tag:blogger.com,1999:blog-26608690522249245492024-03-14T00:39:09.983-05:00The Biologist Is In...and will see you shortly.Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.comBlogger177125tag:blogger.com,1999:blog-2660869052224924549.post-11859031915966710972023-08-29T12:45:00.000-05:002023-08-29T12:45:06.253-05:00The Color of Beans 6<p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCG-5dmuEtmh-0TYrXdJN4tVv98AfgzsZIoPI7U7gaKqqYyX5B9Xf3soIn2pF2GbeCSFR76PlbMaMj_Ji6XU7zz0ZXST-Yonvoj5rdLdsmxN-c6yNc2J--ejB1Dm9emZDr3ryODyRDUKUpDTc7zcQ9ny3Dq2pV9vT4rnrD4xPu1iVQAXyhNGCHwgTrVENJ/s1685/blue_x_coccineus__flower.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Cluster of bright red bean flowers." border="0" data-original-height="1684" data-original-width="1685" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCG-5dmuEtmh-0TYrXdJN4tVv98AfgzsZIoPI7U7gaKqqYyX5B9Xf3soIn2pF2GbeCSFR76PlbMaMj_Ji6XU7zz0ZXST-Yonvoj5rdLdsmxN-c6yNc2J--ejB1Dm9emZDr3ryODyRDUKUpDTc7zcQ9ny3Dq2pV9vT4rnrD4xPu1iVQAXyhNGCHwgTrVENJ/w200-h200/blue_x_coccineus__flower.jpg" width="200" /></a>My ongoing project to produce distinctly blue dry beans occasionally throws a surprise at me. This spring, two plants with bright red flowers appeared in one of my gardens. The blue lines had until now showed a mix of white and pale pink flowers, so this change was rather dramatic.</p><p>I immediately began thinking about how these plants came to be. They clearly grew from blue seeds I'd planted, but that was all I knew initially. Last year I had some (more or less) intentional hybrids turn up in my blue bush bean patch, so I thought they might have represented back crosses to the parental blue line.</p><p>In another garden this year is filled with an F2 population from that intentional hybrid I mentioned. If the red flower color came from a back cross, then the same color should also turn up among the F2 plants. Only white and pale pink flowers were evident when they started blooming, thus the red flower did not come from a back cross.</p><p>I did have one red-flowered <i>Phaseolus coccineus</i> (var "Insuk's Wang Kong") growing last year. The seed germinated late and the vine never prospered. It had only one small flower cluster and produced a single pod with a single seed. It was also on the far end of the garden from the blue bush population, with rows of large tomato and other bean plants in between. I didn't expect there would be any chance for pollen transfer like this, even though I was hoping there might be some crosses with more nearby plants because I'd been wanting to work with a <i>P. vulgaris x P. coccineus</i> hybrid for years.</p><p><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiK6krCJ-UWpSrQkGIUS1KQZX723LIJezm6MJEOOlsys7nn7qc-4OP79qkGfG8YB40ImiQcCDpF0BYY85antqUKgdUsv8-QX5BerEwWq0wS_rzr0X2hmf_4Z0FpFCMvIpC-DHnGDgRTkCJ7iHhkEDOblqOl2w0CZVL1gCfBuEFTEejwXDt_LWn8Z7VwnMyl/s4032/blue_x_coccineus__seed.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img alt="Dry beans. Most are tan with dark brown streaks, but a few are solid blue." border="0" data-original-height="4032" data-original-width="3024" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiK6krCJ-UWpSrQkGIUS1KQZX723LIJezm6MJEOOlsys7nn7qc-4OP79qkGfG8YB40ImiQcCDpF0BYY85antqUKgdUsv8-QX5BerEwWq0wS_rzr0X2hmf_4Z0FpFCMvIpC-DHnGDgRTkCJ7iHhkEDOblqOl2w0CZVL1gCfBuEFTEejwXDt_LWn8Z7VwnMyl/w150-h200/blue_x_coccineus__seed.jpg" width="150" /></a></p><p></p><p>I was eagerly waiting for the first seed pods from the red flowered plants to mature, as their seed color would likely be the definitive evidence for the plants being hybrids. The first pods broke open to reveal tan seeds marked with dark blue. The speckled trait came from the <i>P. coccineus</i> parent and the blue color came from the <i>P. vulgaris</i> parent (the blue seeds here for comparison purposes).</p><p>Hybrids between <i>P. vulgaris</i> and <i>P. coccinues</i> are often described as having growth issues or have poor seed-set, though the literature and experience of others seems to be quite variable. Fortunately, my hybrids show no such issues but perhaps they may show up in the next generations.</p><p><br /></p><hr width="50%" /><p><br /></p><p>Because the <i>P. coccineus</i> parent's seeds were a pale purple, I was expecting the hybrid to turn up with a distinctly purple color and I wouldn't see the blue again until the next generation. Since the speckled trait seems to be dominant, I would expect 75% of the next generation to also show speckles. I can't really predict what the colors in the next generation will be, since I don't have a good idea of what the mixed up genetics will do.</p><p>I have read from a few references that the <i>P. coccineus</i> chromosomes are preferentially lost vs the <i>P. vulgaris</i> chromosomes in subsequent generations, so any predictable genetics ratios are likely to be distorted significantly. I'll just have to find out. Because of this tendency, similar crosses have been used before to introgress traits into <i>P. vulgaris</i>, such as disease resistance factors. I'm hoping I can stabilize the flower color over the next few years, as well as the tendency to bloom very well.</p><p>References:</p><p></p><ol style="text-align: left;"><li>Interspecific hybridization between cultivated american species of the genus Phaseolus.</li><ul><li><a href="https://link.springer.com/article/10.1007/BF01902923">https://link.springer.com/article/10.1007/BF01902923</a></li></ul><li>Embryo development in reciprocal cross of Phaseolus vulgaris L. and P. coccineus Lam.</li><ul><li><a href="https://pubmed.ncbi.nlm.nih.gov/24270536/">https://pubmed.ncbi.nlm.nih.gov/24270536/</a></li></ul></ol><p></p>Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-30002103450990351322023-03-03T12:00:00.001-06:002023-03-03T12:00:00.169-06:00Chile breeding<div dir="ltr" style="text-align: left;" trbidi="on">Plant breeding involves a great deal of luck and you can have some really good success with that. Luther Burbank produced numerous amazing plant varieties, but at the same time, he never believed in genetics. The key aspects of his method were to just try things, to grow large numbers at every stage, and to pay close attention to every plant (to find the differences). He tried crossing a strawberry and a raspberry... and actually got <a href="https://the-biologist-is-in.blogspot.com/2015/01/hybrid-sterility-and-speciation.html">something</a>.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">With some knowledge, you can make predictions about what is more likely to work. To that end, plant breeders have researched what techniques are needed to hybridize different species. Usually there is limited success with hybridizing species in different genera, where the plants are less closely related, but there are <a href="https://www.aos.org/orchids/additional-resources/intergeneric-hybrids.aspx">exceptions</a>. In the end, species labels are things we make for our convenience. Nature is under no obligation to follow what we think a species is or should be.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">
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<br />In peppers there are several domesticated or partially domesticated species:</div><div dir="ltr" style="text-align: left;" trbidi="on"><ul style="text-align: left;"><li><i>Capsicum annum</i> : common sweet & hot peppers in North America.</li><li><i>C. baccatum</i> : more common in South America.</li><li><i>C. chinense</i> : habanero type peppers.</li><li><i>C. frutescens</i> : generally smaller, less common peppers. </li><li><i>C. pubescens </i>: rocoto, manzano, locoto; tropical peppers with black seeds.</li></ul><div>There are many more wild species that are only occasionally or rarely grown by gardeners. Those species contain a wealth of potentially useful genes though. Disease resistances, agronomic traits, and novel flavors can all potentially be moved from the crop wild-relatives into domesticated peppers. Towards that end, researchers have tried crossing almost any pair of species related to domesticated peppers. The following figure shows a crossability polygon, summarizing the results from attempts to hybridize between eleven species in the pepper genus.</div>
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<a href="http://2.bp.blogspot.com/-ME03rYv-1hw/VGwmwXJXndI/AAAAAAAAAy8/c-jgA8GnImw/s1600/8302757528_baaaf572dd_o.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://2.bp.blogspot.com/-ME03rYv-1hw/VGwmwXJXndI/AAAAAAAAAy8/c-jgA8GnImw/s1600/8302757528_baaaf572dd_o.jpg" /></a></div>
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<br /></div>I found the figure several years ago at: <a href="http://www.plantsciences.ucdavis.edu/vc221/pepper/PEPPERrd.htm">www.plantsciences.ucdavis.edu/vc221/pepper/PEPPERrd.htm</a>. I have not yet been able to find the paper in which this figure was first published.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">There are other wild pepper species, which could maybe be included in a more recent version of the figure.</div><div dir="ltr" style="text-align: left;" trbidi="on"><ul style="text-align: left;"><li><div dir="ltr" trbidi="on"><i>C. lanceolatum</i>: a cloud-forest species sharing the trait of black seeds with <i>C. pubescens</i>.<br /><i>C. rhomboideum</i>: a species barely considered to belong to the genus <i>Capsicum</i>, with yellow flowers, sweet berries, and brown seeds.</div></li><li><div><i>C. annum var glabriusculum</i> : tiny, very hot, wild pepper of the desert southwest US.</div></li><li><div>And many others...</div></li></ul></div><div dir="ltr" trbidi="on"><br /></div><div dir="ltr" trbidi="on"><hr width="50%" /><br />What this diagram suggests is that you could transfer an interesting trait from any one of these species into any other species you're interested in working with, either directly or through intermediaries. It would just take motivation, time, and money to do so. More generally, hybrids between the species would let one introduce much more genetic diversity into their pepper breeding projects, even if there wasn't a specific trait of interest.</div><div dir="ltr" style="text-align: left;" trbidi="on">
<br /></div><div dir="ltr" style="text-align: left;" trbidi="on">I'm working with lines that include <i>C. annum var glabriusculum</i> in their recent ancestry. This was the wild pepper which grew in San Antonio and Austin Texas where I grew up. I started by growing seeds for the species which I (or friends and family) had collected from the wild. At one point, a few seeds collected from a large, seemingly wild plant grew up showing the parent plant had been a hybrid with some unknown domesticated type. I've been growing the descendants of those plants since.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimVMRUMeG1CruNIcsBgXZVxUnbBJ6EpjsnypMbclgIx-VmP9VZ0SvPRcSotb6lVi8doff3hKw3mcKPWQkZ21eQhdO0I8v0i29cDSJ7aVgQVLy4b1Yl_Mtr3OYAG9Bna_ukeqT0y4cukTS_CrheqtfCliTn-OoZiTM0fwd-PAxQqOPnKy_ThuFMX9jIDw/s4096/miniatures.jpeg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Left half shows several miniature pepper plants growing in two rows. Right half shows numerous tiny black and red pepper pods drying." border="0" data-original-height="1536" data-original-width="4096" height="120" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimVMRUMeG1CruNIcsBgXZVxUnbBJ6EpjsnypMbclgIx-VmP9VZ0SvPRcSotb6lVi8doff3hKw3mcKPWQkZ21eQhdO0I8v0i29cDSJ7aVgQVLy4b1Yl_Mtr3OYAG9Bna_ukeqT0y4cukTS_CrheqtfCliTn-OoZiTM0fwd-PAxQqOPnKy_ThuFMX9jIDw/w320-h120/miniatures.jpeg" width="320" /></a></div>At left is an side view of a patch of miniature pepper plants grown in 2022. Here they're about 4.5 inches tall and the tallest matured to about 8 inches in height. The smallest stayed under an inch (and didn't mature any pods). This line has the small leaves and pods of its wild ancestor, but has a far more dense branching structure and short stems. They produced more and more dark purple/black pigment in the leaves as the season went on. The pods matured from black to bright red at final maturity. The pods range from very hot to volcanic. The plants were covered in black and red pods at the end of the season.</div><div dir="ltr" style="text-align: left;" trbidi="on"></div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFk0gOWFN7UAkCphqRzX1nDPrKm6ZDCnw0AzjlCex-YWXCfTltDCwpjbk2MqpP-xFudgv7TUZz8eGlYC54pqLVSXoq0fpTJ1N2fN__kmpP7_5pQb1rJo1ocwyA-U4tw1-gQzoFERA3axkwTB8UtIXpCRa3zKeFNKTSKXYWIKpVnU7s1M3G5UFywfcvfg/s2048/F1_00.jpeg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="2048" data-original-width="1536" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjFk0gOWFN7UAkCphqRzX1nDPrKm6ZDCnw0AzjlCex-YWXCfTltDCwpjbk2MqpP-xFudgv7TUZz8eGlYC54pqLVSXoq0fpTJ1N2fN__kmpP7_5pQb1rJo1ocwyA-U4tw1-gQzoFERA3axkwTB8UtIXpCRa3zKeFNKTSKXYWIKpVnU7s1M3G5UFywfcvfg/w150-h200/F1_00.jpeg" width="150" /></a></div>Other plants derived from that initial wild hybrid had larger, more typical forms, though they were still small in size compared to many garden types. Among those, one plant (at right) stood out as extra productive in 2021. I had been hoping to select up a productive hot pepper type since the more standard types have been not doing so well with my short growing season. I grew 25 plants in 2022 from seeds saved from this plant.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">Those plants made it clear the productive parent plant had been a new hybrid, between the wild hybrid derived plants I was growing and the Pimenta da Neyde pepper I had been growing the year before. In addition to a wild range of leaf color and plant growth habit in these F2 plants, I also found several with decently large pods at various heat levels.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbGDgonbHLQJasO1wQpHtXCgNVK9_LzNfDTV7IGcoiLiVYPIfVnKYXcG8VvxOMJIdBV_d81IId-cC6fzxKB-irobSpguGWW0m3N7pp9alXB64uJIiL-AH7X8ub-Ndml8ucIXe-SJw9jsfZHV0fQrWYLHNkPmmMISmuRiBDe6vZBfB1REkbYiRNgwRrzA/s4094/hab_jal_F2s.jpeg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="At left a single habanero type pepper cut open to show orange capsaicin oil rich internal membranes; at right four small jalapeno type peppers with longitudinal corked surface cracks. Both peppers are bright red." border="0" data-original-height="2048" data-original-width="4094" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbGDgonbHLQJasO1wQpHtXCgNVK9_LzNfDTV7IGcoiLiVYPIfVnKYXcG8VvxOMJIdBV_d81IId-cC6fzxKB-irobSpguGWW0m3N7pp9alXB64uJIiL-AH7X8ub-Ndml8ucIXe-SJw9jsfZHV0fQrWYLHNkPmmMISmuRiBDe6vZBfB1REkbYiRNgwRrzA/w200-h100/hab_jal_F2s.jpeg" width="200" /></a></div>The split pod at left came from a single plant which seemed to mimic a habanero. The pods had very thin walls and had a heat comparable or higher than habaneros. The internal membranes look so enriched in capsaicin oils that I was hesitant to try tasting them. Other plants seemed to mimic jalapenos, with their thick flesh and corked skin. These peppers are smaller than real jalapenos with a moderate heat level. The plants with both types of pods were far more productive than any habanero or jalapeno I had grown in my gardens, so I took this as a win.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">Though I can't be sure, I have a pretty good feeling that all of these peppers are able to grow as well as they do for me in part because of some genes inherited from their recent wild ancestor. They handle the poor soil and limited water in my garden far better than usual garden types. The miniature peppers absolutely have their size and growth habit in part due to their wild ancestry.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">In the next several years I hope to stabilize several new varieties from this project. Even if I don't, I'll be getting plenty of hot peppers along the way.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">References:</div><div dir="ltr" style="text-align: left;" trbidi="on"><ul style="text-align: left;"><li>Burbank's strawberry/raspberry hybrid: <a href="https://the-biologist-is-in.blogspot.com/2015/01/hybrid-sterility-and-speciation.html">https://the-biologist-is-in.blogspot.com/2015/01/hybrid-sterility-and-speciation.html</a></li><li>Intergeneric hybrid orchids: <a href="https://www.aos.org/orchids/additional-resources/intergeneric-hybrids.aspx">https://www.aos.org/orchids/additional-resources/intergeneric-hybrids.aspx</a></li></ul></div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com3tag:blogger.com,1999:blog-2660869052224924549.post-53519937367709775012023-02-24T12:00:00.326-06:002023-02-24T12:00:00.182-06:00The Color of Beans 5<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJVZCK5VN6nimaBqukRrVl-nNdVU1BaSUQL0UVK4mFvxrTMbmZFY4Lq4_gCX3wyw20QGiDgeqAWdjPTNDTUFVE7qC52Z0ILGI2FwcnNFcklDpi4u_gMgluPfDaXQcwLBx6jVLgHWpVQQPnQrLCetNkwiK58GLN-m_TyDTcHb8tjmG1Vxd51h8dDltRPw/s2048/2022_blue.jpeg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Pile of blue dry beans." border="0" data-original-height="2048" data-original-width="2048" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJVZCK5VN6nimaBqukRrVl-nNdVU1BaSUQL0UVK4mFvxrTMbmZFY4Lq4_gCX3wyw20QGiDgeqAWdjPTNDTUFVE7qC52Z0ILGI2FwcnNFcklDpi4u_gMgluPfDaXQcwLBx6jVLgHWpVQQPnQrLCetNkwiK58GLN-m_TyDTcHb8tjmG1Vxd51h8dDltRPw/w200-h200/2022_blue.jpeg" width="200" /></a></div><p>After several years of looking for a truly blue dry bean, I started actively working to produce my own variety in 2018 when I was gifted a few bluish-black hybrid seeds from a bean collector. At the end of 2022, I was essentially done. Five years of selecting the best blue seeds each season and my new variety finally produced a consistently blue crop.</p><p>There's probably still going to be a few more years of increasing the seed before I'm prepared to distribute them in some fashion. Along the way I'll be selecting for increased productivity and having to figure out where I can grow more of them each year.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1uTORzlvbLpPa0S2o7BoBOw23cKRo65xgsR1_hAHAEq6aSAZrzY1dI_F0_WKOtg9hZ-dfvd1u-7sICeaib-MvV0r94L1uFse339iLG5FZERbR9VI7nZaU4c49QZiyVc4aJvHPyc3qSfRCT9Ng5S6VbXh4unXHqutW99dk1q-jHwDZKrlKBXn9UzViMQ/s924/anthocyanin_pathway-2d.png" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Anthocyanin pathway diagram, emphasizing red and blue anthocyanins, as well as yellow astragalin." border="0" data-original-height="636" data-original-width="924" height="138" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1uTORzlvbLpPa0S2o7BoBOw23cKRo65xgsR1_hAHAEq6aSAZrzY1dI_F0_WKOtg9hZ-dfvd1u-7sICeaib-MvV0r94L1uFse339iLG5FZERbR9VI7nZaU4c49QZiyVc4aJvHPyc3qSfRCT9Ng5S6VbXh4unXHqutW99dk1q-jHwDZKrlKBXn9UzViMQ/w200-h138/anthocyanin_pathway-2d.png" width="200" /></a><p style="text-align: left;">Since harvesting the most recent crop, I've been digging into what research literature there is about the genetics and biology of color in beans. This was initially just to get a better idea of what was going on in my beans. Along the way I realized I could probably use the knowledge I had gained to intentionally make new blue varieties.</p>
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<p style="text-align: left;">The initial random hybrid was between a black variety (<a href="https://exchange.seedsavers.org/page/variety/id/193592">Haudenosaunee Skunk</a>) and a yellow-tan variety (<a href="https://www.seedsavers.org/arikara-yellow-bean">Arikara Yellow</a>). That color combination would clearly work as parents in a new cross, but I realized there was a combination of parental color genetics that would probably make it easier to recover the right combination of genes to produce a blue color.</p><p style="text-align: left;">The color of black beans is caused by a combination of red, blue, and yellow-brown pigments at high intensity. In <i>Phaseolus vulgaris</i>, a small number of genes lead to this color: R ("red"; likely a transcription factor driving enzyme F3'H), V ("violet"; enzyme F3'5'H), and then B ("brown"; transcription factors enhancing CHS/CHI, darkening all downstream pigments). A yellow-brown bean is caused by all three genes being inactive (written as "rvb"). There are a few other genes that seem to impact exactly what shade of brown color may result, but there doesn't seem to be as much clarity in the research literature about that part of the pigment pathway.</p><p style="text-align: left;">The difference between a purple and a black bean is that the purple bean has an inactive version of B (b). Crossing a purple bean (RVb) to a yellow bean (rvb), where both have the recessive inactive b allele, reduces the genetic possibilities in the F2s to only those impacting the red and blue pigments. Among the F2 plants, we should see the ratios of a dihybrid cross play out. 9 purples, 3 reds, 3 blues, and 1 yellow-brown. 3/16 isn't that bad and I can easily grow enough plants to expect to be able to find the blues I'm looking for.</p><p style="text-align: left;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_StWOEi5YZNDKrK8yQOhRm9QdgSjubzRlmtl_nHJdsZpqRjl-DBd_TFlaBgl-0rNwHeP3otWwseeZmwyfFuaVU_amfluWQa1pWVs8gTeM3HAxDYAy78IFILvpROWiYmv9L--f3ukgm9IarMOz8kVmIATOdL5jGpjipTRKzYzwvJoAgwYfyhNCCvZVsg/s6048/P_coccineus_purple-yellow.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="At left, purple dry beans. At right, yellow dry beans." border="0" data-original-height="3024" data-original-width="6048" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_StWOEi5YZNDKrK8yQOhRm9QdgSjubzRlmtl_nHJdsZpqRjl-DBd_TFlaBgl-0rNwHeP3otWwseeZmwyfFuaVU_amfluWQa1pWVs8gTeM3HAxDYAy78IFILvpROWiYmv9L--f3ukgm9IarMOz8kVmIATOdL5jGpjipTRKzYzwvJoAgwYfyhNCCvZVsg/w200-h100/P_coccineus_purple-yellow.jpg" width="200" /></a></div><div style="text-align: left;">To test this model I've been building, I decided maybe I could try to make a blue version of one of the other domesticated bean species. Most <i>P. coccineus</i> (runner or ayacote) beans I'd ever seen before were lilac and heavily spotted with black. After digging around for a while, I eventually ordered some mixed color packages from some Mexican bean importers in the south-west. Among those, I was able to select out seeds with the colors I was looking for.</div><p></p><p style="text-align: left;"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKqN2xqMVzUaOKUj8n3EVWp9P6hbSeZu--bsj-FwktAzEFWshR-VdjI0xp3kwtHiFPI9HhPjYxHcnEWW7zV0aF3kejzs6GANk7Y77tEl2G0ZhgG5iJPyPm9xfyJ8CsC6nrCc63Gu1A_rpKmz6-3aBbFzMJ9vERgbovxmtRIywOXo8suG2NCmbe2Bjjpg/s6048/P_lunatus_purple-yellow.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" data-original-height="3024" data-original-width="6048" height="100" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhKqN2xqMVzUaOKUj8n3EVWp9P6hbSeZu--bsj-FwktAzEFWshR-VdjI0xp3kwtHiFPI9HhPjYxHcnEWW7zV0aF3kejzs6GANk7Y77tEl2G0ZhgG5iJPyPm9xfyJ8CsC6nrCc63Gu1A_rpKmz6-3aBbFzMJ9vERgbovxmtRIywOXo8suG2NCmbe2Bjjpg/w200-h100/P_lunatus_purple-yellow.jpg" width="200" /></a></div><div style="text-align: left;">While I was waiting for those to arrive, I was also looking for <i>P. lunatus</i> (lima) beans with the same colors. The yellow-brown variety I found is called <a href="https://www.nativeseeds.org/products/pl011">Pima Orange</a>. I ordered the purple variety from someone on Ebay and am still waiting for them to arrive.</div><p></p><p style="text-align: left;">I wasn't able to find any sign of a purple version of <i>P. acutifolius</i> (tepary) beans. I did find <a href="https://www.nativeseeds.org/collections/tepary-beans/products/pt082">black</a> and <a href="https://www.nativeseeds.org/collections/tepary-beans/products/pt120">yellow</a> versions that I could use with more difficulty. I'll keep looking for a purple version and may eventually decide to try using a black variety instead, but for now I'll hold off on trying to make a blue variety of this species.</p><hr width="50%" /><p style="text-align: left;">The color of a seed is determined by the genes of the mother plant, so it can take some tricks to sort things out. The plan will take a few years to play out.</p><p style="text-align: left;"></p><ul style="text-align: left;"><li>2023 : Plant purple & yellow seeds on a common trellis. Some harvested seeds may be hybrids, but we can't identify them yet. Save them separated by color.</li><li>2024 : Plant yellow seeds only. Save harvested seeds by color.</li><ul><li>Yellow seeds : mother plant wasn't hybrid.</li><li>Purple seeds : mother plant was a hybrid between purple & yellow plants. These seeds will grow into F2 plants.</li></ul><li>2025 : Plant purple seeds only. Save harvested seeds by color.</li><ul><li>The F2 plants should fall into four categories (9 purple : 3 red : 3 blue : 1 yellow). I've already determined I can grow F2 plants in a mass planting and observe the expected ratios in the cumulative produced seed counts.</li></ul></ul><p style="text-align: left;"><i>P. coccineus</i> and <i>P. lunatus</i> are strong out-crossers, so I can rely on bees and other pollinators to do the work of transferring pollen for me. The two species can't cross, so I can do both parallel experiments in a relatively small garden space. To increase the odds of the yellow seeds produced in 2023 being hybrids, I can plant many more purple seeds than yellow (or even only one yellow seed among many purple). This will result in most flowers that a yellow-seed plant can cross with being those from purple-seed plants.</p><p style="text-align: left;">If no purple seeds turn up in 2024, then no useful cross-pollinations happened in 2023. In 2025 I would then plant purple and yellow seeds to try and find crosses again. There may be some hybrid seeds among the purples, but distinguishing them from the non-hybrids would take a couple more years and require individual plants to be grown on separate trellises. That's more work than I want to put into it, hence designing the plan the way I have.</p><hr width="50%" /><p style="text-align: left;">This plan assumes the genes driving F3'H (red anthocyanins) and F3'5'H (blue anthocyanins) are unlinked in these species. I know in <i>P. vulgaris</i> the two genes are not tightly linked. If they were, I would not expect to have been able to find the initial blue-seeded plant so easily as I did. That it <a href="https://link.springer.com/article/10.1007/BF01902923">is possible</a> to make hybrids between <i>P. vulgaris</i> and <i>P. coccineus</i> tells us their genomes are organized in largely the same fashion, so the two genes should be similarly not tightly linked in <i>P. coccineus</i>. Making hybrids with <i>P. lunatus</i> is harder, but <a href="https://www.semanticscholar.org/paper/Hybrid-plant-of-Phaseolus-vulgaris-L.-and-P.-L.-by-Kuboyama-Shintaku/c20048408e38632b8ae8fe45d234e967ad57df2d">still possible</a>, so similarly I don't expect the two genes to be tightly linked.</p><p style="text-align: left;">Why aren't there already blue varieties of these species available? I don't know, but I feel it might be the same reason that blue varieties of <i>P. vulgaris</i> are so very rare, whatever that is. That and the vast majority of people who have ever grown beans have not been geneticists backed up with decades of published research into the biology of bean pigments. In a few years, I hope to have remedied this absence.</p><p style="text-align: left;"><br /></p>
<div style="text-align: left;">References:</div><div><ol style="text-align: left;"><li>Bean varieties:</li><ol><li>Haudenosaunee Skunk: <a href="https://exchange.seedsavers.org/page/variety/id/193592">https://exchange.seedsavers.org/page/variety/id/193592</a></li><li>Arikara Yellow: <a href="https://www.seedsavers.org/arikara-yellow-bean">https://www.seedsavers.org/arikara-yellow-bean</a></li><li>Pima Orange : <a href="https://www.nativeseeds.org/products/pl011">https://www.nativeseeds.org/products/pl011</a></li><li>Black Tepary : <a href="https://www.nativeseeds.org/collections/tepary-beans/products/pt082">https://www.nativeseeds.org/collections/tepary-beans/products/pt082</a></li><li>S'oam Baw Tepary : <a href="https://www.nativeseeds.org/collections/tepary-beans/products/pt120">https://www.nativeseeds.org/collections/tepary-beans/products/pt120</a></li></ol><li>Blog posts:</li><ol><li><a href="https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html">https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html</a></li><li><a href="https://the-biologist-is-in.blogspot.com/2022/12/the-color-of-beans-2.html">https://the-biologist-is-in.blogspot.com/2022/12/the-color-of-beans-2.html</a></li><li><a href="https://the-biologist-is-in.blogspot.com/2023/01/the-color-of-beans-3.html">https://the-biologist-is-in.blogspot.com/2023/01/the-color-of-beans-3.html</a></li><li><a href="https://the-biologist-is-in.blogspot.com/2023/02/the-color-of-beans-4.html">https://the-biologist-is-in.blogspot.com/2023/02/the-color-of-beans-4.html</a></li></ol><li>Bean species hybrds:</li><ol><li><a href="https://link.springer.com/article/10.1007/BF01902923">https://link.springer.com/article/10.1007/BF01902923</a></li><li><a href="https://www.semanticscholar.org/paper/Hybrid-plant-of-Phaseolus-vulgaris-L.-and-P.-L.-by-Kuboyama-Shintaku/c20048408e38632b8ae8fe45d234e967ad57df2d">https://www.semanticscholar.org/paper/Hybrid-plant-of-Phaseolus-vulgaris-L.-and-P.-L.-by-Kuboyama-Shintaku/c20048408e38632b8ae8fe45d234e967ad57df2d</a></li></ol></ol></div></div>Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com08PM6C4WQ+6243.4456216 104.137501616.175084156464905 68.981251600000007 70.7161590435351 139.29375159999998tag:blogger.com,1999:blog-2660869052224924549.post-29657738041464090612023-02-10T12:00:00.002-06:002023-02-10T12:00:00.181-06:00The Color of Beans 4<p></p>In my last post (<a href="https://the-biologist-is-in.blogspot.com/2023/01/the-color-of-beans-3.html">https://the-biologist-is-in.blogspot.com/2023/01/the-color-of-beans-3.html</a>), I shared a couple figures illustrating the flavonoid/anthocyanin pigment pathway in plants and in common beans (<i>Phaseolus vulgaris</i>) specifically. A couple days later, I found some additional evidence which led me to feel the need to update my figures somewhat.<div><br /><hr width="50%" /><br />
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj44qECxtXu7h7XUZfSoGWqgPMLJGAou4-YDtPLa8lWtQQb-WAdhsBTmgrTPWzfVA5VjtjunFGmsjEwI1ZcCCpmRyW0RSRjFSTfqHVWNKLRqgIT_MAoBKggpTEMcDea-4igh_SJ9ghyZF4AiuDjEk4XryQv-s02ubsBeVEFpIQtfC7dXJ2e_yc4lxSYKg/s951/anthocyanin_pathway-1b.png" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Starting section from the top: phenylalanine to cinnaminate to 4-coumerate to p-coumaroyl-CoA (+ 3x malonyl-CoA) to naringen chalcone to naringen. Naringen goes left and right to eriodictyol and pentahydroxy flavone. Eriodictyol goes left to flavan-4-ols and then to phlobaphenes (highlighted in red). Eriodictyol goes right to tricetin. Naringen goes right to apigentin (highlighte light brown). Pentahydroxy falvanone goes right to luteolin (highlighted pale yellow). Naringenin goes down to dihydrokaempferol. Eriodictyol and dihydrokaempferol go left to dihydroquercetin. Pentahydroxy flavanone and dihydrokaempferol go right to dihydromyricetin. Dihydroquercetin goes right to quercetin (highlighted in yellow). Dihydrokaempferol goes right to kaempferol (highlighted in yellow) and then down to astragalin (highlighted in yellow). Kaempferol goes to a series of question marks highlighted in a gradient from white to brown. Dihydromyricetin goes right to myricetin (highlighted light brown). Dihydroquercetin goes down to leuocyanidin. Dihydrokaempferol goes down to leucopelargonidin. Dihydromyricetin goes down to leucodelphinidin. Leucocyanidin goes down to cyanidin and then cyanin (both highlighted red). Leucopelargonidin goes down to pelargonidin and pelargonin (both highlighted orange). Leucodelphinidin goes down to delphinidin and delphinin (both highlighted blue). Leucocyanidin, leucopelargonidin, and leucodelphinidin go left to 2,3-trans-flaven-3-ols (catechin) (highlighted in in a gradient from white to brown). Cyanidin, pelargonidin, and delphinidin go left to 2,3-cis-flaven-3-ols (epecatechin) (highlighted in a gradient from white to brown). Catechin and epicatechin go down to proanthocyanidins (highlighted in a gradient from white to brown). Luteolin, apigenin, and tricetin have a group label 'flavones'. Myrictein, kaempferol, and quercetin have a group label 'flavonols'. The figure has enzyme labels at most steps. In the top starting section: PAL, C4H, 4CL, CHS, and CHI. Naringenin to eriodictyol is F3'H. Naringenin to pentahydroxy flavanone is F3'5'H. Eriodictyol, naringenin, and pentahydroxy flavanone to tricetin, apigenin, and luteolin are FNS. Eriodictyol, naringenin, and pentahydroxy flavanone to to dihydroquercetin, dihydrokaempferol, and dihydromyrecetin are F3'H. Eriodictyol to flavan-4-ols is DFR. Dihydrokaempferol to dihydroquercetin is F3'H. Dihydrokaemperol to dihydromyricetin is F3'5'H. Dihydroquercetin, dihydrokaempferol, and dihydromyricetin to quercetin, kaempferol, and myricetin are FLS. Dihydroquercetin, dihydrokaempferol, and dihydromyricetin to leucocyanidin, leucopelargonidin, and leucodelphindin are DFR. Leucocyanidin, leucopelargonidin, and leucodelphindin to cyanidin, pelargonidin, and delphinidin are ANS. Cyanidin, pelargonidin, and delphinidin to cyanin, pelargonin, and delphinin are GT. Leucocyanidin, leucopelargonidin, and leucodelphindin to catechin are LAR. Cyanidin, pelargonidin, and delphinidin to epicatechin are ANR." border="0" data-original-height="636" data-original-width="951" height="134" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj44qECxtXu7h7XUZfSoGWqgPMLJGAou4-YDtPLa8lWtQQb-WAdhsBTmgrTPWzfVA5VjtjunFGmsjEwI1ZcCCpmRyW0RSRjFSTfqHVWNKLRqgIT_MAoBKggpTEMcDea-4igh_SJ9ghyZF4AiuDjEk4XryQv-s02ubsBeVEFpIQtfC7dXJ2e_yc4lxSYKg/w200-h134/anthocyanin_pathway-1b.png" width="200" /></a></div>Certain combinations of published genes lead to production of a brown pigment when an excess of yellow astragalin would be expected. Here I've made up an enzyme called FNR (FlavoNol Reductase) leading to production of the pigment, modeled after the production of proanthocyanidins by ANR (Anthocyanin Reductase).<p></p><p>The evidence for a brown pigment derived from the yellow pigment pathway comes from the gene B changing a bean color from yellow-brown to mineral/dark-brown when present. B is thought to be a transcription factor that enhances the expression of other pathway genes. Yellow can only arise when red and blue pigment branches are absent, so the brown pigment produced with B can't be the brown proanthocyanidins derived from the red and blue pigment branches. Instead it must be an analogous pigment produced from kaempferol and/or astragalin. I haven't found any research papers discussing this pigment pathway branch, but all the evidence seems to point to it being there anyhow.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzIKOH_pcl0_bZSxQ-En-zZFHshidbO7qXamOqYi66bUtDQHo3TI8qLnKP29VoFSSQvA_wKxhbdcIr_8Oj5kHzE8ttgPhPBMY3iTLU8U4htJTc2D_kHHCVt3QQtStdgtv_CWQS3mc8tdYJLHrP2eERf3j5JS8_f20QZ78n_sl4dT8xCl-wT_oRJ2pjZg/s924/anthocyanin_pathway-2c.png" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="This version of the flavonoid pigment pathway is trimmed to be limited to the main pigments (cyanidin, pelargonidin, delphinidin, & astragalin) along with the core of the pathway leading to them and the metabolites derived from them." border="0" data-original-height="636" data-original-width="924" height="221" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzIKOH_pcl0_bZSxQ-En-zZFHshidbO7qXamOqYi66bUtDQHo3TI8qLnKP29VoFSSQvA_wKxhbdcIr_8Oj5kHzE8ttgPhPBMY3iTLU8U4htJTc2D_kHHCVt3QQtStdgtv_CWQS3mc8tdYJLHrP2eERf3j5JS8_f20QZ78n_sl4dT8xCl-wT_oRJ2pjZg/w320-h221/anthocyanin_pathway-2c.png" width="320" /></a></div>The figure trimmed to the metabolites and pigments significant in common beans... now includes pelargonidins. This version of the figure has different thickness arrows in places to illustrate when one branch has a higher priority, when one branch of metabolites is more likely than another.<p></p><p>Dihydrokaempferol is a central metabolite for all the different pigment branches in the pathway. F3'H and F3'5'H leading to red and blue pigments have the strongest branches, followed by FLS leading to yellow pigments, and then last is DFR leading to orange pigments. For the orange pigments to dominate the final color, it looks like the other three branches have to be disabled or significantly reduced.</p><p></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiy0MkG5oJbzazX1xSKdp0WGf3OftplfsrdNEbqc7XYubKTtKBqDwlFjdL99qkv3eDth-tHU6Agpru7zENvH_HVZKZMSdNQnVvPNnjQ6P6tXk8bqTbQqm1dcCgXbwMP7UkZNppr3_wCbtH_-1Obo2tbfu0HcjT7tdcuEbbEAifn6-7A3pjxFLsnzZUgpg/s520/from_g3netic_lottery_on_instagram.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="pale tan beans with orange-toned eyes." border="0" data-original-height="520" data-original-width="390" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiy0MkG5oJbzazX1xSKdp0WGf3OftplfsrdNEbqc7XYubKTtKBqDwlFjdL99qkv3eDth-tHU6Agpru7zENvH_HVZKZMSdNQnVvPNnjQ6P6tXk8bqTbQqm1dcCgXbwMP7UkZNppr3_wCbtH_-1Obo2tbfu0HcjT7tdcuEbbEAifn6-7A3pjxFLsnzZUgpg/w150-h200/from_g3netic_lottery_on_instagram.jpg" width="150" /></a></div>So. Are there orange varieties of common bean? Maybe. Instagram user @g3netic_lottery shared a mixed variety of beans they grew this year and some of them had a distinctly orange-ish color, especially in the hilium ring. Now, I'm not entirely sure that is the color of pelargonidin, but it is the closest to orange I've seen in common beans. It's enough of a suggestion that I decided to rework the pathway figure to include it for this species.<p></p><p>I still think it would be really cool to find (or breed up) a variety that had distinctly orange color all over the seed. These beans at right hint that it is feasible if one has the right sort of luck. <a href="https://www.instagram.com/g3netic_lottery/">@g3netic_lottery on Instagram</a> grows beans and other crops in South Africa. I'll be keeping my eye out for useful seeds more accessible to me that might help me get to a nicely orange common bean.</p><hr width="50%" /><p>The other domesticated bean species will have very similar pathways as the common bean, but the specific available mutations are going to be different. Maybe we can find a good pelargonidin orange color in one of them. I spent some time looking around for orange seeded varieties of the other species, with limited luck.</p><ul style="text-align: left;"><li>Runner beans (<i>P. coccineus</i>): This photo of "<a href="http://dualsnatural.com/products/ayocote-mexican-beans">Ayacote Mexican" beans</a> includes some very orange looking seeds, but I have no idea how much that reflects reality.</li><li>Lima beans (<i>P. lunatus</i>): <a href="http://www.nativeseeds.org/products/pl011">"Pima Orange"</a> has seeds that look yellow-brown or orange depending on the photo. Again, it is hard to say what they really look like.</li><li>Tepary beans (<i>P. acutifolius</i>) : There are <a href="https://sanpeteready.org/gardening-in-sanpete-tepary-beans/">some photos around</a> of very orange tepary beans, but I can't find any varieties available for sale that look anything near orange.</li><li>Year-long beans (<i>P. dumosus</i>) : This species is interesting, but only grown in a limited area. I found several articles about it, but I have yet to find anyone selling seeds.</li></ul><div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1W2u3xMHHr7fVd8O5FATuwE3cq3OK36be9RBh-0APqyBdbB54LPokrEr71lGcAyg2NW69v-0TQipsC1YEnC9HErQwqL1fLh_9YXLcCPCv6_9QhlXPqIsykZYiw3nzPWpwvvlDfM2qMBV2ZTgNQFTOcGjTgeazJy8Nsa-aTbxZ9Y1BjcDqK5hDAqDPyQ/s2936/P.coccinus_ayacote_purple_2.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Mix of dark purple and black beans." border="0" data-original-height="2936" data-original-width="2936" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1W2u3xMHHr7fVd8O5FATuwE3cq3OK36be9RBh-0APqyBdbB54LPokrEr71lGcAyg2NW69v-0TQipsC1YEnC9HErQwqL1fLh_9YXLcCPCv6_9QhlXPqIsykZYiw3nzPWpwvvlDfM2qMBV2ZTgNQFTOcGjTgeazJy8Nsa-aTbxZ9Y1BjcDqK5hDAqDPyQ/w200-h200/P.coccinus_ayacote_purple_2.jpg" width="200" /></a></div>I ordered the runner and lima bean varieties above, so I can see what their colors actually look like. It is so very easy to intentionally or accidentally tweak the color of a photo, so the color of photos online isn't always something you should trust.</div><div><br /></div><div>The runner beans turned up first. Unfortunately, there was nothing like orange among them. I did get the lovely dark purple beans at left though, which are perfect for another project I'll describe in another post. After further looking around, I found a <a href="https://masienda.com/products/ayocote-beans">different vendor</a> selling ayacote beans that are at least advertised with some nice orange tones. As they too are selling the beans intended for food use, there's no guarantee any yellow seeds will turn up.</div><div><br /></div><div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQJmVF9auSqxiYkUV_Kkq5y65wpHSKPOuONO3VHkX0iR8gvPiw2yWxNMjMylQmx2j9-SLjSuUaKVgN-VOJDN4gYNmFHChtM1_TcLfAPFB_E9c7tEGvxcKGW9T9B7c4V3To7-1HE2LAcy195b9B9owI3I30cUs-GN38_xy1RnO3krEMMjdWO0rkiFAXOQ/s2854/P.lunatus_Pima-Orange_orange_3.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Mix of orange colored beans with variable dark markings." border="0" data-original-height="2854" data-original-width="2854" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQJmVF9auSqxiYkUV_Kkq5y65wpHSKPOuONO3VHkX0iR8gvPiw2yWxNMjMylQmx2j9-SLjSuUaKVgN-VOJDN4gYNmFHChtM1_TcLfAPFB_E9c7tEGvxcKGW9T9B7c4V3To7-1HE2LAcy195b9B9owI3I30cUs-GN38_xy1RnO3krEMMjdWO0rkiFAXOQ/w200-h200/P.lunatus_Pima-Orange_orange_3.jpg" width="200" /></a></div>The lima beans arrived a few days later. When I opened the package, I was greeted by seeds with a surprisingly nice orange color! Now, this isn't anything like the orange you get from beta-carotene in some carrots and tomatoes, but this might just be what a pelargonidin orange looks like.</div><div><br /></div><div>Alternately, this could be a mix of a yellow and a brown pigment. There may be some simple basement-lab tests I can do to help me identify the pigment, but that will take some further research.</div><div><br /></div><div>In either case, I think it is entirely reasonable to expect a similar orange colored common bean should be possible. It's just a matter of finding the right mutations and crossing them into the same plant.</div><div><br /></div></div><div>References:</div><div><ul style="text-align: left;"><li>Some seed sources:</li><ul><li><a href="https://dualsnatural.com/products/ayocote-mexican-beans">dualsnatural.com/products/ayocote-mexican-beans</a> : <i>P. coccineus</i> "Ayacote Mexican".</li><li><a href="https://masienda.com/products/ayocote-beans">https://masienda.com/products/ayocote-beans</a> : <i>P. coccineus</i> "Ayacote Pinto".</li><li><a href="https://www.nativeseeds.org/products/pl011">www.nativeseeds.org/products/pl011</a>: <i>P. lunatus</i> "Pima Orange"</li><li><a href="https://www.nativeseeds.org/collections/indigenous-seeds-bean-tepary">www.nativeseeds.org/collections/indigenous-seeds-bean-tepary</a>: <i>P. acutifolius</i> varieties.</li></ul></ul></div>Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-79430762045900128642023-02-03T12:00:00.004-06:002023-02-07T17:44:34.721-06:00Potatoes<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTQLFeAFvU5X6y6dl60QTmuSierNbnq9cM5Ol33j_GMFEBO9zBpTOL0odFEFzkMzPBNOu2PQ_XOs0RsWHmurgTm42Eo5n87y5zUq_lnUrBD5q4BqPobne0b5PjsVHVx2CI_vwkmShnJ8rrlxYOX4z36cSM5_vl1DmqrQgPw472xU_qcB5e7ow30u42mw/s2156/FbcLq1QWAAQnwoa.jpeg" style="clear: left; display: inline; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Two pale blue potato plant flowers." border="0" data-original-height="2155" data-original-width="2156" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgTQLFeAFvU5X6y6dl60QTmuSierNbnq9cM5Ol33j_GMFEBO9zBpTOL0odFEFzkMzPBNOu2PQ_XOs0RsWHmurgTm42Eo5n87y5zUq_lnUrBD5q4BqPobne0b5PjsVHVx2CI_vwkmShnJ8rrlxYOX4z36cSM5_vl1DmqrQgPw472xU_qcB5e7ow30u42mw/w200-h200/FbcLq1QWAAQnwoa.jpeg" width="200" /></a></div><div dir="ltr" style="text-align: left;" trbidi="on">Years ago I heard a story. The story teller's cousin has been growing potatoes and tomatoes each of the last several years. Some years, her cousin reported finding hybrid plants that produce edible potatoes and green tomatoes.<br />
<br />
From the story, second-hand as it was, I imagined ripe-red tomatoes on a plant that when pulled up had mature potatoes hanging from the roots. There is usually some truth behind a story like this, but perhaps not what the originally teller or the later hearer initially thought.<br />
<br />
The two species (tomato, <i>Solanum lysopersicum</i>; potato, <i>S. tuberosum</i>) are in the same genus, but are distantly related enough that they can't cross to form hybrids. Plants with the important traits of both species can be <a href="http://www.territorialseed.com/product/grafted-tomtato-ketchup-n-fries/new_for_spring_2015">purchased</a> or <a href="https://www.youtube.com/watch?v=6V_X77CeTcs">made at home</a>, but they are the result of actively grafting separate plants together and wouldn't accidentally form in the garden.<br />
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<div class="separator" style="clear: both; text-align: center;"><div style="text-align: left;"><div class="separator" style="clear: both; text-align: left;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEig8AiFMQUnIpFWGEIYmo3GTogKFsgI7AI9AWxriTE8M-nyzFKujz01YRN2Uq9QdtfelZJuIp0Pff2f5StbDFWiLNxoICt8Lj-hUh0B0xvpMP7ymMmobOPAicVQllPC6BhBy6FpIpOW7i5wfW-P1aVk4oSD3W_yPzLgmEeTulIjqx7ietZULcfpz-65ag/s1827/FeZeIsEXwAI4sy8.jpeg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img alt="Single potato plant stem with several leaves and two light purple flowers. Stems are dark purple." border="0" data-original-height="1827" data-original-width="1826" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEig8AiFMQUnIpFWGEIYmo3GTogKFsgI7AI9AWxriTE8M-nyzFKujz01YRN2Uq9QdtfelZJuIp0Pff2f5StbDFWiLNxoICt8Lj-hUh0B0xvpMP7ymMmobOPAicVQllPC6BhBy6FpIpOW7i5wfW-P1aVk4oSD3W_yPzLgmEeTulIjqx7ietZULcfpz-65ag/w200-h200/FeZeIsEXwAI4sy8.jpeg" width="200" /></a></div>As potatoes are in the same genus as tomatoes, they do produce fruit which is very similar to those of tomatoes. However, instead of being large and colorful, potato fruit are small and generally remain green. Most people who've grown potatoes have never seen the fruit because many commercial varieties rarely flower and even more rarely set fruit. Commercial varieties have been bred to not flower and/or produce fruit because that would take energy wasted that could otherwise be used to grow tubers.<br />
<br />
The fruit are generally considered to be poisonous (due to high solanine content) like the other non-tuber parts of the plant. Solanine can usually be detected as a bitter taste, but
sensitivity to it varies and people have been sickened or killed by
consuming too much of it. <br />
<br />
Professional potato breeders have been actively reducing the level of solanine in potatoes for decades. A side-effect of this selection process could be the reduction of solanine in the berries as well as the tubers, but nobody seems to have been researching this possibility.<br />
<br />The story teller's cousin could have been growing a potato variety that coincidentally had extra-low solanine levels in its fruit, or they could have a low sensitivity to solanine. Either way, they probably wouldn't have been able to collect enough fruit from the potato plants to be at risk of being in any real danger from the amount of solanine.<br />
<br />A weekend prior to when I first started writing this post, I gathered a batch of fruit from some Yukon Gold potato plants. I tasted one and found it mildly bitter. My mother in law tasted it and found it terribly bitter. We had sampled a similar amount of the fruit and so our different reactions likely reflect different abilities to taste the solanine.<br />
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<div style="text-align: left;"><br /></div><div style="text-align: left;"><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcicGxhjAZknk-VBW3AxmosuT8Nh8QMS5k0nTF2F-YB9DqNOiFwvqU8M5okJNqNl002TDfoWQ308XK1bmDrdHaylibvKw7MJdQeazRG-A6JwA3dNrrqb1sqvKKSGsDX1K6RMlJN_8qY3QUWvWPoSfVyw79Kl1WqiOZn3owBtNcVw7_KuEaV8XEIv4miA/s2048/FUrbZxlWAAARYZ4.jpeg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em; text-align: left;"><img alt="Four small piles of small potatoes. At bottom-right is five red potatoes. At top-left is two larger brown/purple potatoes. At bottom-right is four dark purple potatoes. At top-right are four black potatoes." border="0" data-original-height="1537" data-original-width="2048" height="150" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcicGxhjAZknk-VBW3AxmosuT8Nh8QMS5k0nTF2F-YB9DqNOiFwvqU8M5okJNqNl002TDfoWQ308XK1bmDrdHaylibvKw7MJdQeazRG-A6JwA3dNrrqb1sqvKKSGsDX1K6RMlJN_8qY3QUWvWPoSfVyw79Kl1WqiOZn3owBtNcVw7_KuEaV8XEIv4miA/w200-h150/FUrbZxlWAAARYZ4.jpeg" width="200" /></a></div>I wouldn't advise eating the tomato-like berries to be found occasionally on potato plants, but they have other uses.</div>Potatoes are typically grown from seed potatoes (either saved from the previous year or bought anew from tissue-culture labs) and thus are genetic clones that will grow/produce very consistently from year to year. The true potato seeds (TPS), however, are the result of a cross- or self-pollination. The mixing up of the parents' genetics means every plant grown from true seed will be different.</div><div style="text-align: left;"><br /></div>
<div dir="ltr" style="text-align: left;" trbidi="on">
As the only potatoes growing in the patch were Yukon Gold, the seeds in the gathered fruit likely represent the result of a self-pollination. Every plant that grows from TPS is instantly a new variety that can then be cloned by saving the tubers. Over a few years one could grow a significant number of new varieties from any given cross, in time developing an appreciation for the genetics that are found in the parent(s). Yukon Gold is a popular variety and others have already performed exactly this experiment. </div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">A <a href="http://www.tomatoville.com/showthread.php?t=6761">forum discussion about TPS</a> about the likely results of growing seeds from Yukon Gold, written by Tom Wagner, a notable tomato and potato breeder:</div>
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<blockquote>
<span style="color: #990000;"><span style="font-size: x-small;">I have been testing Yukon Gold OP berries for 25 years or more ever since the experimental clone was first accessed by me. In controlled self pollinated berries, as opposed to OP berries, I get a rather predictable segregation of types each time I grow out seedlings. If you grow out seedlings yourself enjoy the following:</span></span><br />
<ul>
<li><span style="color: #990000;"><span style="font-size: x-small;">whites with white flesh</span></span></li>
<li><span style="color: #990000;"><span style="font-size: x-small;">whites with light yellow flesh</span></span></li>
<li><span style="color: #990000;"><span style="font-size: x-small;">yellows with light yellow flesh</span></span></li>
<li><span style="color: #990000;"><span style="font-size: x-small;">yellows with medium yellow flesh</span></span></li>
<li><span style="color: #990000;"><span style="font-size: x-small;">yellows with deeper yellow flesh</span></span></li>
<li><span style="color: #990000;"><span style="font-size: x-small;">repeat of above but with either light pink eyes/red eye</span></span></li>
<li><span style="color: #990000;"><span style="font-size: x-small;">all of the above with templates of size, yield, shape, flavor, etc., differences.</span></span></li>
</ul>
<span style="color: #990000;"><span style="font-size: x-small;"><b>Yukon Gold</b> was selected from a cross between Norgleam (female) and W5279-4 (a yellow-fleshed diploid hybrid of <i>S. phureja</i> and haploid cv <b>Katahdin</b>). Yukon Gold is a tetraploid because of the unreduced gamete from it pollen parent.
</span></span></blockquote>
Yukon Gold is a tetraploid with a complex parentage, potentially giving it a wide range of possible genetic combinations. That most of those possibilities seem to fall into a distinct set of combinations just means that for those visible traits there isn't that much diversity hiding inside the parent. If you want to play with intensely-colored tubers you would have to <a href="http://www.tom8toes.com/index.php/potatoes.html">look elsewhere</a>.<br />
<br />
The really interesting thing about growing potatoes from TPS is all the minor variations in the plant that might impact production or how the plants grow. Over a few years one could select a variety perfectly-suited to the peculiar conditions of your garden, rather than hoping that the default clones available in the store will work for you. At least that's the theory, if you've got enough time and space to dedicate to the task.<br /><br /><hr width="50%" /><br /><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUgy2gCnGXk4IlkW73NP79au1KdbujAFz_zbJr9872Qh67cCmB6uEh6hFq5m4IanPog-h0ML-thmr91YafxFeHfLuKHYV-xnUbA-Yztne6aD4_uq63CgLp7k4L5k1FMIVssA-R6xl2JVv2asEeoNlejEGxu2LIW1ZXiULbNrW4KOr2BoRqYWhWYFSojQ/s597/Fe4y_WlWAAgSGEM.jpeg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Bowl of small tan potatoes with small purple marks." border="0" data-original-height="491" data-original-width="597" height="164" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgUgy2gCnGXk4IlkW73NP79au1KdbujAFz_zbJr9872Qh67cCmB6uEh6hFq5m4IanPog-h0ML-thmr91YafxFeHfLuKHYV-xnUbA-Yztne6aD4_uq63CgLp7k4L5k1FMIVssA-R6xl2JVv2asEeoNlejEGxu2LIW1ZXiULbNrW4KOr2BoRqYWhWYFSojQ/w200-h164/Fe4y_WlWAAgSGEM.jpeg" width="200" /></a></div>A few years back I ordered some true potato seed from <a href="https://www.cultivariable.com/">cultivariable.com</a> to start experimenting with in my garden. Most of the seedlings each year have failed for one reason or another.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">A few plants didn't produce a single tuber. Most of those that produced tubers got infected with what might have been late-blight (<i>Phytophthora infestans</i>). For my purposes, the specific disease didn't matter. Any with an obvious infection were discarded.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">Of those that made it to harvest, some didn't survive winter storage. A very few didn't taste good. One tasted like fresh-mowed grass. (In retrospect, I wish I had kept that one for its prank value alone.) A few that made it through all those steps didn't manage to grow any tubers in the next year.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">I did end up with a handful of varieties which seem to grow well enough in my environment, produce tubers that store well, and importantly also taste good. A selection of my varieties can be seen in the photos above. Some even ended up having very nice flowers, though one would never mistake the plants for garden flowers. This year I'm planning to grow a commercial type along side mine, to get a better sense for how well they produce vs the commercial control. Every year in the garden is a new experiment.</div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on"><br /></div><div dir="ltr" style="text-align: left;" trbidi="on">
References:<br />
<ul style="text-align: left;">
<li>Grafted tomato/potato</li>
<ul>
<li><a href="http://www.territorialseed.com/product/grafted-tomtato-ketchup-n-fries/new_for_spring_2015">www.territorialseed.com/product/grafted-tomtato-ketchup-n-fries/new_for_spring_2015</a></li>
<li><a href="https://www.youtube.com/watch?v=6V_X77CeTcs">www.youtube.com/watch?v=6V_X77CeTcs </a></li>
</ul>
<li>Solanine</li>
<ul>
<li><a href="http://www.food-info.net/uk/qa/qa-fp95.htm">www.food-info.net/uk/qa/qa-fp95.htm</a> </li>
<li><a href="http://www.smithsonianmag.com/arts-culture/horrific-tales-of-potatoes-that-caused-mass-sickness-and-even-death-3162870/?no-ist">www.smithsonianmag.com/arts-culture/horrific-tales-of-potatoes-that-caused-mass-sickness-and-even-death-3162870/?no-ist</a></li>
</ul>
<li>Tom Wagner</li>
<ul>
<li><a href="http://www.tomatoville.com/showthread.php?t=6761">www.tomatoville.com/showthread.php?t=6761</a></li>
</ul>
<ul>
<li><a href="http://gardenrant.com/2012/01/an-interview-with-the-true-potato-seed-man.html">gardenrant.com/2012/01/an-interview-with-the-true-potato-seed-man.html</a></li>
</ul>
<li>Potato Seeds</li>
<ul>
<li><a href="http://www.tom8toes.com/index.php/potatoes.html">www.tom8toes.com/index.php/potatoes.html</a></li>
<li><a href="http://tatermaterseeds.com/shop/index.php?main_page=index&cPath=2&zenid=c96f378a548b3b7031d204e6f608f617">tatermaterseeds.com/shop/index.php?main_page=index&cPath=2&zenid=c96f378a548b3b7031d204e6f608f617</a> </li>
<li><a href="http://www.doublehelixfarms.com/true-potato-seed-TPS">www.doublehelixfarms.com/true-potato-seed-TPS</a></li><li><a href="https://www.cultivariable.com/">www.cultivariable.com/</a></li>
</ul>
</ul>
</div>
</div>
</div></div>Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-75157616062893220882023-01-20T12:00:00.007-06:002023-01-31T03:26:17.048-06:00The Color of Beans 3<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEIjZe-cZyLs7KiSv_d3FoPpI_cOWkVte0yteNdYIeeKNFZUCiT2qqd_DNzo63aMNFTzaT0wigxGjTC4wxHvo9dwKDD-dPENoJh_1g61Krg7eDvl6PCUwR21P0rgXuLvkcZsErZMrNfJx0QdkXVy00BkQ0DFljY0cSk6yeiERVdVbtVSY9EWxkUh9H3Q/s931/anthocyanin_pathway-1.png" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Diagram illustrating the flavone pigment pathway.
Starting section from the top: phenylalanine to cinnaminate to 4-coumerate to p-coumaroyl-CoA (+ 3x malonyl-CoA) to naringen chalcone to naringen. Naringen goes left and right to eriodictyol and pentahydroxy flavone. Eriodictyol goes left to flavan-4-ols and then to phlobaphenes (highlighted in red). Eriodictyol goes right to tricetin. Naringen goes right to apigentin (highlighte light brown). Pentahydroxy falvanone goes right to luteolin (highlighted pale yellow). Naringenin goes down to dihydrokaempferol. Eriodictyol and dihydrokaempferol go left to dihydroquercetin. Pentahydroxy flavanone and dihydrokaempferol go right to dihydromyricetin. Dihydroquercetin goes right to quercetin (highlighted in yellow). Dihydrokaempferol goes right to kaempferol (highlighted in yellow) and then down to atragalin (highlighted in yellow). Dihydromyricetin goes right to myricetin (highlighted light brown). Dihydroquercetin goes down to leuocyanidin. Dihydrokaempferol goes down to leucopelargonidin. Dihydromyricetin goes down to leucodelphinidin. Leucocyanidin goes down to cyanidin and then cyanin (both highlighted red). Leucopelargonidin goes down to pelargonidin and pelargonin (both highlighted orange). Leucodelphinidin goes down to delphinidin and delphinin (both highlighted blue). Leucocyanidin, leucopelargonidin, and leucodelphinidin go left to 2,3-trans-flaven-3-ols (catechin) (highlighted in in a gradient from white to brown). Cyanidin, pelargonidin, and delphinidin go left to 2,3-cis-flaven-3-ols (epecatechin) (highlighted in a gradient from white to brown). Catechin and epicatechin go down to proanthocyanidins (highlighted in a gradient from white to brown). Luteolin, apigenin, and tricetin have a group label 'flavones'. Myrictein, kaempferol, and quercetin have a group label 'flavonols'.
The figure has enzyme labels at most steps.
In the top starting section: PAL, C4H, 4CL, CHS, and CHI. Naringenin to eriodictyol is F3'H. Naringenin to pentahydroxy flavanone is F3'5'H. Eriodictyol, naringenin, and pentahydroxy flavanone to tricetin, apigenin, and luteolin are FNS. Eriodictyol, naringenin, and pentahydroxy flavanone to to dihydroquercetin, dihydrokaempferol, and dihydromyrecetin are F3'H. Eriodictyol to flavan-4-ols is DFR. Dihydrokaempferol to dihydroquercetin is F3'H. Dihydrokaemperol to dihydromyricetin is F3'5'H. Dihydroquercetin, dihydrokaempferol, and dihydromyricetin to quercetin, kaempferol, and myricetin are FLS. Dihydroquercetin, dihydrokaempferol, and dihydromyricetin to leucocyanidin, leucopelargonidin, and leucodelphindin are DFR. Leucocyanidin, leucopelargonidin, and leucodelphindin to cyanidin, pelargonidin, and delphinidin are ANS. Cyanidin, pelargonidin, and delphinidin to cyanin, pelargonin, and delphinin are GT. Leucocyanidin, leucopelargonidin, and leucodelphindin to catechin are LAR. Cyanidin, pelargonidin, and delphinidin to epicatechin are ANR." border="0" data-original-height="636" data-original-width="931" height="219" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiEIjZe-cZyLs7KiSv_d3FoPpI_cOWkVte0yteNdYIeeKNFZUCiT2qqd_DNzo63aMNFTzaT0wigxGjTC4wxHvo9dwKDD-dPENoJh_1g61Krg7eDvl6PCUwR21P0rgXuLvkcZsErZMrNfJx0QdkXVy00BkQ0DFljY0cSk6yeiERVdVbtVSY9EWxkUh9H3Q/s320/anthocyanin_pathway-1.png" width="320" /></a></div>A great deal of research has gone into our understanding of how colors are made in plants. I've previously written about the carotenoid pigment pathways in <a href="https://the-biologist-is-in.blogspot.com/2014/04/the-color-of-tomatoes.html">tomatoes [1]</a> and <a href="https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html">peppers [2]</a>, condensing a great deal of published literature in the process. Until recently, I didn't have a solid grasp of the pathway plants use to make a second major category of pigments, the flavonoid pigments. These pigments are responsible for many of the red/purple/blue colors you see in flowers and other plant parts, but I've been learning about them through my focus on the various colors of dry beans.<div><br /></div><div>The carotenoid pigment pathway I discussed in those earlier articles was relatively simple. A single main pathway, with a couple branches. The anthocyanin pathway figure at above-right is a bit more complicated. The figure is a consensus pathway, built from research in a few different species. There are definitely more pieces that could be added, but this amount is a good start. The colored highlights are intended to represent the colors of those chemicals. The lower red, orange, and blue pigments are anthocyanins, the pigments responsible for the color of many flowers (and other plant parts). The white-to-brown gradient highlight is for the proanthocyanidins. They oxidize over time, changing from clear to brown. The red pigment at upper-left is found in some trees, but I wasn't able to find too much information about them. The yellow pigments at right are found in various plants and plant parts, but they're not generally the source for bright yellows in flowers. (The enzyme FGT leading to astragalin at far right is something I made up, since I couldn't find any research naming the enzyme performing that step.)</div><div><br /></div><div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjl4fltZ6PMr7zxok03pAc2oOpJs67i0LgBrT_mZOKlBg6azaHajdOYagKA-uJXdQ3M0ECZnZzT6tB9fxqka2Za4WvOsKgDR9o0CcqxFEJfQK2AxE7UPeDm_H4mlNkTmLE_ovw2ECFCIdnWqXWE0J4KY-X7SytNkQZLTQoKoOfaZhnf3DfAxt_ce2vFIg/s904/anthocyanin_pathway-2.png" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Diagram illustrating the flavone pigment pathway as found in common dry beans.
Starting section from the top: phenylalanine to cinnaminate to 4-coumerate to p-coumaroyl-CoA (+ 3x malonyl-CoA) to naringen chalcone to naringen to dihydrokaempferol. Dihydrokaempferol goes left to dihydroquercetin and right to dihydromyricetin. Dihydroquercetin goes right to quercetin (highlighted in yellow). Dihydrokaempferol goes right to kaempferol (highlighted in yellow) and then down to atragalin (highlighted in yellow). Dihydromyricetin goes right to myricetin (highlighted light brown). Dihydroquercetin goes down to leuocyanidin. Dihydromyricetin goes down to leucodelphinidin. Leucocyanidin goes down to cyanidin and then cyanin (both highlighted red). Leucodelphinidin goes down to delphinidin and delphinin (both highlighted blue). Leucocyanidin and leucodelphinidin go left to 2,3-trans-flaven-3-ols (catechin) (highlighted in in a gradient from white to brown). Cyanidin and delphinidin go left to 2,3-cis-flaven-3-ols (epecatechin) (highlighted in a gradient from white to brown). Catechin and epicatechin go down to proanthocyanidins (highlighted in a gradient from white to brown). Myrictein, kaempferol, and quercetin have a group label 'flavonols'.
The figure has enzyme labels at most steps.
In the top starting section: PAL, C4H, 4CL, CHS, CHI, and F3H. Dihydrokaempferol to dihydroquercetin is F3'H. Dihydrokaemperol to dihydromyricetin is F3'5'H. Dihydroquercetin, dihydrokaempferol, and dihydromyricetin to quercetin, kaempferol, and myricetin are FLS. Dihydroquercetin and dihydromyricetin to leucocyanidin and leucodelphindin are DFR. Leucocyanidin and leucodelphindin to cyanidin and delphinidin are ANS. Cyanidin and delphinidin to cyanin and delphinin are GT. Leucocyanidin and leucodelphindin to catechin are LAR. Cyanidin and delphinidin to epicatechin are ANR." border="0" data-original-height="636" data-original-width="904" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjl4fltZ6PMr7zxok03pAc2oOpJs67i0LgBrT_mZOKlBg6azaHajdOYagKA-uJXdQ3M0ECZnZzT6tB9fxqka2Za4WvOsKgDR9o0CcqxFEJfQK2AxE7UPeDm_H4mlNkTmLE_ovw2ECFCIdnWqXWE0J4KY-X7SytNkQZLTQoKoOfaZhnf3DfAxt_ce2vFIg/s320/anthocyanin_pathway-2.png" width="320" /></a></div>At left is a heavily reduced version of the first figure, trimmed to an approximation of what seems to be going on in common beans (<i>Phaseolus vulgaris</i>). Combinations of the yellow, red, blue, and brown pigments seem to be responsible for most of the variations in color that we see in dry beans. I've seen some evidence for a brown pigment derived from the yellow ones here, but I haven't found any research clarifying the chemistry involved. There's the possibility of some green pigments made up from a different metabolic pathway, but I haven't found sufficient research about them to know if they're represented in beans.<br />Various of the trimmed compounds are also found in common beans, but they don't seem to be found in significant amounts. The orange pelargonidin pigments have been reported in some bean varieties, but I've never come across a common bean that has a color dominated by orange pigment. There might be orange examples from <i>P. coccineus</i>, the scarlet runner bean, but I'm still investigating this.</div><br /><hr width="50%" /><br />The colors of beans drew attention far before we had any understanding of the physiology of the pigments involved. Much of the early published research into bean colors sought to identify different genes responsible for the traits. Eventually the gene labels assigned by different authors got correlated with each other and the set of labels for important color genes became standardized. Even more recently, there have been efforts to identify the molecular mechanism behind the different classical gene labels. Some gene labels are now associated with specific enzymes or other genes important in the flavonoid pathway.<div><br /></div><div><ul style="text-align: left;"><li>R [red] : Enzyme F3'H, or more likely a transcription factor driving F3'H in the seed coat. F3'H is important for stress response in plant tissues and so is unlikely to be absent even when the enzyme isn't active in the pathway.</li><li>V [violet] : Enzyme F3'5'H. This one isn't as important as F3'H and is entirely absent in many plants.</li><li>J : Pretty solidly identified as the enzyme DFR.</li><li>P : A transcription factor driving expression of several genes important in the flavonoid pathway. In the figures above, the regulated enzyme targets are drawn in blue.</li><li>B : A transcription factor driving expression of chalcone synthase (CHS) and/or chalcone isomerase (CHI).</li><li>G : A transcription factor leading to increased levels of astragalin, perhaps by driving expression of FLS and/or FGT. Likely has other impacts, but I haven't found sufficient research.</li></ul></div><div><div><br /></div><div>Tracking down which gene was associated with which step in the pathway was tricky. Many of the older papers had models for what a given gene did, but then those models were overturned by more recent research. The <a href="https://www.frontiersin.org/articles/10.3389/fpls.2022.869582/full#ref33">paper identifying V as being the gene for the enzyme F3'5'H</a> was only published in March 2022. Finding that paper got me interesting in trying to see how many of the others could also be associated with a specific part of the pathway. The other gene notes above came from the scattered papers linked in the references section, though few were specifically the point of the papers.</div><div><br /></div><div>My goal was to better understand what the gene labels were doing, so I could better figure out what genes were likely to be involved in the beans I was growing and crossing. I'll write more on that another time.</div><br /><br />
<div>References</div><div><ol style="text-align: left;"><li>Related blog posts:</li><ol><li><a href="https://the-biologist-is-in.blogspot.com/2014/04/the-color-of-tomatoes.html">https://the-biologist-is-in.blogspot.com/2014/04/the-color-of-tomatoes.html</a></li><ul><li>Carotenoid pigments in tomatoes.</li></ul><li><a href="https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html">https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html</a></li><ul><li>Carotenoid pigments in peppers.</li></ul><li><a href="https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html">https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html</a></li><ul><li>Introduction of my #BlueBeanProject.</li></ul><li><a href="https://the-biologist-is-in.blogspot.com/2022/12/the-color-of-beans-2.html">https://the-biologist-is-in.blogspot.com/2022/12/the-color-of-beans-2.html</a></li><ul><li>Status update of my #BlueBeanProject.</li></ul><li><a href="https://the-biologist-is-in.blogspot.com/2019/11/biology-of-blue.html">https://the-biologist-is-in.blogspot.com/2019/11/biology-of-blue.html</a></li><ul><li>Discussions around the chemistry of blue in biology.</li></ul></ol><li>Papers related to anthocyanin pathway in bean, cotton, etc:</li><ol><li><a href="http://arsftfbean.uprm.edu/bic/wp-content/uploads/2018/04/ChemistrySeedCoatColor.pdf">http://arsftfbean.uprm.edu/bic/wp-content/uploads/2018/04/ChemistrySeedCoatColor.pdf</a></li><li><a href="https://nph.onlinelibrary.wiley.com/doi/full/10.1002/ppp3.10132">https://nph.onlinelibrary.wiley.com/doi/full/10.1002/ppp3.10132</a></li><li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602603/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602603/</a></li><li><a href="https://link.springer.com/article/10.1007/s11738-011-0858-x">https://link.springer.com/article/10.1007/s11738-011-0858-x</a></li><li><a href="https://pubmed.ncbi.nlm.nih.gov/28981784/">https://pubmed.ncbi.nlm.nih.gov/28981784/</a></li><li><a href="https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-2065-7">https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-2065-7</a></li><li><a href="https://pubmed.ncbi.nlm.nih.gov/35289870/">https://pubmed.ncbi.nlm.nih.gov/35289870/</a></li><li><a href="https://squashpractice.com/2011/10/08/bean-genes/">https://squashpractice.com/2011/10/08/bean-genes/</a></li><li><a href="https://journals.ashs.org/jashs/view/journals/jashs/124/5/article-p514.xml">https://journals.ashs.org/jashs/view/journals/jashs/124/5/article-p514.xml</a></li><li><a href="https://www.frontiersin.org/articles/10.3389/fpls.2022.869582/full#ref33">https://www.frontiersin.org/articles/10.3389/fpls.2022.869582/full#ref33</a></li><li><a href="https://journals.ashs.org/downloadpdf/journals/jashs/120/6/article-p896.pdf">https://journals.ashs.org/downloadpdf/journals/jashs/120/6/article-p896.pdf</a></li><li><a href="https://journals.ashs.org/downloadpdf/journals/jashs/125/1/article-p52.pdf">https://journals.ashs.org/downloadpdf/journals/jashs/125/1/article-p52.pdf</a></li><li><a href="https://www.semanticscholar.org/paper/Allelism-Found-between-Two-Common-Bean-Genes%2C-Hilum-Bassett-Shearon/f9cef3175289b7d2822461b9d495d8885bb67a48">https://www.semanticscholar.org/paper/Allelism-Found-between-Two-Common-Bean-Genes%2C-Hilum-Bassett-Shearon/f9cef3175289b7d2822461b9d495d8885bb67a48</a></li><li><a href="https://www.semanticscholar.org/paper/Inheritance-of-Reverse-Margo-Seedcoat-Pattern-and-J-Bassett-Lee/7557538290b700d1fd980a24fba3148846861690">https://www.semanticscholar.org/paper/Inheritance-of-Reverse-Margo-Seedcoat-Pattern-and-J-Bassett-Lee/7557538290b700d1fd980a24fba3148846861690</a></li><li><a href="https://www.semanticscholar.org/paper/The-Margo-%28mar%29-Seedcoat-Color-Gene-Is-a-Synonym-%28-Bassett/d1c58ec1fa0bf9e500d8bd48364a61568b0b7a11">https://www.semanticscholar.org/paper/The-Margo-%28mar%29-Seedcoat-Color-Gene-Is-a-Synonym-%28-Bassett/d1c58ec1fa0bf9e500d8bd48364a61568b0b7a11</a></li><li><a href="https://naldc.nal.usda.gov/catalog/IND92036951">https://naldc.nal.usda.gov/catalog/IND92036951</a></li></ol></ol></div></div>Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-83820481464395827762023-01-13T12:00:00.002-06:002023-02-07T12:48:10.176-06:00The Color of Pineapple<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhFN8o-w-HvfZ8Y0JCRXdg3bT_953peYGrpg1YoGQaw5MWISAdPXQe0pZGQFF1B7ziH78rS3CSWqXJGQOWXBNSGRJAth3OuyrDw2bp-ayXChYI7mnR9sQSV73hMl8RFQVFxbwZGjHPFv--ijkOlFHqJPg--P24bYOizzHBF-0K30DWTCQyXUq6m7otB5Q/s2048/PinkGlow_Pineapple.jpeg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Clear glas bowl filled with chunks of cut pink pineapple." border="0" data-original-height="2048" data-original-width="2048" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhFN8o-w-HvfZ8Y0JCRXdg3bT_953peYGrpg1YoGQaw5MWISAdPXQe0pZGQFF1B7ziH78rS3CSWqXJGQOWXBNSGRJAth3OuyrDw2bp-ayXChYI7mnR9sQSV73hMl8RFQVFxbwZGjHPFv--ijkOlFHqJPg--P24bYOizzHBF-0K30DWTCQyXUq6m7otB5Q/w200-h200/PinkGlow_Pineapple.jpeg" width="200" /></a>
The pineapple we all grew up with is a bright yellow color. The pineapples of today isn't necessarily the same shade. Del Monte is now selling a variety with a distinctly pink flesh, called PinkGlow<sup>TM</sup> or Rosé pineapple. This is a bio-engineered variety, first conceptualized way back in 2005. A patent for the variety was issued in 2012 and the US <a href="https://www.fda.gov/food/cfsan-constituent-updates/fda-concludes-consultation-pink-flesh-pineapple">FDA deregulated the variety in 2016</a>, deciding the variety was essentially the same as other varieties with regards to safety and regulatory concerns.<br />The variety started as an extra sweet variety grown in Hawaii called MD2. This pink version shares the extra sweet and low acid traits of that original variety. I think it is a worthwhile product, even though (in my limited experience) most people's reactions to seeing the pink cut pieces at left was to think they looked like pieces of meat.<br /><hr width="50%" /><br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjh5e1V8Dvz6JjlmggQnMK3MJdbSzj2vdsZdr13Gd8E0JGekW1u7BwfCCJFMqFLEnUp8LTS0PsFY4blywhLM_yVZn6ncxFO_a2h4rPqRmMZ2rYtabSJh5rFFGpgrrYKfUHev96jfPNmjtdI-m6TsbXsicW9vDihAHewDHfbLlHu2AM69Jp8fCGYIS7D7w/s943/pigment_pathway_pineapple.png" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Figure depicting the carotenoid biosynthesis pathway in plants. Starting at top: Acetyl-CoA -> Isopentyl pyrophosphate -> Geranyl pyrophosphate -> Farnesyl pyrophosphate -> Geranylgeranyl pyrophosphate -> Phytoene. An arrow also goes from Geranylgeranyl pyrophosphate to Phytol -> Chlorophyll ->->-> Un-colored metabolites. From Phytoene -> Phytofluene -> Ksi-carotene -> Neurosporene -> Prolycopene -> Lycopene -> Delta-carotene -> Alpha-carotene -> Lutein. A second branch from Lycopene -> Gamma-carotene -> Beta-carotene -> Beta-cryptoxanthin -> Zeaxanthin -> Antheraxanthin -> Violaxanthin -> Xanthoxin -> Abscisic Acid aldehyde -> Abscisic acid. A side brance from Gamma-carotene -> Torulene. A side brance from Violaxanthin -> Neoxanthin -> Xanthoxin (already in the pathway described)." border="0" data-original-height="943" data-original-width="413" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjh5e1V8Dvz6JjlmggQnMK3MJdbSzj2vdsZdr13Gd8E0JGekW1u7BwfCCJFMqFLEnUp8LTS0PsFY4blywhLM_yVZn6ncxFO_a2h4rPqRmMZ2rYtabSJh5rFFGpgrrYKfUHev96jfPNmjtdI-m6TsbXsicW9vDihAHewDHfbLlHu2AM69Jp8fCGYIS7D7w/w88-h200/pigment_pathway_pineapple.png" width="88" /></a>
The <a href="https://patents.google.com/patent/USPP25763">patent</a> is a bit of a pain to read, as they generally are. The "<span face="Roboto, sans-serif" style="font-size: 13px;">DETAILED DESCRIPTION OF THE INVENTION" section is where they describe the details of the alterations they made.<br /><br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYF1L38KaWPI7H4zAJ8ec5AxllG_jNQ_2EPnX5AQoqpspEu7yUghs-WxufHxCg99OmNE4WSQiKcliXee911kqWmzc3asC0u42kGCW72kVu3yZc83cpYOgiTuLMPo37S40RHM85RotK5jkO_IqXrccLOP5e250HwUv9MUnM9HKXxTqPbYJQ2psxIbqbQg/s418/pigment_pathway_pineapple_2.png" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="A figure representing part of the carotenoid pathway described in the previous image. A larger arrow goes from Geranylgeranyl pyrophosphate to Phytoene. A large X covers each arrow leading away from Lycopene." border="0" data-original-height="418" data-original-width="258" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYF1L38KaWPI7H4zAJ8ec5AxllG_jNQ_2EPnX5AQoqpspEu7yUghs-WxufHxCg99OmNE4WSQiKcliXee911kqWmzc3asC0u42kGCW72kVu3yZc83cpYOgiTuLMPo37S40RHM85RotK5jkO_IqXrccLOP5e250HwUv9MUnM9HKXxTqPbYJQ2psxIbqbQg/w124-h200/pigment_pathway_pineapple_2.png" width="124" /></a>
At left is a sketch of the carotenoid pathway in pineapples. There is limited published information about the specifics of the pathway in pineapple, so this diagram was constructed from more general research in <a href="https://the-biologist-is-in.blogspot.com/2014/04/the-color-of-tomatoes.html">tomatoes</a>, <a href="https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html">peppers</a>, and other species. At right is a closeup of the pathway altered to illustrate the changes that were made in the pink pineapple, as described in the patent.<br /><br />The first modification was to introduce a second copy of the phytoene synthase gene, driving increased amounts of metabolic energy through the carotenoid pathway. This is represented in the figure by a larger arrow at the top. The added gene was combined with a pineapple fruit flesh specific promotor, so the rest of the plant doesn't have its carotenoid pathway messed around with.<br /><br />The second modification was to shut down two enzymes, lycopene beta-cyclase and lycopene epsilon-cyclase, normally responsible for converting lycopene into the next steps in the two branches of the carotenoid pathway after lycopene. The consequence of this is all the metabolic energy passing through the pathway is stopped at lycopene. Shutting down these genes was performed by RNA interference (RNAi), also driven by a copy of the same fruit flesh specific promotor. Again, this prevents the modification from interfering with the carotenoid pathway elsewhere in the pineapple plant.<br /><br />The carotenoid pathway is important for a plant's stress response and other systems. It is likely a pineapple plant would survive more dramatic alterations to the carotenoid pathway that impacted the entire plant, but doing so would throw off the existing balance. The efforts they've taken to limit the pathway tweaks to only happen within the fruit flesh were important to ensure the plants generally are as productive and healthy as the pineapple they started with.<br /><br /><hr width="50%" /><br />A third modification was atempted, but how the patent is written indicates they're not exactly sure the alteration worked. Commercial pineapple production relies on precision planning. To get a pineapple crop to mature at a specific planned time, the plants are treated with a hormone which induces flowering. In pineapple, the hormone that triggers flowering is the simple gas ethylene. Either ethylene or the similar shaped molecule acetylene is used to induce a crop to start blooming at a specific time. The problem is, pineapple plants will initiate blooming all on their own, when the growers may not want the plants to do so. This is called "natural flowering" and interferes with the plans of the growers.<br /><br />So, to try and reduce the rate of natural flowering, the third modification was to try and supress the ACC synthase gene important for normal ethylene biosynthesis. They again used RNAi for this, targeted to growing meristems where the gene enzyme activity is important for normal flower induction. I suspect the reason the patent expresses uncertainty about this modification working is because at the time of patent filing, they didn't have enough experience with growing the new pineapple in field conditions to be able to see a reduction in the rate of natural flowering. By now they'll know for sure if it worked.
<br /><br />References:<ol style="text-align: left;"><li>Marketing piece: <a href="https://specialtyproduce.com/produce/Pinkglow_Pineapple_17105.php">https://specialtyproduce.com/produce/Pinkglow_Pineapple_17105.php</a></li><li>Patent: <a href="https://patents.google.com/patent/USPP25763">https://patents.google.com/patent/USPP25763</a></li><li>FDA statement: <a href="https://www.fda.gov/food/cfsan-constituent-updates/fda-concludes-consultation-pink-flesh-pineapple">https://www.fda.gov/food/cfsan-constituent-updates/fda-concludes-consultation-pink-flesh-pineapple</a></li><li>Carotenoids in tomatoes: <a href="https://the-biologist-is-in.blogspot.com/2014/04/the-color-of-tomatoes.html">https://the-biologist-is-in.blogspot.com/2014/04/the-color-of-tomatoes.html</a></li><li>Carotenoids in peppers: <a href="https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html">https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html</a></li><li>Pineapple flower induction: <a href="https://www.echocommunity.org/resources/f0e9cfeb-ba1d-435e-a515-7705ca79b409">https://www.echocommunity.org/resources/f0e9cfeb-ba1d-435e-a515-7705ca79b409</a></li></ol></span>Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com1tag:blogger.com,1999:blog-2660869052224924549.post-6822635055471719632022-12-30T12:00:00.044-06:002022-12-30T15:47:17.688-06:00The Color of Beans 2<p>A few years back I wrote a short post to introduced a project I had started to breed up a nicely blue colored dry bean. </p><p style="text-align: center;"><a href="https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html">https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html</a></p><p>The project as been moving forward nicely since then. This year's crop was very consistently blue in color, the first time I didn't harvest a large fraction of tan/blue seeds as well.</p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgvwvWt1nhz-Z3vX32dvgcvBlyOsY7SR9yYMAbJB94iRXF-MZjmH9OSB5bcXTOk_2j7oxFj9Ezdrl0GjCpkneAoCOnVljp-rDMukCuCJT4ka6xz60gPcY2cE4W3X2bffzTFHgmjOpY4XZ0nDJTjkbll2d50koqdZ1d5KRw_8OujiNLhx-lrz_cqcpWMig/s2048/old-blue-beans.jpeg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Dry beans in mixed colors. Browns, blues, and dark greys." border="0" data-original-height="2047" data-original-width="2048" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgvwvWt1nhz-Z3vX32dvgcvBlyOsY7SR9yYMAbJB94iRXF-MZjmH9OSB5bcXTOk_2j7oxFj9Ezdrl0GjCpkneAoCOnVljp-rDMukCuCJT4ka6xz60gPcY2cE4W3X2bffzTFHgmjOpY4XZ0nDJTjkbll2d50koqdZ1d5KRw_8OujiNLhx-lrz_cqcpWMig/w200-h200/old-blue-beans.jpeg" width="200" /></a></div>The picture at left looks very similar to the one I included in the post linked above, but this photo is from a few days ago. These beans are the extras I had saved from earlier generations, including many from 2018. This tells me the best blue colored seeds are able to maintain their color well in long-term storage.<div><br /></div><div>The other truly blue varieties I have come across all seem to darken towards brown during storage. "San Berdardo Blue" and the rarer "Pragerhof" beans both have a nice blue color at harvest, but that color doesn't last. My blues keeping their color for a few years in storage is a nice improvement.</div><div><br /></div><div>Over the first several years, I selected the best blue colored seeds from each harvest to plant the following spring. Until this year's harvest, each year I kept finding brown/tan seeds. This tells me the brown color was due to recessive alleles, which means it can be very hard to filter out the brown-seed trait. Any given blue seed could be hiding the recessive brown color allele.</div><div><br /></div><div><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3ieF0ZaxsQj7TXYZ9LYP36lWxLXdpytlCJrz9ERebS30zzrLgFrgEurIRc_hSHV3oMGnWZP8RoAjEivHkj5xQyn_cNAwYipMU9cYS1zd_AspqHIQXg15uItz1ieqVaaqoYX3JmIGeI84kt80dql7TXOuKkatRdclD-uwYuso0InOiD_aae0txsdRRVA/s2048/2022_blue.jpeg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Dark blue dry beans." border="0" data-original-height="2048" data-original-width="2048" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3ieF0ZaxsQj7TXYZ9LYP36lWxLXdpytlCJrz9ERebS30zzrLgFrgEurIRc_hSHV3oMGnWZP8RoAjEivHkj5xQyn_cNAwYipMU9cYS1zd_AspqHIQXg15uItz1ieqVaaqoYX3JmIGeI84kt80dql7TXOuKkatRdclD-uwYuso0InOiD_aae0txsdRRVA/w200-h200/2022_blue.jpeg" width="200" /></a></div>This year I was lucky and the entire harvest had the rich blue color I had been working towards. The recessive allele for brown color could still be hiding among these. I won't be more certain I have finished filtering out that trait for at least a couple more years, but I am hopeful. Because I didn't have to select on color this year, I instead selected for larger seed size and pods (or pod clusters) with more seeds in them.</div><div><br /></div><div>Right now I am working to figure out how I can distribute this new variety, but it may not happen this year. I have very limited seed stock and any method of selling or distributing them comes with some significant costs.</div><div><br /></div><div>You can find more about these beans with the tag #BlueBeanProject on various social media systems. I'll also be writing more posts here, so stay tuned.</div><div><br /></div><hr width="50%" /><div><br /></div><div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjp7gpOe06lSeGtXq-Pi4pbif3r5Wx4RUuaKjecr2gM5mhZ1UWx-_UlAjRWYpJja_OnQtHpJMAe4A--0IzfCEAQuD72UB9Q8Nr6wk7BVyEj6ZtImBflB1kpvKne-QQdNQz4kPFN4BK_-H0aPxj2WIBLE1rsFmEghPKmrdGHTdO749UPxF1043ktU-KmWw/s1440/eyeshadow-beans.jpeg" style="clear: right; display: inline; float: right; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img alt="Eleven pale blue bean seeds, each with a black ring around the hilium." border="0" data-original-height="1440" data-original-width="1440" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjp7gpOe06lSeGtXq-Pi4pbif3r5Wx4RUuaKjecr2gM5mhZ1UWx-_UlAjRWYpJja_OnQtHpJMAe4A--0IzfCEAQuD72UB9Q8Nr6wk7BVyEj6ZtImBflB1kpvKne-QQdNQz4kPFN4BK_-H0aPxj2WIBLE1rsFmEghPKmrdGHTdO749UPxF1043ktU-KmWw/w200-h200/eyeshadow-beans.jpeg" width="200" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWC7nANf0qxWeeLeKjTqEe7Pp5bVsfWSu99YVFg7DIbsQC_ECFZVFILLgdX3uDRZ2rJIQvWHEk9sMKgQ8WHyS120zuukLI4eIgUT2H1-oBU_ZuAkfnArxGOfyM-batvZIMUIGRuJamzmv7t58WnqIu-iTyYfE9Haa6v-qY5oeS5UBqhSRFHwHJ7oLC2w/s1440/starry-night-beans.jpeg" style="clear: left; display: inline; float: left; margin-bottom: 1em; margin-right: 1em; text-align: center;"><img alt="Five dark blue bean seeds with tan speckles." border="0" data-original-height="1440" data-original-width="1440" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWC7nANf0qxWeeLeKjTqEe7Pp5bVsfWSu99YVFg7DIbsQC_ECFZVFILLgdX3uDRZ2rJIQvWHEk9sMKgQ8WHyS120zuukLI4eIgUT2H1-oBU_ZuAkfnArxGOfyM-batvZIMUIGRuJamzmv7t58WnqIu-iTyYfE9Haa6v-qY5oeS5UBqhSRFHwHJ7oLC2w/w200-h200/starry-night-beans.jpeg" width="200" /></a>I also have a couple new blue lines, unrelated to those above. These samples are F2s from a cross between "Pragerhof" and an unknown black bean.<br /><br /></div>One blue is darker than my main line and the other is lighter. I don't know for sure what these will become during the several years it will take to stabilize their genetics, but I aim to find out!<br /><div><br /></div><div>References:</div><div><p></p><ol style="text-align: left;"><li><a href="https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans.html" style="text-align: center;">https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans.html</a></li><li>"San Berdardo Blue" beans: <a href="https://store.experimentalfarmnetwork.org/products/nonna-agness-blue-bean">https://store.experimentalfarmnetwork.org/products/nonna-agness-blue-bean</a></li><li>"Pragerhof" beans: <a href="https://oroseeds.com/wp-content/uploads/2019/02/download-18.png">https://oroseeds.com/wp-content/uploads/2019/02/download-18.png</a></li><ul><li>No longer offered for sale by OroSeeds, but their photo remains online.</li></ul></ol><p></p></div>Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com013650 Thunderbird Cir, Prior Lake, MN 55379, USA44.752596 -93.45334531.883158848289877 -111.03147 57.622033151710113 -75.87522tag:blogger.com,1999:blog-2660869052224924549.post-34542926138217127352021-05-20T14:11:00.005-05:002021-05-20T14:11:53.254-05:00Viable Interspecific Eggplant Hybrids<p>The last year has been a mess. I'm fine. My family is fine. Most of my friends are fine. The increased anxiety and stress basically shut off any motivation or ability I had to write posts here. I was still active over on twitter or instagram, as those require less focused thought, but I just couldn't will myself to sit down at a computer and type up anything I felt was worthwhile to post.</p><p>I'm now fully vaccinated against covid19, but I know there are many people who still have not been able to access a vaccine. Some in my family. Many in the broader community. Covid cases in my community are dropping, but they're still higher than the peak we had in May of last year. I worry about recent CDC guidance and how people broadly seem to think it means the pandemic is over. It is not. Not here, and not elsewhere.</p><p>For now, most people locally seem to still be keeping up distancing and masking practices gained over the last year. As always, the next few weeks will be informative.</p><p>Even with the persistent writer's block, I routinely thought about
writing something. This post is the first something to come of that. It isn't really the long and information or photo rich posts I like to write, but it is what it is <br /></p>
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<p>My plant breeding projects have continued without interruption. My gardens have provided me with useful exercise and amusement. <br /></p><p>Most of my plant breeding projects start with hybrids between divergent varieties within one species. The F1 generally stands out from the two parental lines, so Iit is fairly easy to have confidence that the cross took. In the F2 generation, there are almost always useful and unexpected traits which segregates out.</p><p></p><p>Last year I grew out a F2 population of scarlet eggplant. Every plant was different, but two stood out. One was extra productive and ripened fruit far earlier than any others. The other developed fruit that were white when immature, but ripened to the typical red later. This season I have F3 populations from those two plants.</p><p>I still haven't figured out how to like eating eggplant, especially the more bitter flavors of the scarlet eggplant, but I like the plants and will continue to try.</p><p>Recently I found some references describing successful hybrids between the scarlet eggplant (<i>Solanum aethiopicum</i>) and more common purple eggplant (<i>S. melongena</i>), with some significant effort in the lab. This got me thinking about what species one could make hybrids with among the eggplant. Any such hybrids would allow for much more diverse F2 populations, with their higher potential for selection towards interesting new traits.</p><p>This led to some discussion about primary (1'), secondary (2'), and tertiary (3') germplasm. 1' germplasm includes plants in the same or related species which can cross readily to your subject species. 2' germplasm includes plants which can cross to your subject species with significant reduction in fertility. 3' germplasm is then plants that can cross with your subject only with intensive laboratory operations such as embryo rescue or induced genome duplication.</p><p>In the case of eggplants, there has been much more exploration of 2' and 3' germplasm for the common eggplant. The scarlet eggplant is an important crop for many communities, but it has not attracted as much attention in communities with higher levels of biological research investment. As such, the 2' and 3' germplasm lists below for scarlet eggplant are very much incomplete.<br /></p>
<p style="margin-left: 40px; text-align: left;"> Asian Eggplant (<i>Solanum melongena</i>)<br /></p><p style="margin-left: 40px; text-align: left;"></p><ol style="margin-left: 40px; text-align: left;"><li>primary: <i>S. incanum</i> and <i>S. insanum.</i></li><li>secondary: <i>S. anguivi</i>, <i>S. dasyphyllum</i>, <i>S. lichtensteinii</i>, <i>S. linnaeanum</i>, <i>S. pyracanthos</i>, <i>S. tomentosum</i>, and <i>S. violaceum</i>.<i><br /></i></li><li>tertiary: <i>S. elaeagnifolium</i>, <i>S. sisymbriifolium</i>, <i>S. torvum</i>, and <i>S. aethiopicum</i>. <br /></li></ol><p style="margin-left: 40px; text-align: left;">Scarlet Eggplant (<i>Solanum aethiopicum</i>)<span class="Eq0J8 LrzXr kno-fv"></span></p><ol style="margin-left: 40px; text-align: left;"><li><span class="Eq0J8 LrzXr kno-fv">primary: <i>S. anguivi</i>, <i>S. </i></span><span class="Eq0J8 LrzXr kno-fv"><span><i>macrocarpon</i>, and <i>S. dasyphyllum</i></span></span><i><span class="Eq0J8 LrzXr kno-fv"><span><br /></span></span></i></li><li><span class="Eq0J8 LrzXr kno-fv">secondary: <br /></span></li><li><span class="Eq0J8 LrzXr kno-fv">tertiary: <i>S. melongena</i>. <br /></span></li></ol><p></p>
<p>Professional plant breeders pursue traits from related species like these to improve disease resistance, drought resistance, or other traits important to growing large crops.</p><p>Independent plant breeders can afford to use traits from related species (among the 1' and 2' germplasm resources at least) to express their creativity towards developing new varieties. Even if you're not sure what to do with them (as I am), they're still lovely plants which might be fun to work with in the garden. <br /></p><p>I hope you are and remain well as the pandemic continues.<br /></p>
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<p>References</p><ul style="text-align: left;"><li>S. melongena germplasm. <br /></li><ul><li><a href="https://journals.ashs.org/jashs/view/journals/jashs/141/1/article-p34.xml">https://journals.ashs.org/jashs/view/journals/jashs/141/1/article-p34.xml</a></li></ul><li>S. aethiopicum germplasm</li><ul><li><a href="http://www.researchgate.net/publication/264393961_Conventional_and_phenomics_characterization_provides_insight_into_the_diversity_and_relationships_of_hypervariable_scarlet_Solanum_aethiopicum_L_and_gboma_S_macrocarpon_L_eggplant_complexes">www.researchgate.net/publication/264393961_Conventional_and_phenomics_characterization_provides_insight_into_the_diversity_and_relationships_of_hypervariable_scarlet_Solanum_aethiopicum_L_and_gboma_S_macrocarpon_L_eggplant_complexes</a></li><li><a href="https://www.sciencedirect.com/science/article/abs/pii/S088915751500232X">www.sciencedirect.com/science/article/abs/pii/S088915751500232X</a></li><li><a href="https://www.frontiersin.org/articles/10.3389/fpls.2017.01484/full">https://www.frontiersin.org/articles/10.3389/fpls.2017.01484/full</a> </li></ul><li>Fertility restoration in S. melongena x S. aethiopicum hybrids.</li><ul><li><a href="https://link.springer.com/article/10.1023/B:EUPH.0000003883.39440.6d">https://link.springer.com/article/10.1023/B:EUPH.0000003883.39440.6d</a><br /></li></ul><li>Primary, secondary, and tertiary gene pools. <br /></li><ul><li><a href="https://www.frontiersin.org/articles/10.3389/fpls.2014.00068/full">https://www.frontiersin.org/articles/10.3389/fpls.2014.00068/full</a></li></ul></ul>Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com1tag:blogger.com,1999:blog-2660869052224924549.post-16826797624225708302020-02-21T11:00:00.001-06:002023-02-07T17:58:43.510-06:00Photoshop again.<div dir="ltr" style="text-align: left;" trbidi="on">
Online seed vendors vary dramatically from the largely respectable, to the folks selling "peppers" like those below that I found on the Amazon or Ebay marketplaces.<br />
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To you, the botanically savvy purchaser, these vendors stand out as clearly fraudulent. But not everyone is botanically savvy. People who don't instantly know these wonderful colored peppers are just photoshopped versions of a red pepper photo are such vendors intended "customers".<br />
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<td><img alt="Pile of cayenne peppers photo edited to look cyan in color." border="0" height="200" src="https://1.bp.blogspot.com/-qwefc4Oqtag/VlA5zl0VusI/AAAAAAAABq4/qZdtyTuAVng/w133-h200/c4ca3712ad269eff9d5d419a5268c4d9.jpg" width="133" /></td>
<td><img alt="Pile of cayenne peppers photo edited to look blue in color." border="0" height="200" src="https://4.bp.blogspot.com/-ZJdOFFB2ooM/VlA5zCC6SUI/AAAAAAAABqs/PpXLEXGvJPI/w133-h200/5efdb937e2038dc45751586e468da673.jpg" width="133" /></td>
<td><img alt="Pile of cayenne peppers photo edited to look purple in color." border="0" height="200" src="https://2.bp.blogspot.com/-QwJHTV6l3KM/VlA5y1I85hI/AAAAAAAABqo/oiQmui33U9E/w132-h200/1606869_1240709415955085_6768060320307667737_n.jpg" width="132" /></td>
<td><img alt="Pile of cayenne peppers photo edited to look magenta in color." border="0" height="200" src="https://2.bp.blogspot.com/-_h6Z48sMUkg/VlA5zECGPSI/AAAAAAAABqw/2u6XyHRnt7c/w133-h200/5127756ae5afdd92a1ed9d16b31e8215.jpg" width="133" /></td>
<td><img alt="Pile of cayenne peppers; original photo the others here were modified from." border="0" height="200" src="https://1.bp.blogspot.com/-hGjx1PFeEqs/VlA5znqa2sI/AAAAAAAABq0/msyvQoJd19Q/w133-h200/bce70c6e-038a-4c97-a917-c5e56ca0f55c.jpg" width="133" /></td>
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Even among the largely respectable vendors, there are a wide range of philosophical or political stances that may impact your decisions of who to buy from. Does the company support white supremacists? Do they sell patented plant varieties? Do they push pseudo-science in their catalogs?<br />
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It can take some digging to be certain you agree with the politics behind any given company. It can take significant effort to bring such considerations into your buying decisions, so I understand if you choose not to do so.<br />
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But please, don't buy seeds from vendors selling off-hue peppers, blue strawberries, rainbow roses, rainbow onions, or the many other scams that are out there. If something looks too good to be true, at the very least investigate further. These online vendors rely on people clicking "buy" when seeing something interesting. By the time you've grown up the seeds and realize you were scammed, the time to contest the purchase in the marketplaces the vendors work through will have long since expired.</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com1tag:blogger.com,1999:blog-2660869052224924549.post-2055860369034532912020-02-14T11:00:00.001-06:002023-02-07T18:00:37.456-06:00Tomatillo Breeding (4/n)<div dir="ltr" style="text-align: left;" trbidi="on">
The last couple posts have looked at simulations for selection of a single gene, for recessive or dominant alleles. Increasing the number of genes actively under selection results in it taking longer and longer for the population to converge.
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<a href="https://1.bp.blogspot.com/-NfA6MsEmwBc/XkO3B48-36I/AAAAAAAAHwo/h-YL41jDdlMbB49PbHpWDXm3lyZ7woSEgCLcBGAsYHQ/s1600/Recessive_largePop.multiple.png" style="margin-left: 1em; margin-right: 1em;"><img alt="Plot titled "Multiple recessive traits, large population", illustrating selection for a trait in an out-crossing population." border="0" data-original-height="543" data-original-width="552" height="314" src="https://1.bp.blogspot.com/-NfA6MsEmwBc/XkO3B48-36I/AAAAAAAAHwo/h-YL41jDdlMbB49PbHpWDXm3lyZ7woSEgCLcBGAsYHQ/w320-h314/Recessive_largePop.multiple.png" width="320" /></a></div>
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<a href="https://1.bp.blogspot.com/-f3Osn8iVlPs/XkO3FTreGJI/AAAAAAAAHws/4X9fD-yjve0s4r9fR14C8OI7O2-SocV8ACLcBGAsYHQ/s1600/Dominant_largePop.multiple.png" style="margin-left: 1em; margin-right: 1em;"><img alt="Plot titled "Multiple dominant traits, large population", illustrating selection for a trait in an out-crossing population. It takes more years for the trait of interest to reach saturation in the population." border="0" data-original-height="543" data-original-width="552" height="314" src="https://1.bp.blogspot.com/-f3Osn8iVlPs/XkO3FTreGJI/AAAAAAAAHws/4X9fD-yjve0s4r9fR14C8OI7O2-SocV8ACLcBGAsYHQ/w320-h314/Dominant_largePop.multiple.png" width="320" /></a></div>
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The change in code to simulate multiple genetic loci is really simple if we assume the different alleles we're selecting on are found sufficiently distant from each other on the chromosomes. This is referred to as "un-linked" and means the probability calculations for each are independent of the others.<br />
<br />
<pre style="background-color: #eeeeee; border: 1px dashed rgb(153, 153, 153); color: black; font-family: "andale mono", "lucida console", monaco, fixed, monospace; font-size: 12px; line-height: 14px; margin-bottom: -1px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;">R Script 5: Multiple recessive traits, large population.</pre>
<pre style="background-color: #eeeeee; border: 1px dashed rgb(153, 153, 153); color: black; font-family: "andale mono", "lucida console", monaco, fixed, monospace; font-size: 12px; line-height: 14px; margin-top: 0px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;"><code># One recessive trait, infinite population.
# Stabilize progeny for recessive trait via selection.
# Save seeds from double-recessive plants each generation.
years <- 10;
# Define F2 population.
P_AA <- vector();
P_Aa <- vector();
P_aa <- vector();
P_AA <- 0.25;
P_Aa <- 0.50;
P_aa <- 0.25;
# Save seeds only from aabb plants, unknown pollen donor. Iterate over years.
for(i in 1:years) {
P_AA <- append(P_AA, 0);
P_Aa <- append(P_Aa, P_aa[i]*P_AA[i]*1.00 + P_aa[i]*P_Aa[i]*0.50);
P_aa <- append(P_aa, P_aa[i]*P_aa[i]*1.00 + P_aa[i]*P_Aa[i]*0.50);
P_sum <- P_aa[i+1] + P_Aa[i+1];
P_Aa[i+1] <- P_Aa[i+1]/P_sum;
P_aa[i+1] <- P_aa[i+1]/P_sum;
}
# Make figure.
plot( 0:years, P_aa^1, col="red", main="Multiple recessive traits, large population.", xlab="Years", ylab="%aa pollen donors", xlim=c(0,years), ylim=c(0,1), axes=TRUE, frame.plot=TRUE);
lines(0:years, P_aa^1, col="red");
lines(0:years, 1-P_aa^1, col="blue", lty="dashed");
lines(c(0,years),c(0.95,0.95), col="black", lty="dotted");
lines(c(0,years),c(0.99,0.99), col="black", lty="dashed");
for(i in 2:20) {
lines(0:years, P_aa^i, col="red");
lines(0:years, 1-P_aa^i, col="blue", lty="dashed");
}</code></pre>
<br />
<pre style="background-color: #eeeeee; border: 1px dashed rgb(153, 153, 153); color: black; font-family: "andale mono", "lucida console", monaco, fixed, monospace; font-size: 12px; line-height: 14px; margin-bottom: -1px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;">R Script 6: Multiple dominant traits, large population.</pre>
<pre style="background-color: #eeeeee; border: 1px dashed rgb(153, 153, 153); color: black; font-family: "andale mono", "lucida console", monaco, fixed, monospace; font-size: 12px; line-height: 14px; margin-top: 0px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;"><code># One dominant trait, infinite population.
# Stabilize progeny for dominant trait via selection.
# Save seeds from dominant plants each generation.
years <- 10;
# Define F2 population.
P_AA <- vector();
P_Aa <- vector();
P_aa <- vector();
P_AA <- 0.25;
P_Aa <- 0.50;
P_aa <- 0.25;
# Save seeds only from (AA and Aa) plants, unknown pollen donor. Iterate over years.
for(i in 1:years) {
P_AA <- append(P_AA, P_AA[i]*P_AA[i]*1.00 + P_AA[i]*P_Aa[i]*0.50 + P_Aa[i]*P_Aa[i]*0.25);
P_Aa <- append(P_Aa, P_AA[i]*P_aa[i]*1.00 + P_AA[i]*P_Aa[i]*0.50 + P_Aa[i]*P_aa[i]*0.50 + P_Aa[i]*P_Aa[i]*0.50);
P_aa <- append(P_aa, 0);
P_sum <- P_AA[i+1] + P_Aa[i+1];
P_AA[i+1] <- P_AA[i+1]/P_sum;
P_Aa[i+1] <- P_Aa[i+1]/P_sum;
}
# Make figure.
plot( 0:years, P_AA, col="red", main="Multiple dominant traits, large population.", xlab="Years", ylab="%AA pollen donors", xlim=c(0,years), ylim=c(0,1), axes=TRUE, frame.plot=TRUE);
lines(0:years, P_AA, col="red");
lines(0:years, 1-P_AA, col="blue", lty="dashed");
lines(c(0,years),c(0.95,0.95), col="black", lty="dotted");
lines(c(0,years),c(0.99,0.99), col="black", lty="dashed");
for(i in 2:20) {
lines(0:years, P_AA^i, col="red");
lines(0:years, 1-P_AA^i, col="blue", lty="dashed");
}</code></pre>
<br />
<hr width="50%" />
<br />
The probability of an F2 plant having two copies of recessive alleles for multiple genes drops to minimal very quickly when we increase the number of genes. In a small population this low probability means we might not find an F2 with all the recessive alleles stacked up the way we might want. All is not lost.<br />
<br />
With our small F2 population, roughly a quarter would be expected to be in the double-recessive condition for the first gene of interest.<br />
<br />
<div style="text-align: center;">
25% AA; 50% Aa; 25% aa</div>
<br />
If we were unlucky and couldn't find a single plant that was also double-recessive for the second gene of interest, we can go ahead with plants showing the dominant trait for that second gene. The probability is that two thirds of the plants showing the dominant trait for the second gene will be heterozygous, carrying one copy of the recessive allele.<br />
<br />
<div style="text-align: center;">
aaB_ (â…“BB; â…”Bb)</div>
<br />
In the next generation we have pretty good odds of recovering that second recessive trait that we were looking for. This way we can progressively collect multiple recessive traits without finding them in that first F2 generation. With this strategy, we need to keep seeds from prior generations. If we can't recover that next recessive trait in the next year, then we managed to find plants that were not heterozygous for the gene of interest. We need to grow more plants from the previous generation again, to try and find some carrying a copy of the recessive allele.<br />
<br />
<hr width="50%" />
<br />
With plants that typically self-pollinate (like peppers and tomatoes), it can be pretty simple to intentionally remove recessive alleles for genes of interest. If you grow out the seeds produced by a plant and find any double-recessive progeny, you know that plant was heterozygous. If you don't find any double-recessive progeny, if you grow enough seeds, you can be pretty confident of that plant being homozygous for the dominant allele.<br />
<br />
With plants that can't self-pollinate (like tomatillos), it can take more work/time. Lets say we have one plant that is showing the dominant trait. If we cross it with a plant showing the recessive trait, the resulting progeny will tell us if that first plant is "AA" or "Aa". If all the progeny show the dominant trait, then the plant we were testing is "AA". If the progeny show a mix of dominant and recessive traits, then the plant we were testing is "Aa" (and can be discarded). This is called a "test-cross" because it is used to test the genetics of a specific individual, even though we have no interest in using the progeny that result for further breeding work.<br />
<br />
Since tomatilloes can be kept alive over several years, you can use such test crosses to progressively collect multiple plants with just the dominant alleles for your genes of interest. Once you have a few such plants, you can then allow them to inter-cross and be confident you won't have the recessive allele turning up in the next generations.</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-64043481251485790902020-02-07T11:00:00.000-06:002020-02-12T02:19:42.247-06:00Tomatillo Breeding (3/n)<div dir="ltr" style="text-align: left;" trbidi="on">
I've been doing some math to help me think about breeding strategies with tomatillos. Last week I showed some code for calculating how populations of different sizes converge under selection for a single recessive trait. Here I'll show similar code for a single dominant trait.<br />
<br />
<hr width="50%" />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-zDv4ZeNlLT4/XjzsaI7_lyI/AAAAAAAAHt0/KWjVLxrC9uU9iQeEhQec317HUFarwtnOgCLcBGAsYHQ/s1600/Dominant_largePop.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="X-axis, years going from 0 to 10. Y-axis, "%AA pollen donors" going from 0 to 1. Red curve for %AA goes from lower left, rises slowly towards 1, and then smooths out to approach 1. Blue curve descends in a mirror image." border="0" data-original-height="543" data-original-width="552" height="313" src="https://1.bp.blogspot.com/-zDv4ZeNlLT4/XjzsaI7_lyI/AAAAAAAAHt0/KWjVLxrC9uU9iQeEhQec317HUFarwtnOgCLcBGAsYHQ/s320/Dominant_largePop.png" title="One dominant trait, large population." width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Solid red curve with circles: %AA pollen donors. <br />
Dashed blue curve: %Aa & %aa pollen donors.</td></tr>
</tbody></table>
Like before, we'll start with an infinite population.<br />
<br />
Since we can't tell the difference between plants with one or two copies of the dominant trait ("AA" or "Aa"), we can't tell what the genetic status is of any one plant that we save seeds from. Our goal is a population entirely consisting of "AA" plants, so that is what the code will plot.<br />
<br />
The zero year is our F2 population. It takes seven years for the "AA" individuals to represent 95% (dotted horizontal line) of the population. Three years later the level crosses above 99% (dashed horizontal line) of the population.<br />
<br />
Because this is the infinite population scenario, there will always be a small percentage of the population carrying the recessive allele.<br />
<br />
<pre style="background-color: #eeeeee; border: 1px dashed #999999; color: black; font-family: "andale mono" , "lucida console" , "monaco" , "fixed" , monospace; font-size: 12px; line-height: 14px; margin-bottom: -1px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;">R Script 3: One dominant trait, infinite population.</pre>
<pre style="background-color: #eeeeee; border: 1px dashed #999999; color: black; font-family: "andale mono" , "lucida console" , "monaco" , "fixed" , monospace; font-size: 12px; line-height: 14px; margin-top: 0px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;"><code># One dominant trait, infinite population.
# Stabilize progeny for dominant trait via selection.
# Save seeds from dominant plants each generation.
years <- 10;
# Define F2 population.
P_AA <- vector();
P_Aa <- vector();
P_aa <- vector();
P_AA <- 0.25;
P_Aa <- 0.50;
P_aa <- 0.25;
# Save seeds only from (AA and Aa) plants, unknown pollen donor. Iterate over years.
for(i in 1:years) {
P_AA <- append(P_AA, P_AA[i]*P_AA[i]*1.00 + P_AA[i]*P_Aa[i]*0.50 + P_Aa[i]*P_Aa[i]*0.25);
P_Aa <- append(P_Aa, P_AA[i]*P_aa[i]*1.00 + P_AA[i]*P_Aa[i]*0.50 + P_Aa[i]*P_aa[i]*0.50 + P_Aa[i]*P_Aa[i]*0.50);
P_aa <- append(P_aa, 0);
P_sum <- P_AA[i+1] + P_Aa[i+1];
P_AA[i+1] <- P_AA[i+1]/P_sum;
P_Aa[i+1] <- P_Aa[i+1]/P_sum;
}
# Make figure.
plot( 0:years, P_AA, col="red", main="One dominant trait, large population.", xlab="Years", ylab="%AA pollen donors", xlim=c(0,years), ylim=c(0,1), axes=TRUE, frame.plot=TRUE);
lines(0:years, P_AA, col="red");
lines(0:years, P_Aa+P_aa, col="blue", lty="dashed");
lines(c(0,years),c(0.95,0.95), col="black", lty="dotted");
lines(c(0,years),c(0.99,0.99), col="black", lty="dashed")
</code></pre>
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-JfyKjwWpSNQ/XjzxP9PIM8I/AAAAAAAAHuM/kmXKoEjylkc4H4R9yiIgRihiORNAebdtACLcBGAsYHQ/s1600/Recessive_vs_Dominant_largePop.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="X-axis, years going from 0 to 10. Y-axis, "%target Pollen Donors" going from 0 to 1. Cyan curve for recessive percentage goes from lower left, rises sharply towards 1, and then smooths out to approach 1. Red curve for dominant percentage goes from lower left, rises slowly towards 1, and then smooths out to approach 1. Yellow curve descends in a mirror image of cyan curve. Blue curve descends in a mirror image of red curve." border="0" data-original-height="543" data-original-width="552" height="196" src="https://1.bp.blogspot.com/-JfyKjwWpSNQ/XjzxP9PIM8I/AAAAAAAAHuM/kmXKoEjylkc4H4R9yiIgRihiORNAebdtACLcBGAsYHQ/s200/Recessive_vs_Dominant_largePop.png" title="Recessive vs dominant trait, large population." width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Cyan line w/circles: recessive selection.<br />
Red line w/circles: dominant selection.</td></tr>
</tbody></table>
To compare the trajectory for selection on the recessive allele vs on the dominant allele, I overlaid the two curves in an image editor. I inverted the colors for the recessive curves to better distinguish them from the added dominant curves.<br />
<br />
Selection on a dominant trait progresses at a slower rate initially than selection on a recessive trait, but by about ten years the two approaches would be expected to reach a similar degree of completeness.<br />
<br />
With smaller population sizes, we'd expect the selected allele (dominant or recessive) to reach complete saturation by about that time point.<br />
<br />
<hr width="50%" />
<br />
With recessive traits, I only had to consider "aa" plants as seed producers. With dominant traits, I have to consider "AA" and "Aa" plants. This seems like a small difference, but for simulating small numbers this adds significant complexity.<br />
<br />
<table><tbody>
<tr><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-qr6SF_EBc9s/Xj0POZ4_7PI/AAAAAAAAHu0/gsU7xEpw8hgar30HPoLxAKhoH_CqxDTPQCLcBGAsYHQ/s1600/Dominant_smallPop_1000.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img alt="Similar to above figure, but each curve is replaced by a tight cluster of overlapping curves representing individual runs of the simulation." border="0" data-original-height="543" data-original-width="552" height="196" src="https://1.bp.blogspot.com/-qr6SF_EBc9s/Xj0POZ4_7PI/AAAAAAAAHu0/gsU7xEpw8hgar30HPoLxAKhoH_CqxDTPQCLcBGAsYHQ/s200/Dominant_smallPop_1000.png" title="One dominant trait, small population." width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Population = 1000</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-gloJqWTin6g/Xj0PR950kAI/AAAAAAAAHu4/KWrcrBAUKOYabhwB2zy_Jg_FdoJbD-9hACLcBGAsYHQ/s1600/Dominant_smallPop_50.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img alt="Similar to above figure, but each curve is replaced by a very loose cluster of overlapping curves representing individual runs of the simulation." border="0" data-original-height="543" data-original-width="552" height="196" src="https://1.bp.blogspot.com/-gloJqWTin6g/Xj0PR950kAI/AAAAAAAAHu4/KWrcrBAUKOYabhwB2zy_Jg_FdoJbD-9hACLcBGAsYHQ/s200/Dominant_smallPop_50.png" title="One dominant trait, small population." width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Population = 50</td></tr>
</tbody></table>
</td><td><table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-ZUBIO-6MnYI/Xj0TZzgpW3I/AAAAAAAAHvQ/TJ_8UG_xobYbuPXEQEPK2w5523aVN8iuQCEwYBhgL/s1600/Dominant_smallPop_10.png" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Similar to above figure, but each curve is replaced by an extremely loose cluster of overlapping curves representing individual runs of the simulation. These curves occupy almost the entire figure." border="0" data-original-height="543" data-original-width="552" height="196" src="https://1.bp.blogspot.com/-ZUBIO-6MnYI/Xj0TZzgpW3I/AAAAAAAAHvQ/TJ_8UG_xobYbuPXEQEPK2w5523aVN8iuQCEwYBhgL/s200/Dominant_smallPop_10.png" title="One dominant trait, small population." width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Population = 10</td></tr>
</tbody></table>
</td></tr>
</tbody></table>
<br />
If you compare these plots to those for the recessive selection scenario (<a href="https://the-biologist-is-in.blogspot.com/2020/01/tomatillo-breeding-2n.html">https://the-biologist-is-in.blogspot.com/2020/01/tomatillo-breeding-2n.html</a>), you'll see that this scenario has a much higher level of noise in the trajectories. For the smallest population level, it takes 30 years (not shown in figures) for the majority of the experimental replicates to converge on the targeted "AA" condition. <br />
<br />
<pre style="background-color: #eeeeee; border: 1px dashed #999999; color: black; font-family: "andale mono" , "lucida console" , "monaco" , "fixed" , monospace; font-size: 12px; line-height: 14px; margin-bottom: -1px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;">R Script 4: One dominant trait, small population.</pre>
<pre style="background-color: #eeeeee; border: 1px dashed #999999; color: black; font-family: "andale mono" , "lucida console" , "monaco" , "fixed" , monospace; font-size: 12px; line-height: 14px; margin-top: 0px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;"><code># One dominant trait, small population.
# Stabilize progeny for dominant trait via selection.
# Save seeds from dominant plants each generation.
years <- 10;
population <- 1000; # 1000, 50, 10
trials <- 100;
# Intialize figure.
plot( c(0,years),c(0,years), col="red", main="One dominant trait, small population.", xlab="Years", ylab="%AA pollen donors", xlim=c(0,years), ylim=c(0,1), axes=TRUE, frame.plot=TRUE);
lines(c(0,years),c(0.95,0.95), col="black", lty="dotted");
lines(c(0,years),c(0.99,0.99), col="black", lty="dashed");
for (ii in 1:trials) {
# Define F2 population probabilities for selection on AA plants.
P_AA_1 <- vector();
P_Aa_1 <- vector();
P_aa_1 <- vector();
P_AA_1 <- 0.25;
P_Aa_1 <- 0.50;
P_aa_1 <- 0.25;
# Define F2 population probabilities for selection on Aa plants.
P_AA_2 <- vector();
P_Aa_2 <- vector();
P_aa_2 <- vector();
P_AA_2 <- 0.25;
P_Aa_2 <- 0.50;
P_aa_2 <- 0.25;
# Save seeds only from (AA and Aa) plants, which can't self-polinate.
for (i in 1:(years+2)) {
# Generate actual population.
rands <- runif(population, 0, 1);
Genotypes <- vector();
for (j in 1:population) {
if (rands[j] < P_AA_1[i]) {
Genotypes <- append(Genotypes, "AA");
} else if (rands[j] < P_AA_1[i]+P_Aa_1[i]) {
Genotypes <- append(Genotypes, "Aa");
} else {
Genotypes <- append(Genotypes, "aa");
}
}
Genotype_counts <- table(Genotypes);
# Determine actual genotype probabilities for pollen donors. (Assuming "AA" plant in case 1, "Aa" plant in case 2.)
if (is.na(Genotype_counts["AA"])) {
P_AA_1[i] <- 0;
P_AA_2[i] <- 0;
} else {
P_AA_1[i] <- (Genotype_counts["AA"]-1)/(population-1); # The plant we're saving seeds from can't be polinated by itself.
P_AA_2[i] <- Genotype_counts["AA"]/(population-1);
}
if (is.na(Genotype_counts["Aa"])) {
P_Aa_1[i] <- 0;
P_Aa_2[i] <- 0;
} else {
P_Aa_1[i] <- Genotype_counts["Aa"]/(population-1);
P_Aa_2[i] <- (Genotype_counts["AA"]-1)/(population-1); # The plant we're saving seeds from can't be polinated by itself.
}
if (is.na(Genotype_counts["aa"])) {
P_aa_1[i] <- 0;
P_aa_2[i] <- 0;
} else {
P_aa_1[i] <- Genotype_counts["aa"]/(population-1);
P_aa_2[i] <- Genotype_counts["aa"]/(population-1);
}
# Generate new theoretical genotype probabilities.
P_AA_1 <- append(P_AA_1, P_AA_1[i]*P_AA_1[i]*1.00 + P_AA_1[i]*P_Aa_1[i]*0.50 + P_Aa_1[i]*P_Aa_1[i]*0.25);
P_Aa_1 <- append(P_Aa_1, P_AA_1[i]*P_aa_1[i]*1.00 + P_AA_1[i]*P_Aa_1[i]*0.50 + P_Aa_1[i]*P_aa_1[i]*0.50 + P_Aa_1[i]*P_Aa_1[i]*0.50);
P_aa_1 <- append(P_aa_1, 0);
P_AA_2 <- append(P_AA_2, P_AA_2[i]*P_AA_2[i]*1.00 + P_AA_2[i]*P_Aa_2[i]*0.50 + P_Aa_2[i]*P_Aa_2[i]*0.25);
P_Aa_2 <- append(P_Aa_2, P_AA_2[i]*P_aa_2[i]*1.00 + P_AA_2[i]*P_Aa_2[i]*0.50 + P_Aa_2[i]*P_aa_2[i]*0.50 + P_Aa_2[i]*P_Aa_2[i]*0.50);
P_aa_2 <- append(P_aa_2, 0);
P_sum_1 <- P_AA_1[i+1] + P_Aa_1[i+1];
P_AA_1[i+1] <- P_AA_1[i+1]/P_sum_1;
P_Aa_1[i+1] <- P_Aa_1[i+1]/P_sum_1;
P_sum_2 <- P_AA_2[i+1] + P_Aa_2[i+1];
P_AA_2[i+1] <- P_AA_2[i+1]/P_sum_2;
P_Aa_2[i+1] <- P_Aa_2[i+1]/P_sum_2;
# Weighted average of the two probability sets by proportion of "AA" vs "Aa" plants.
# Only _1 values carry over to next iteration.
if (is.na(Genotype_counts["AA"])) {
count_AA <- 0; } else {
count_AA <- Genotype_counts["AA"];
}
if (is.na(Genotype_counts["Aa"])) {
count_Aa <- 0; } else {
count_Aa <- Genotype_counts["Aa"];
}
weight1 <- count_AA/(count_AA+count_Aa);
weight2 <- 1-weight1;
val_AA_1 <- P_AA_1[i+1];
val_AA_2 <- P_AA_2[i+1];
val_Aa_1 <- P_Aa_1[i+1];
val_Aa_2 <- P_Aa_2[i+1];
P_AA_1[i+1] <- val_AA_1*weight1 + val_AA_2*weight2;
P_Aa_1[i+1] <- val_Aa_1*weight1 + val_Aa_2*weight2;
if (is.na(P_AA_1[i+1]) == TRUE) { P_AA_1[i+1] <- 0; }
if (is.na(P_Aa_1[i+1]) == TRUE) { P_Aa_1[i+1] <- 0; }
if ((P_AA_1[i+1]+P_Aa_1[i+1]) == 0) {
# End simulation cycle if no "AA" or "Aa" plants.
for (j in (length(P_aa_1)):years) {
P_AA_1 <- append(P_AA_1, 0);
P_Aa_1 <- append(P_Aa_1, 0);
P_aa_1 <- append(P_aa_1, 0);
}
break;
}
## Debugging output.
#message("Iteration ", i);
#print(Genotypes);
#message(" ");
}
# Add current simulation cycle to figure.
points(0:years, P_AA_1[1:(years+1)], col="red");
lines( 0:years, P_AA_1[1:(years+1)], col="red");
lines( 0:years, 1-P_AA_1[1:(years+1)], col="blue", lty="dashed");
}</code></pre>
<br />
<hr width="50%" />
<br />
This essentially means it isn't possible to selectively breed a dominant trait to complete saturation in a small population just using simple selection.<br />
<br />
Unlike in the recessive case, we can't just save a few plants over winter to reset the population with only the exact genetics we want. A similar strategy should allow for more rapid progress towards the goal, however.<br />
<br />
I'll explore this topic further next time. </div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-71809266595217635032020-01-31T10:00:00.000-06:002020-02-07T01:41:01.211-06:00Tomatillo Breeding (2/n)<div dir="ltr" style="text-align: left;" trbidi="on">
I thought it would take me a week to get back to this, but that didn't happen. Oops. Sorry.<br />
<br />
<hr width="50%" />
<br />
The big difficulty with tomatillo breeding is that they're very strong out-crossers. Unlike tomatoes, peppers, eggplant, beans, etc., you can't just grow one plant from each generation to help reduce control the genetics during the process of making a new variety. If you grow a dozen tomatillo plants and don't like how half of them grew, you can be sure that seeds saved from the plants you liked will have genetics from the ones you didn't.<br />
<br />
I worked out some of the math long-hand, showing how this difficulty plays out over several generations. I faltered when it came to the task of outlining all those calculations via text. It is easy enough to throw a few equations into text, but I didn't want to post pages of derivations for you to read through. (And I'd have most assuredly made silly typos along the way.)<br />
<br />
Instead, I wrote up some simulations in R. These can be run using RStudio if you want to play around with them, or you can just look at my summary figures here.<br />
<br />
<hr width="50%" />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-w0olkHcOBZk/XjO8x6FHLcI/AAAAAAAAHpw/s2PTiw1-DQsQwfh7-PImxHY-nw_iyAsiwCLcBGAsYHQ/s1600/Recessive_largePop.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="X-axis, years going from 0 to 10. Y-axis, "%aa pollen donors" going from 0 to 1. Red curve for %aa goes from lower left, rises rapidly towards 1, and then smooths out to approach 1. Blue curve descends in a mirror image." border="0" data-original-height="543" data-original-width="552" height="314" src="https://1.bp.blogspot.com/-w0olkHcOBZk/XjO8x6FHLcI/AAAAAAAAHpw/s2PTiw1-DQsQwfh7-PImxHY-nw_iyAsiwCLcBGAsYHQ/s320/Recessive_largePop.png" title="One recessive trait, large population." width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Solid red curve with circles: %aa pollen donors. <br />
Dashed blue curve: %Aa & %AA pollen donors.</td></tr>
</tbody></table>
We'll start with the simple case of a single recessive trait in an infinite
population. (Sometimes infinity makes the math hard to do, other times it
makes it very easy.)<br />
<br />
If we seeds only from plants showing the recessive trait, we can rapidly select away the dominant allele. The zero year of this plot is the F2 generation, where traits first start assorting. It takes five years for the recessive trait to be at 95% (dotted horizontal line) of the population and another three for it to be at 99% (dashed horizontal line) of the population.<br />
<br />
Because the population is infinite, we can never quite reach 100%. There will always be a small amount of the dominant allele hanging around.<br />
<br />
<pre style="background-color: #eeeeee; border: 1px dashed #999999; color: black; font-family: "andale mono" , "lucida console" , "monaco" , "fixed" , monospace; font-size: 12px; line-height: 14px; margin-bottom: -1px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;">R Script 1: One recessive trait, infinite population.</pre>
<pre style="background-color: #eeeeee; border: 1px dashed #999999; color: black; font-family: "andale mono" , "lucida console" , "monaco" , "fixed" , monospace; font-size: 12px; line-height: 14px; margin-top: 0px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;"><code># One recessive trait, infinite population.
# Stabilize progeny for recessive trait via selection.
# Save seeds from double-recessive plants each generation.
years <- 10;
# Define F2 population.
P_AA <- vector();
P_Aa <- vector();
P_aa <- vector();
P_AA <- 0.25;
P_Aa <- 0.50;
P_aa <- 0.25;
# Save seeds only from aa plants, unknown pollen donor. Iterate over years.
for(i in 1:years) {
P_AA <- append(P_AA, 0);
P_Aa <- append(P_Aa, P_aa[i]*P_AA[i]*1.00 + P_aa[i]*P_Aa[i]*0.50);
P_aa <- append(P_aa, P_aa[i]*P_aa[i]*1.00 + P_aa[i]*P_Aa[i]*0.50);
P_sum <- P_aa[i+1] + P_Aa[i+1];
P_Aa[i+1] <- P_Aa[i+1]/P_sum;
P_aa[i+1] <- P_aa[i+1]/P_sum;
}
# Make figure.
plot( 0:years, P_aa, col="red", main="One recessive trait, large population.", xlab="Years", ylab="%aa pollen donors", xlim=c(0,years), ylim=c(0,1), axes=TRUE, frame.plot=TRUE);
lines(0:years, P_aa, col="red");
lines(0:years, P_Aa+P_AA, col="red", lty="dashed");
lines(c(0,years),c(0.95,0.95), col="black", lty="dotted");
lines(c(0,years),c(0.99,0.99), col="black", lty="dashed")
</code></pre>
<br />
<hr width="50%" />
<br />
We can extend this simulation to better model a realistic situation where you can only grow a limited number of plants. Coding this is much more complicated. If we run it with a large population, we see a pattern much like the infinite one above. If we run it with a small population, we get very noisy trajectories that vary a lot from run to run. At small population numbers, it is fairly easy to accidentally end the experiment with no "aa" plants to save seeds from. (In real life, we'd just go back to seeds from the previous generation.)<br />
<br />
<table align="center"><tbody>
<tr><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-zRJ1g1Un_u8/XjPFxL9yyII/AAAAAAAAHqY/q47FEDcg5v4GT5kKjqMyOTcjiLtQ5PSWgCLcBGAsYHQ/s1600/Recessive_smallPop_1000.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img alt="Similar to above figure, but each curve is replaced by a tight cluster of overlapping curves representing individual runs of the simulation." border="0" data-original-height="543" data-original-width="552" height="196" src="https://1.bp.blogspot.com/-zRJ1g1Un_u8/XjPFxL9yyII/AAAAAAAAHqY/q47FEDcg5v4GT5kKjqMyOTcjiLtQ5PSWgCLcBGAsYHQ/s200/Recessive_smallPop_1000.png" title="One recessive trait, small population." width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Population = 1000</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-Dm9bENNH8ws/XjPFzZESEeI/AAAAAAAAHqc/UPsxBCTL098fVY3J0AD0JvSnDBUfmZXxwCEwYBhgL/s1600/Recessive_smallPop_50.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img alt="Similar to above figure, but each curve is replaced by a loose cluster of overlapping curves representing individual runs of the simulation." border="0" data-original-height="543" data-original-width="552" height="196" src="https://1.bp.blogspot.com/-Dm9bENNH8ws/XjPFzZESEeI/AAAAAAAAHqc/UPsxBCTL098fVY3J0AD0JvSnDBUfmZXxwCEwYBhgL/s200/Recessive_smallPop_50.png" title="One recessive trait, small population." width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Population =50</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-SrUTkFpF53w/XjPF6j6IgkI/AAAAAAAAHqg/Kwgp6gFTtJAaj4U4eKtPGq-sq31bsOL1ACLcBGAsYHQ/s1600/Recessive_smallPop_10.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img alt="Similar to above figure, but each curve is replaced by a very loose cluster of overlapping curves representing individual runs of the simulation. The curves are so noisy that the cluster is spread over much of the plot." border="0" data-original-height="543" data-original-width="552" height="196" src="https://1.bp.blogspot.com/-SrUTkFpF53w/XjPF6j6IgkI/AAAAAAAAHqg/Kwgp6gFTtJAaj4U4eKtPGq-sq31bsOL1ACLcBGAsYHQ/s200/Recessive_smallPop_10.png" title="One recessive trait, small population." width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Population =10</td></tr>
</tbody></table>
</td></tr>
</tbody></table>
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
The upshot of the simulations is that if we grow small numbers of plants each generation, we can eventually eliminate the pesky dominant alleles for the trait of interest. It will take a while, but it is doable if you're willing to wait several years to a decade.<br />
<br />
<pre style="background-color: #eeeeee; border: 1px dashed #999999; color: black; font-family: "andale mono" , "lucida console" , "monaco" , "fixed" , monospace; font-size: 12px; line-height: 14px; margin-bottom: -1px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;">R Script 2: One recessive trait, small population.</pre>
<pre style="background-color: #eeeeee; border: 1px dashed #999999; color: black; font-family: "andale mono" , "lucida console" , "monaco" , "fixed" , monospace; font-size: 12px; line-height: 14px; margin-top: 0px; max-height: 150px; overflow: auto; padding: 5px; text-align: left; width: 100%;"><code># One recessive trait, small population.
# Stabilize progeny for recessive trait via selection.
# Save seeds from double-recessive plants each generation.
years <- 10;
population <- 50; # 1000, 50, 10
trials <- 100;
# Intialize figure.
plot( c(0,years),c(0,years), col="red", main="One recessive trait, small population.", xlab="Years", ylab="%aa pollen donors", xlim=c(0,years), ylim=c(0,1), axes=TRUE, frame.plot=TRUE);
lines(c(0,years),c(0.95,0.95), col="black", lty="dotted");
lines(c(0,years),c(0.99,0.99), col="black", lty="dashed");
for (ii in 1:trials) {
# Define F2 population probabilities
P_AA <- vector();
P_Aa <- vector();
P_aa <- vector();
P_AA <- 0.25;
P_Aa <- 0.50;
P_aa <- 0.25;
# Save seeds only from "aa" plants, which can't self-polinate.
for (i in 1:(years+2)) {
# Generate actual population.
rands <- runif(population, 0, 1);
Genotypes <- vector();
for (j in 1:population) {
if (rands[j] < P_AA[i]) {
Genotypes <- append(Genotypes, "AA");
} else if (rands[j] < P_AA[i]+P_Aa[i]) {
Genotypes <- append(Genotypes, "Aa");
} else {
Genotypes <- append(Genotypes, "aa");
}
}
Genotype_counts <- table(Genotypes);
# Determine actual genotype probabilities for pollen donors.
if (is.na(Genotype_counts["AA"])) {
P_AA[i] <- 0; } else {
P_AA[i] <- Genotype_counts["AA"]/(population-1);
}
if (is.na(Genotype_counts["Aa"])) {
P_Aa[i] <- 0; } else {
P_Aa[i] <- Genotype_counts["Aa"]/(population-1);
}
if (is.na(Genotype_counts["aa"])) {
P_aa[i] <- 0; } else {
P_aa[i] <- (Genotype_counts["aa"]-1)/(population-1); # The plant we're saving seeds from can't be polinated by itself.
}
# Generate new theoretical genotype probabilities.
P_AA <- append(P_AA, 0);
P_Aa <- append(P_Aa, P_aa[i]*P_AA[i]*1.00 + P_aa[i]*P_Aa[i]*0.50);
P_aa <- append(P_aa, P_aa[i]*P_aa[i]*1.00 + P_aa[i]*P_Aa[i]*0.50);
P_sum <- P_aa[i+1] + P_Aa[i+1];
P_Aa[i+1] <- P_Aa[i+1]/P_sum;
P_aa[i+1] <- P_aa[i+1]/P_sum;
if (is.na(P_Aa[i+1]) == TRUE) { P_Aa[i+1] <- 0; }
if (is.na(P_aa[i+1]) == TRUE) { P_aa[i+1] <- 0; }
if (P_aa[i+1] == 0) {
# End simulation cycle if no "aa" plants.
for (j in (length(P_aa)):years) {
P_AA <- append(P_AA, 0);
P_Aa <- append(P_Aa, 0);
P_aa <- append(P_aa, 0);
}
break;
}
}
# Add current simulation cycle to figure.
points(0:years, P_aa[1:(years+1)], col="red");
lines( 0:years, P_aa[1:(years+1)], col="red");
lines( 0:years, 1-P_aa[1:(years+1)], col="blue", lty="dashed");
}</code></pre>
<br />
<hr width="50%" />
<br />
However, there's a much faster way to complete the process. It might even only take a couple years.<br />
<br />
Tomatilloes are perennial where it is warm enough for them to survive through winter. They also easily root from cuttings. These traits combined mean we can pot up rooted cuttings from each plant at the end of one year and continue growing selected plants the next year after we've had a chance to evaluate their fruit characteristics.<br />
<br />
You'd have to grow enough plants the first year to be able to find multiple individuals with the recessive traits you're interested in. The next year, you can continue growing only those few plants and allow them to cross-pollinate. Every seed they produce in their second year will contain those recessive traits you selected the parents for. The dominant alleles will be gone from your population.<br />
<br />
You're done in one year of selection and another for seed production. No waiting around for a decade or more, gambling with the whims of chance. You may have your new tomatillo variety complete and ready to go.<br />
<br />
<hr width="50%" />
<br />
I didn't talk about dominant traits here. They're a bit more involved and I'll have to do another post about that case. I'll also have to do another post talking about the case where you're looking for multiple specific genes (recessive or dominant) at once.<br />
<br />
It looks like my planned two part series is going to be a bit longer in the end.</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-8977570637065903522019-12-05T13:00:00.000-06:002020-02-06T22:25:51.838-06:00Tomatillo Breeding (1/n)<div dir="ltr" style="text-align: left;" trbidi="on">
Tomatillos are a wonderful vegetable plant to grow. There are several distinct varieties available, but nowhere near the numbers we see for tomatoes, peppers, or other crops. What's the difference?<br />
<br />
Tomatillos are almost exclusively out-breeders. You need two or more plants growing in an area to get good production of fruit. As a result, every plant is a new hybrid and a population will maintain a high degree of genetic diversity. This also makes it difficult for different varieties to be grown in the same area, as they will generally cross and meld into one diverse population.<br />
<br />
<hr width="50%" />
<br />
A few years back I started an experiment with breeding tomatillos. I grew one plant of a variety with small purple fruit next to one plant of a variety with large green fruit. I had saved seeds from a CSA and the local grocer, so I don't have any specific variety names to give you. (If you want to replicate the experiment, the purple variety was similar to: <a href="https://www.edenbrothers.com/store/purple-tomatillo-seeds.html">https://www.edenbrothers.com/store/purple-tomatillo-seeds.html</a>; the green to: <a href="https://www.edenbrothers.com/store/rio-grande-verde-tomatillo-seeds.html">https://www.edenbrothers.com/store/rio-grande-verde-tomatillo-seeds.html</a>.)<br />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-SE-4gas6AMY/XdYxA5nPDOI/AAAAAAAAHPM/tX0PM10qRXw6VOJT8cyxzgsG4mWiGWQ_ACLcBGAsYHQ/s1600/2017_F1s.a.jpeg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Four tomatillo fruit, from left to right. 1) Medium purple. 2) Small purple. 3) Large green. 4) Medium purple." border="0" data-original-height="400" data-original-width="1600" height="50" src="https://1.bp.blogspot.com/-SE-4gas6AMY/XdYxA5nPDOI/AAAAAAAAHPM/tX0PM10qRXw6VOJT8cyxzgsG4mWiGWQ_ACLcBGAsYHQ/s200/2017_F1s.a.jpeg" title="" width="200" /></a></td></tr>
<tr align="left"><td class="tr-caption">#1. Medium purple fruit.<br />
#2. Small purple fruit.<br />
#3. Large green fruit, with purple dots.<br />
#4. Medium purple fruit.</td></tr>
</tbody></table>
Because the plants are such extreme out-crossers, every seed that year was expected to be a hybrid between the two different varieties. The next year I grew four plants, from seeds I saved from the purple plant. Each plant grew distinct fruit. (1-4, left to right in photo at right.) This diversity tells us that both parental varieties were highly heterogeneous, so the specifics of each hybrid plant depended on exactly which allele they inherited from each parent. As none of my neighbors were growing tomatillos, we can be pretty sure each one was pollinated by the other three.<br />
<br />
<hr width="50%" />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-nDwJXBKCYto/XdY9_asYvzI/AAAAAAAAHPw/1PpPiLVL4PQgiHEpgdjc3ep86Z8Q9TnFACLcBGAsYHQ/s1600/2018_F2-3.b.jpeg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Two large green tomatillo fruit at right. Six small pale purple tomatillo fruit at left." border="0" data-original-height="1421" data-original-width="1420" height="200" src="https://1.bp.blogspot.com/-nDwJXBKCYto/XdY9_asYvzI/AAAAAAAAHPw/1PpPiLVL4PQgiHEpgdjc3ep86Z8Q9TnFACLcBGAsYHQ/s200/2018_F2-3.b.jpeg" title="" width="199" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">F2s from F1#3.</td></tr>
</tbody></table>
<br />
The next year I planted seeds I had saved from plant #3. I grew 11 plants, but only 5 produced any fruit. The plants looked like they'd been exposed to an herbicide from the commercial garden soil I had added to the garden at the start of the season (<a href="https://lee.ces.ncsu.edu/2016/03/herbicide-carryover-in-hay-manure-compost-and-grass-clippings/">Herbicide carryover</a>). All the fruit were green, with some later developing some purple pigment as they ripened off the plant.<br />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-J2ENLqFgGIQ/XdY_g3sARpI/AAAAAAAAHQA/ypmt0qTEbj4GDnD8F8akpvSsPqghXb8KwCLcBGAsYHQ/s1600/2019_F2-4.png" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Ten bowls filled with tomatillo fruit. Contents of each bowl are different sizes and/or shades of green and purple." border="0" data-original-height="540" data-original-width="720" height="150" src="https://1.bp.blogspot.com/-J2ENLqFgGIQ/XdY_g3sARpI/AAAAAAAAHQA/ypmt0qTEbj4GDnD8F8akpvSsPqghXb8KwCLcBGAsYHQ/s200/2019_F2-4.png" title="" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">F2s from F1#4.</td></tr>
</tbody></table>
This year I planted seeds I had saved from plant #4. I grew 12 plants and all produced fruit. These showed a much wider range of pigment levels, including a pair of plants with visible purple pigment and large fruit.<br />
<br />
One plant had a trait I didn't like at all. The fruit from spoiled very rapidly after picking. (Previous year's fruit stored for months.) That plant was one of two in an isolated garden, so I immediately culled all of the fruit from both plants. I didn't want to risk the genetics associated with spoilage turning up in the garden again next year.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://1.bp.blogspot.com/-u7kkVMz3vvw/XdZBJ-gxwlI/AAAAAAAAHQM/OnU5yg9d6HELj30Me6PlsDB-gQeGIgdjACLcBGAsYHQ/s1600/2019_F2-4.a.jpeg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Overhead view of orange plastic bowl filled with large tomatillos. The fruit are combinations of green and dark purple. One fruit at center is mostly green with three purple stripes starting at the bottom." border="0" data-original-height="1600" data-original-width="1600" height="200" src="https://1.bp.blogspot.com/-u7kkVMz3vvw/XdZBJ-gxwlI/AAAAAAAAHQM/OnU5yg9d6HELj30Me6PlsDB-gQeGIgdjACLcBGAsYHQ/s200/2019_F2-4.a.jpeg" title="" width="200" /></a></div>
One plant had fruit I really liked. The fruit were large and developed purple pigment, the traits I have been trying to combine in one plant. I wasn't expecting the fruit to develop stripes as they were maturing, however. These fruit are not lasting as long as I'd like, but the other good traits means I'll be saving seeds from them anyhow.<br />
<a href="https://1.bp.blogspot.com/-csOW63Nqw9A/XdZC0IJLpJI/AAAAAAAAHQY/VY24-R2PhMwq-karYvmIIFwMBpAIOeuOQCLcBGAsYHQ/s1600/2019_F2-4.b.jpeg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Overhead view of green plastic bowl filled with medium tomatillos. The fruit are dark purple, with the most ripe looking black.." border="0" data-original-height="672" data-original-width="672" height="200" src="https://1.bp.blogspot.com/-csOW63Nqw9A/XdZC0IJLpJI/AAAAAAAAHQY/VY24-R2PhMwq-karYvmIIFwMBpAIOeuOQCLcBGAsYHQ/s200/2019_F2-4.b.jpeg" title="" width="200" /></a><br />
A couple other plants produced intensely dark purple fruit, appearing ink-black. This is the color I've been looking for, but the fruit aren't as large as I want. I'll save seeds from these as well.<br />
<br />
Because the plants are out-crossers, I know they will have been pollinated by the others in the garden. Even though these two have trait combinations I really like, it will be unlikely to find offspring with the same traits because of all the other traits in the garden.<br />
<br />
I've tried to diagram the overall history of the project so far. (I didn't have any photos of the original varieties, so they get cartoon representations.) <br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-61OxX5yoaFo/XdZDq3QB2cI/AAAAAAAAHQg/eXtUg0DLCK86ztf-7w04J-UzFZPTNs12gCLcBGAsYHQ/s1600/tomatillo_history.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img alt="At top are a small dark purple and large green circle, representing the original varieties I crossed. From the dark circle, a black line goes down to a second row consisting of four tomatillo fruit pictures. (From left to right: medium purple, small purple, large green, & medium purple.) Black lines are drawn from beneath the right two fruit downwards to photos. Left line goes to a photo of 5 bowls of green fruit, with a photo of pale purple fruit to the left. The right line goes to a photo of 10 bowls of fruit with varying colors of purple and green." border="0" data-original-height="1600" data-original-width="1211" height="320" src="https://1.bp.blogspot.com/-61OxX5yoaFo/XdZDq3QB2cI/AAAAAAAAHQg/eXtUg0DLCK86ztf-7w04J-UzFZPTNs12gCLcBGAsYHQ/s320/tomatillo_history.jpg" title="" width="242" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Tomatillo project history so far.</td></tr>
</tbody></table>
<div class="separator" style="clear: both; text-align: center;">
</div>
<br />
About this point I started thinking about how I might get around the issues caused by the potential for genes from every plant in a garden to turn up in the next generation. I don't want to have to cull everything from a garden when something strongly negative turns up in the population. Right now I only have two isolated garden spaces, so that strategy can only go so far.<br />
<br />
<div style="text-align: center;">
<i>For my solution, come back in a week for part 2!</i></div>
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li>Tomatillo varieties:</li>
<ul>
<li>Purple: <a href="https://www.edenbrothers.com/store/purple-tomatillo-seeds.html">https://www.edenbrothers.com/store/purple-tomatillo-seeds.html</a></li>
<li>Rio Grande Verde: <a href="https://www.edenbrothers.com/store/rio-grande-verde-tomatillo-seeds.html">https://www.edenbrothers.com/store/rio-grande-verde-tomatillo-seeds.html</a></li>
</ul>
<li>Herbicide carryover: <a href="https://lee.ces.ncsu.edu/2016/03/herbicide-carryover-in-hay-manure-compost-and-grass-clippings/">https://lee.ces.ncsu.edu/2016/03/herbicide-carryover-in-hay-manure-compost-and-grass-clippings/</a> </li>
<ul>
</ul>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-58907429905512469782019-11-28T13:00:00.001-06:002023-02-07T17:47:24.410-06:00Fava Beans<div dir="ltr" style="text-align: left;" trbidi="on">
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-4jMUb0qKDuk/VbxYO1Dn_7I/AAAAAAAABaE/I2DUG42PD-I/s1600/132-001.crop.JPG" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Cluster of brown/purple flowers on a fava bean plant." border="0" height="200" src="https://4.bp.blogspot.com/-4jMUb0qKDuk/VbxYO1Dn_7I/AAAAAAAABaE/I2DUG42PD-I/w200-h200/132-001.crop.JPG" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">[Photo from <a href="http://growingfoodsavingseeds.blogspot.com/2015/06/colourful-broad-bean-flowers.html">link</a>.]</td></tr>
</tbody></table>
I've eaten fava beans (<i>Vicia faba</i>) from time to time, but I've never grown them. I was recently perusing some postings from blogs I occasion and found <a href="http://growingfoodsavingseeds.blogspot.com/2015/06/colourful-broad-bean-flowers.html">an interesting post</a>. The post contains a wonderful series of photos of fava bean flowers in the author's garden, ranging in shades of red/pink and brown/black. <a href="http://www.growingfoodsavingseeds.co.uk/forum/breeding-and-genetics/new-channel/2938-broad-bean-fava-bean-flower-colour">A forum discussion</a> revealed that these variations were the result of crossing the varieties "<a href="http://www.thompson-morgan.com/vegetables/vegetable-seeds/pea-and-bean-seeds/broad-bean-crimson-flowered/4772TM">Crimson Flowered</a>" and "<a href="http://davesgarden.com/guides/pf/go/40640/">Red Epicure</a>". After searching around a bit, I found that for the vast majority of fava bean varieties the flowers are only red/pink or brown/black. <br />
<br />
The flowers are impressive enough in the garden already. Some improvement in flower size or color range would be awesome. My biology background leads me to think of at least two strategies.<br />
<ol style="text-align: left;">
<li>Hybridize <i>F. faba</i> with related species with different flower colors. </li>
<li>Find rare varieties of <i>F. faba</i> with different colors.</li>
</ol>
1. Hybridization? I like this strategy generally, but the usefulness of the strategy depends on the plant being worked with. It turns out that there are no known species which can be used to produce hybrid seed with <i>V. faba</i>. <a href="https://books.google.com/books?id=toHsCAAAQBAJ&pg=PA202&lpg=PA202&dq=Vicia+faba+hybrids+with+other+species&source=bl&ots=rokyVBhghu&sig=PsZSX6w__E1oM0fPdcvQAgvaX0k&hl=en&sa=X&ved=0CB8Q6AEwAGoVChMI-JuS1P2KxwIVAYuSCh2rngTg#v=onepage&q=Vicia%20faba%20hybrids%20with%20other%20species&f=false">There is some research looking into why crosses don't work.</a> <i>F. faba</i> as seed parent crossed with<i> V. galilaea</i> and <i>V. johannis</i> both appear to result in fertilized eggs. <i>F. faba</i> as pollen parent crossed with<i> V. bithynica</i> also appears to result in fertilized eggs. The fertilized eggs don't seem to result in viable seeds, however. There is some later developmental failure which interferes with the cross. It might be possible to use embryo rescue to allow some of those crosses to grow up. This is well outside my skill set for now.<br />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-nY8kQGbDYHI/VjmRtzb9-RI/AAAAAAAABpo/jbwM27P4RrQ/s1600/Joseph_Simcox_fava_beans.jpg" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Variously colored fava means laid out in a grid, 11 beans wide and 6 beans tall." border="0" height="133" src="https://2.bp.blogspot.com/-nY8kQGbDYHI/VjmRtzb9-RI/AAAAAAAABpo/jbwM27P4RrQ/w200-h133/Joseph_Simcox_fava_beans.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">[Photo from <a href="https://www.facebook.com/photo.php?fbid=10206706337688042&set=a.3890116502345&type=3&theater">link</a>.]</td></tr>
</tbody></table>
2. Finding old/rare varieties relies on such varieties still existing. The internet provides us with an amazing ability to find things, so long as someone, somewhere has put it online in some form. The image at right and others suggest there's a great deal of genetic diversity around, which might include interesting traits impacting flower color. The task of getting seeds to trial may be rather involved, but it is definitely a way forward. <br />
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li><a href="http://growingfoodsavingseeds.blogspot.com/2015/06/colourful-broad-bean-flowers.html">growingfoodsavingseeds.blogspot.com/2015/06/colourful-broad-bean-flowers.html</a> </li>
<li><a href="http://www.growingfoodsavingseeds.co.uk/forum/breeding-and-genetics/new-channel/2938-broad-bean-fava-bean-flower-colour">www.growingfoodsavingseeds.co.uk/forum/breeding-and-genetics/new-channel/2938-broad-bean-fava-bean-flower-colour</a></li>
<li><a href="https://books.google.com/books?id=toHsCAAAQBAJ&pg=PA202&lpg=PA202&dq=Vicia+faba+hybrids+with+other+species&source=bl&ots=rokyVBhghu&sig=PsZSX6w__E1oM0fPdcvQAgvaX0k&hl=en&sa=X&ved=0CB8Q6AEwAGoVChMI-JuS1P2KxwIVAYuSCh2rngTg#v=onepage&q=Vicia%20faba%20hybrids%20with%20other%20species&f=false">books.google.com/books?id=toHsCAAAQBAJ&pg=PA202&lpg=PA202&dq=Vicia+faba+hybrids+with+other+species&source=bl&ots=rokyVBhghu&sig=PsZSX6w__E1oM0fPdcvQAgvaX0k&hl=en&sa=X&ved=0CB8Q6AEwAGoVChMI-JuS1P2KxwIVAYuSCh2rngTg#v=onepage&q=Vicia%20faba%20hybrids%20with%20other%20species&f=false</a> </li>
<li>Fava varieties:</li>
<ul>
<li>"Crimson Flowered": <a href="http://www.thompson-morgan.com/vegetables/vegetable-seeds/pea-and-bean-seeds/broad-bean-crimson-flowered/4772TM">www.thompson-morgan.com/vegetables/vegetable-seeds/pea-and-bean-seeds/broad-bean-crimson-flowered/4772TM</a></li>
<li>"Red Epicure": <a href="http://davesgarden.com/guides/pf/go/40640/">davesgarden.com/guides/pf/go/40640/</a> </li>
<li>misc: <a href="http://www.heritageharvestseed.com/beansbroad.html">www.heritageharvestseed.com/beansbroad.html</a> </li>
<li>misc: <a href="http://www.heritageharvestseed.com/beansbroad.html">prseeds.ca/seed_categories/beans/favas-broad-beans/</a></li>
</ul>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com4tag:blogger.com,1999:blog-2660869052224924549.post-30545889537469786452019-11-21T13:00:00.001-06:002023-02-07T17:48:41.767-06:00The Color of Onions : The Whims of Genetics<div dir="ltr" style="text-align: left;" trbidi="on">
I've previously posted about what might go into changing the color of onions (<a href="http://the-biologist-is-in.blogspot.com/2013/12/the-color-of-onions.html">the-biologist-is-in.blogspot.com/2013/12/the-color-of-onions.html</a>), but now I've gone and done an experiment. It was an accident, really, but many useful experiments start out as accidents.<br />
<br />
We planted out a batch of "red" onion seedlings this last spring. We got them in a trade from someone who had started them. We got a pot of onion threads, and they got a couple squash babies in return. I'd never grown onions before, so I just put them (along with several types of decorative onions, hoping the deer would leave them all alone) into a raised bed that I had recently cleared. I watered the babies a few times when I noticed the soil was dry. I never fertilized or amended the soil. I basically ignored them. In retrospect, this is not the way to get those luxuriant onions you see in the store. Somehow, almost all the plants survived and produced bulbs. Inch-long bulbs, that is.<br />
<br />
I pulled each onion as its leaves died down. They got cleaned, dried, and then left alone on the kitchen windowsill. After too many had accumulated, I moved them to a spare drying rack left over from an ongoing tomato-jerky experiment with a food dehydrator. A couple days later, I happened to notice that one of the bulbs was a much darker color than all the others. An early thought was that this was the color of some mold infesting the bulb, but on close examination there didn't seem to be anything wrong with it. It definitely was a darker shade.<br />
<br />
I started looking at the color of the collected onions. One stood out as being more red than the others... actually red instead of that purplish color that "red" onions typically are. Another was a rich purple color.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-Im4WZ8rAGvQ/Up0aqSxTYVI/AAAAAAAAAJQ/4sC9DfYj8_I/s1600/Red_cabbage_pH_series.jpg" style="margin-left: auto; margin-right: auto;"><img alt="12 vials in a row, filled with clear colored liquid going from red at left, to blue, green, and then yellow at the right." border="0" height="92" src="https://2.bp.blogspot.com/-Im4WZ8rAGvQ/Up0aqSxTYVI/AAAAAAAAAJQ/4sC9DfYj8_I/w320-h92/Red_cabbage_pH_series.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://www.braukaiser.com/wiki/index.php?title=An_Overview_of_pH">www.braukaiser.com/wiki/index.php?title=An_Overview_of_pH</a></td></tr>
</tbody></table>
Since "red" onions are colored by anthocyanins that change their color depending on pH, we can estimate the pH of the cellular structures where the pigment is found. The red bulb approaches a pH of 2, while the purple bulb approaches a pH of 5. If we could drive the pH further to the right by the same interval, we'd get a pH=8 onion that looked blue.<br />
<br />
<hr width="50%" />
<br />
I was planning to save the color outlier bulbs (red, purple, dark) to grow the following year for seed. Unfortunately, they didn't survive the winter. I was pretty sure they wouldn't survive outside, but I didn't think about how best to get them to survive inside.<br />
<br />
I may re-do this initial experiment next year. Onions with unexpected colors would be fun.<br />
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li><a href="http://the-biologist-is-in.blogspot.com/2013/12/the-color-of-onions.html">the-biologist-is-in.blogspot.com/2013/12/the-color-of-onions.html</a> </li>
<li><a href="http://www.braukaiser.com/wiki/index.php?title=An_Overview_of_pH">www.braukaiser.com/wiki/index.php?title=An_Overview_of_pH</a> </li>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com1tag:blogger.com,1999:blog-2660869052224924549.post-61084522848524077452019-11-14T13:00:00.001-06:002023-02-07T17:51:47.815-06:00Biology of Blue<div dir="ltr" style="text-align: left;" trbidi="on">
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-uqWMDzZfEl8/Up4_2KmsMsI/AAAAAAAAAMw/hqosGFRY9XM/s1600/6063041960_c081830a9b_b.jpg" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Two plants on the forest floor, with broad oval leaves growing from the base and a thin stem topped with dark blue berries." border="0" height="320" src="https://2.bp.blogspot.com/-uqWMDzZfEl8/Up4_2KmsMsI/AAAAAAAAAMw/hqosGFRY9XM/w212-h320/6063041960_c081830a9b_b.jpg" width="212" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Blue-Bead Lily (<i>Clintonia borealis</i>)</td></tr>
</tbody></table>
Blue is very hard/expensive for biology to produce.<br />
<br />
Blue light is higher energy than other visible frequencies, so chemistry to absorb everything else but pass/reflect blue light is ... tricky.<br />
<br />
<hr width="50%" />
<br />
The lovely blue feathers of the <a href="https://dnr.wi.gov/wnrmag/html/stories/2003/feb03/jays.htm">Blue Jay</a> (<i>Cyanocitta cristata</i>) and <a href="https://academic.oup.com/beheco/article/14/6/855/269116">Eastern Bluebird</a> (<i>Sialia sialis</i>) have no blue pigment in them. The vibrant blue so often seen <a href="https://jeb.biologists.org/content/207/22/3999.long">in dragonflies</a> is produced without any blue pigment. Even the blue color we see <a href="https://www.sciencealert.com/science-how-blue-eyes-get-their-colour">in the eyes</a> of some people has no blue pigment. These and many more examples of blue in biology all are referred to as structural colors instead.<br />
<br />
Structural colors are produced by the presence of microscopically fine structures that interfere with light. The blue of some human eyes is caused by very small particles of melanin (a brown pigment), for example.<br />
<br />
<hr width="50%" />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-HUmVMVFzrzs/XbZzVucaNdI/AAAAAAAAG1M/piOqb-N5jlcT4PbLkmRzLQGTlmtmZrthgCLcBGAsYHQ/s1600/Flavone_structure.png" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Molecular structure diagram, illustrating the general structure of flavones, with three six-carbon rings." border="0" data-original-height="382" data-original-width="500" height="152" src="https://1.bp.blogspot.com/-HUmVMVFzrzs/XbZzVucaNdI/AAAAAAAAG1M/piOqb-N5jlcT4PbLkmRzLQGTlmtmZrthgCLcBGAsYHQ/w200-h152/Flavone_structure.png" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="https://en.wikipedia.org/wiki/Flavones#/media/File:Flavon_num.svg">Flavone structure.</a></td></tr>
</tbody></table>
Some blue berries, like those of Marbleberry (<i>Pollia condensata</i>) are blue due to a structural color. Others, like the Blue-Bead Lily (<i>Clintonia borealis</i>) I photographed in northern Minnesota (at top-left) have a blue flavinoid pigment. The flavinoid pigments are derived from or structurally similar to flavone (at right).<br />
<br />
Some insects (like the <a href="https://link.springer.com/article/10.1007/BF01880094">Lycaenid butterflies</a>) are blue due to flavoniods like kaempherol. Some of the more common flavinoid pigments are the <a href="http://www.micro-ox.com/chem_antho.htm">anthocyanins</a> responsible for the red/purple/blue colors seen in fruits and other plant tissues. Different compounds in the group have various modifications to the basic flavone structure. Those modifications impact the stability of the ionic form of the molecules at different pH levels, as well as the specific frequencies of light that are absorbed.<br />
<br />
I don't have a solid grasp on the physics that leads to all the differences in color, but the following quote from <a href="https://www.ias.ac.in/article/fulltext/reso/006/03/0066-0075">this paper</a> seems to be illustrative.<br />
<br />
<div style="text-align: center;">
<i>"Confining electrons to a smaller space makes the light absorbed bluer and if they move around in larger space the light absorbed is redder."</i></div>
<br />
When the light absorbed is bluer, the light transmitted (and thus observed) is redder, and vice versa. Thus, when electrons are more de-localized, the molecule will have a more blue color. Conversely, when electrons are more restricted, the molecule will have a more red color.<br />
<br />
<hr width="50%" />
<br />
In the structure of lycopene, responsible for the classical red color of tomatoes, electrons are restricted to travel within very localized regions of the molecule.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-_5PjChkWwQE/XbZ6J9q-LbI/AAAAAAAAG1k/nXqODHpiwL8-muDZ0aFiNW_rKdTlBlSxgCLcBGAsYHQ/s1600/Lycopene_structure.png" style="margin-left: auto; margin-right: auto;"><img alt="Molecular structure figure, single enlongated carbon chain with double and single bonds." border="0" data-original-height="160" data-original-width="452" height="113" src="https://1.bp.blogspot.com/-_5PjChkWwQE/XbZ6J9q-LbI/AAAAAAAAG1k/nXqODHpiwL8-muDZ0aFiNW_rKdTlBlSxgCLcBGAsYHQ/w320-h113/Lycopene_structure.png" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">[From <a href="http://ijsrch.com/IJSRCH18322">Madu & Bello, 2018</a>.]</td></tr>
</tbody></table>
<br />
Compared that to the anthocyains, where the electrons are de-localized into aromatic carbon rings. Here the electrons are much more free to occupy larger spaces. The molecules often absorb more red and appear bluer.<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-Hr50iB-MqSM/XbZ9kHfRjyI/AAAAAAAAG2E/b0sDQL7GN6sxkIPuaZYsDtds3O8ugT_TQCLcBGAsYHQ/s1600/Anthocyanin_structure_2.png" style="margin-left: auto; margin-right: auto;"><img alt="Molecular structure figure, illustrating the basic structure of anthocyanins." border="0" data-original-height="582" data-original-width="800" height="232" src="https://1.bp.blogspot.com/-Hr50iB-MqSM/XbZ9kHfRjyI/AAAAAAAAG2E/b0sDQL7GN6sxkIPuaZYsDtds3O8ugT_TQCLcBGAsYHQ/w320-h232/Anthocyanin_structure_2.png" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">[Modified from <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613902/">Khoo <i>et al</i>, 2017</a>.]</td></tr>
</tbody></table>
<br />
One of the anthocyanins that is more stable at higher pH is called delphinidin. It is responsible for the clear blue color found in delphiniums and can also be found in various purple plant materials. The exact shade it presents us with depends on the specific pH of the cell and the association of the delphinidin with various molecules or ions in ways far more complex than I've been able to become clear about with my readings so far.<br />
<br />
<hr width="50%" />
<br />
So. Why does biology often go with structural colors, when there are commonly available molecules which produce the color? Two partial answers that come to mind are:<br />
<ol style="text-align: left;">
<li>It may be that the flavinoid blue pigments are more energetically expensive to produce than other pigment types.</li>
<li>It may be that structural blues are very easy to come by on accident (like <a href="https://link.springer.com/chapter/10.1007/978-3-642-70280-8_4">iridovirus infection of isopods</a>).</li>
</ol>
Evolution is a tinkerer, not a planner. It can be very hard to ever answer questions of "why" in biology. It is far easier to answer questions about "how" or "what". In the end, biologists often have to say, "I really don't know. Do you have any ideas about how we might find out?"<br />
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li>Structural color:</li>
<ul>
<li><a href="https://en.wikipedia.org/wiki/Structural_coloration">https://en.wikipedia.org/wiki/Structural_coloration</a> </li>
<li><a href="https://medium.com/@rawwerks/what-is-structural-color-536ee6fe46d4">https://medium.com/@rawwerks/what-is-structural-color-536ee6fe46d4</a> </li>
</ul>
<li>Bluejay color: <a href="https://dnr.wi.gov/wnrmag/html/stories/2003/feb03/jays.htm">https://dnr.wi.gov/wnrmag/html/stories/2003/feb03/jays.htm</a> </li>
<li>Eastern Bluebird color: <a href="https://academic.oup.com/beheco/article/14/6/855/269116">https://academic.oup.com/beheco/article/14/6/855/269116</a></li>
<li>Dragonfly color: <a href="https://jeb.biologists.org/content/207/22/3999.long">https://jeb.biologists.org/content/207/22/3999.long</a> </li>
<li>Human eye color: <a href="https://www.sciencealert.com/science-how-blue-eyes-get-their-colour">https://www.sciencealert.com/science-how-blue-eyes-get-their-colour</a> </li>
<li>Bluebead Lily:</li>
<ul>
<li><a href="https://www.fs.fed.us/wildflowers/plant-of-the-week/clintonia_borealis.shtml">https://www.fs.fed.us/wildflowers/plant-of-the-week/clintonia_borealis.shtml</a></li>
<li><a href="https://books.google.com/books?id=YfpVC5aRRZcC&pg=PA69&lpg=PA69&dq=%22Clintonia+borealis%22+pigment&source=bl&ots=qOVVqSmgEi&sig=ACfU3U0QzbH4fUDoQwl2RO0pdEDb4xftZQ&hl=en&sa=X&ved=2ahUKEwio2NXZl7TlAhVJba0KHSmdB4YQ6AEwAXoECAkQAQ#v=onepage&q=%22Clintonia%20borealis%22%20pigment&f=false">https://books.google.com/books?id=YfpVC5aRRZcC&pg=PA69&lpg=PA69&dq=%22Clintonia+borealis%22+pigment&source=bl&ots=qOVVqSmgEi&sig=ACfU3U0QzbH4fUDoQwl2RO0pdEDb4xftZQ&hl=en&sa=X&ved=2ahUKEwio2NXZl7TlAhVJba0KHSmdB4YQ6AEwAXoECAkQAQ#v=onepage&q=%22Clintonia%20borealis%22%20pigment&f=false</a> </li>
</ul>
<li>Butterflies:</li>
<ul>
<li><a href="https://link.springer.com/article/10.1007/BF01880094">https://link.springer.com/article/10.1007/BF01880094</a> </li>
</ul>
<li>Marbleberry (<i>Pollia condensata</i>):</li>
<ul>
<li><a href="https://earthsky.org/earth/brightest-biological-substance-reveals-its-secret">https://earthsky.org/earth/brightest-biological-substance-reveals-its-secret</a></li>
<li><a href="https://www.npr.org/2012/09/11/160894364/how-to-get-birds-to-pick-blue-berries-they-can-t-eat">https://www.npr.org/2012/09/11/160894364/how-to-get-birds-to-pick-blue-berries-they-can-t-eat</a></li>
</ul>
<li>Anthocyanin pigments:</li>
<ul>
<li><a href="http://www.micro-ox.com/chem_antho.htm">http://www.micro-ox.com/chem_antho.htm</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613902/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613902/</a> </li>
<li><a href="https://www.tuscany-diet.net/2014/02/22/anthocyanins-definition-structure-ph/">https://www.tuscany-diet.net/2014/02/22/anthocyanins-definition-structure-ph/</a></li>
</ul>
<li>Chemistry of colors:</li>
<ul>
<li><a href="https://www.ias.ac.in/article/fulltext/reso/006/03/0066-0075">https://www.ias.ac.in/article/fulltext/reso/006/03/0066-0075</a> </li>
</ul>
<li>Lycopene structure:</li>
<ul>
<li><a href="http://ijsrch.com/IJSRCH18322">http://ijsrch.com/IJSRCH18322</a></li>
</ul>
<li>Iridoviruses: <a href="https://link.springer.com/chapter/10.1007/978-3-642-70280-8_4">https://link.springer.com/chapter/10.1007/978-3-642-70280-8_4</a> </li>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com3tag:blogger.com,1999:blog-2660869052224924549.post-73447898829020892972019-11-07T13:00:00.002-06:002023-02-07T17:52:22.675-06:00Botanizing in Alaska: Alpine Blueberry<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/-3gLxzCMcZDg/VbsPjW9Rl6I/AAAAAAAABZE/2ACUSXqQClA/s1600/blueberry.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Small blueberry bush with unripe green berries." border="0" height="320" src="https://2.bp.blogspot.com/-3gLxzCMcZDg/VbsPjW9Rl6I/AAAAAAAABZE/2ACUSXqQClA/w213-h320/blueberry.jpg" width="213" /></a></div>
The Alpine Blueberry (<i>Vaccinium uliginosum</i>) grows throughout Alaska. I took this photo during midsummer. The berries ripen during fall, so I didn't get any on the trip when I took the photo.<br />
<br />
The ripe berries are well-regarded by humans and bears alike. Both can be found collecting them along roadsides in the fall. Ideally not in the same place at the same time, but you have to keep aware of your surroundings while berry picking in case you're lucky/unlucky.<br />
<br />
<hr width="50%" />
<br />
On a more recent trip than when I took this photo, I was lucky enough to find plenty of ripe blueberries to pick as well as a black bear filling itself on blueberries. I was especially lucky in that the two of us were picking berries in different places.<br />
<br />
Within each berry are several tiny seeds. The seeds need a period of cold moist stratification before they will germinate effectively. I'll be planting a batch of seeds in a pot outside to see if I can get any plants to grow next year.<br />
<br />
References:<br />
<ul style="text-align: left;">
<li>Bog/Alpine blueberry:</li>
<ul>
<li><a href="https://www.flora.dempstercountry.org/0.Site.Folder/Species.Program/Species.php?species_id=Vacci.uli">https://www.flora.dempstercountry.org/0.Site.Folder/Species.Program/Species.php?species_id=Vacci.uli</a> </li>
<li><a href="http://plants.alaska.gov/pdf/Blueberry.pdf">http://plants.alaska.gov/pdf/Blueberry.pdf</a></li>
</ul>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-16700798238355674922019-10-31T13:00:00.001-05:002023-02-07T17:56:50.392-06:00Lavendar<div dir="ltr" style="text-align: left;" trbidi="on">
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/--7wUvmoT6ik/XbkdVmxUw7I/AAAAAAAAG6A/bHd6oE2R24oXQyw01wEshfFKO2YFcD3iQCLcBGAsYHQ/s1600/Lavandula_angustifolia_-_K%25C3%25B6hler%25E2%2580%2593s_Medizinal-Pflanzen-087.jpg" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Botanical drawing of lavender plant, showing details of flower structure." border="0" data-original-height="597" data-original-width="438" height="200" src="https://1.bp.blogspot.com/--7wUvmoT6ik/XbkdVmxUw7I/AAAAAAAAG6A/bHd6oE2R24oXQyw01wEshfFKO2YFcD3iQCLcBGAsYHQ/w146-h200/Lavandula_angustifolia_-_K%25C3%25B6hler%25E2%2580%2593s_Medizinal-Pflanzen-087.jpg" width="146" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">[From <a href="https://en.wikipedia.org/wiki/Lavandula_angustifolia#/media/File:Lavandula_angustifolia_-_K%C3%B6hler%E2%80%93s_Medizinal-Pflanzen-087.jpg">link</a>.]</td></tr>
</tbody></table>
Lavender is a wonderfully aromatic plant with gorgeous flowers. When I moved to Minnesota I learned that most lavenders don't survive our winters well. There are a few <a href="https://www.gardeningknowhow.com/garden-how-to/gardening-by-zone/zone-4/lavender-in-zone-4-gardens.htm">varieties listed</a> as surviving here, but they require "some winter protection".<br />
<br />
I want lavender to grow and thrive here without care. This led me to start thinking about how I would go about breeding cold-hardy lavenders.<br />
<br />
<hr width="50%" />
<br />
The first step with any breeding project is to figure out a plan. It can be a simple or complex plan, but something. Anyhow. I wanted to gather seeds from the most cold-hardy varieties available. But since I had never actually grown lavender before, I was hesitant to start with buying several relatively expensive plants that I might just kill the first winter.<br />
<br />
While investigating the available varieties I realized the most cold-hardy ones were all from the species <i>Lavandula angustifolia</i> and that seeds for <i>L. angustifolia</i> were readily (and cheaply) available in any spring-time seed packet kiosk.<br />
<br />
So, I picked up a few packets. <br />
<br />
<hr width="50%" />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-9EpOBri0juw/Xbkcp5aQ5lI/AAAAAAAAG54/fSqMKhqH-F8-sB-2uIPcVttxVI43BSYlgCLcBGAsYHQ/s1600/seedlings.2.jpeg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="View into small square pot with dark soil and tiny green seedlings." border="0" data-original-height="1000" data-original-width="1000" height="200" src="https://1.bp.blogspot.com/-9EpOBri0juw/Xbkcp5aQ5lI/AAAAAAAAG54/fSqMKhqH-F8-sB-2uIPcVttxVI43BSYlgCLcBGAsYHQ/w200-h200/seedlings.2.jpeg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender seedlings in pot.</td></tr>
</tbody></table>
This spring I scattered the -tiny- seeds on to the soil in a larger pot, pressed them in, and waited for something to happen. The seeds may have been old, or lavender may not be quick to start from seeds.<br />
<br />
Eventually I had some little green seedlings that I didn't recognize growing in the pot. One day I was examining the plants closely, trying to figure out if they were stray weeds or not. To my surprise, I could smell lavender. Even the tiny seedlings are exuberant with their scent production.<br />
<br />
Once the seedling had gotten a bit larger, I separated them out and transplanted each one to its own pot. I kept the pots where I could keep an eye on them and keep them watered. A few of the plants began to put on new growth, but most seemed to suffer and remain stunted. (In retrospect, I and our rains may have been keeping them too wet. Oh well, that just counts as a first selection pass. I don't want plants that have to be given special conditions, anyhow.)<br />
<br />
<hr width="50%" />
<br />
Now that winter is coming on, I've brought the three best grown plants
inside to overwinter under lights. I left the others to their fate
outside in a cold-frame.<br />
<br />
Since lavender varieties are propagated by cuttings, I could refer to
these three plants as three new varieties. However, only time will tell
if they're worth propagating. And really, I don't expect them to have
the cold-hardiness that I'm looking for. The odds of one of these three
meeting that criterion are astoundingly low.<br />
<br />
<table align="center"><tbody>
<tr><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-vFnECsE8S-4/XbkQYRbPROI/AAAAAAAAG4k/ALdtEDZqLY4SNBWzqnNroJOgy2fwmL1dgCLcBGAsYHQ/s1600/left_full.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Lavender plant growing under lights." border="0" data-original-height="1500" data-original-width="1000" height="200" src="https://1.bp.blogspot.com/-vFnECsE8S-4/XbkQYRbPROI/AAAAAAAAG4k/ALdtEDZqLY4SNBWzqnNroJOgy2fwmL1dgCLcBGAsYHQ/w133-h200/left_full.2.jpg" width="133" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #1.</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-X85pSHTjNlI/XbkQX1lm7gI/AAAAAAAAG4c/j3P6qLd2GToj_3qWo08v1TvjQpZAXOFnQCLcBGAsYHQ/s1600/milddle_full.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Short lavender plant growing under lights." border="0" data-original-height="1000" data-original-width="1500" height="133" src="https://1.bp.blogspot.com/-X85pSHTjNlI/XbkQX1lm7gI/AAAAAAAAG4c/j3P6qLd2GToj_3qWo08v1TvjQpZAXOFnQCLcBGAsYHQ/w200-h133/milddle_full.2.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #2.</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-LYurqlr2fgo/XbkQYeL_2SI/AAAAAAAAG4g/ewFBemD2FZ4kKYyhGg93oGu9bPrOR9VNQCLcBGAsYHQ/s1600/right_full.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Lavender plant growing under lights." border="0" data-original-height="1500" data-original-width="1000" height="200" src="https://1.bp.blogspot.com/-LYurqlr2fgo/XbkQYeL_2SI/AAAAAAAAG4g/ewFBemD2FZ4kKYyhGg93oGu9bPrOR9VNQCLcBGAsYHQ/w133-h200/right_full.2.jpg" width="133" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #3.</td></tr>
</tbody></table>
</td></tr>
</tbody></table>
<br />
I do like the dwarfed growth habit of the second plant. A closer look shows that it does have shorter internode distances than the other plants. It isn't just behind in its growth, it is actually growing differently.<br />
<br />
<table align="center"><tbody>
<tr><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-SJ0lXcfbCq0/XbkSJSarCPI/AAAAAAAAG5E/FBBQp5EeySAK7g43t1PWbDHT7URNvZA6QCLcBGAsYHQ/s1600/left_close.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Close view of lavender plant stem leaf." border="0" data-original-height="1500" data-original-width="1000" height="200" src="https://1.bp.blogspot.com/-SJ0lXcfbCq0/XbkSJSarCPI/AAAAAAAAG5E/FBBQp5EeySAK7g43t1PWbDHT7URNvZA6QCLcBGAsYHQ/w133-h200/left_close.2.jpg" width="133" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #1, stem.</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-rfRf79_T59M/XbkSJYXXmrI/AAAAAAAAG5I/LMHJi2MQMYY6EiQ10wZrPJ7ASdh1TYikQCLcBGAsYHQ/s1600/middle_close.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Close view of lavender stem tip on short plant." border="0" data-original-height="1000" data-original-width="1500" height="133" src="https://1.bp.blogspot.com/-rfRf79_T59M/XbkSJYXXmrI/AAAAAAAAG5I/LMHJi2MQMYY6EiQ10wZrPJ7ASdh1TYikQCLcBGAsYHQ/w200-h133/middle_close.2.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #2, stem.</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-nU9UpKzcYIM/XbkSJC-kawI/AAAAAAAAG5A/HNzBRbDLvh0QBwPFv_NvR20AAhFWGEN2ACLcBGAsYHQ/s1600/right_close.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Close view of lavender plant stem tip." border="0" data-original-height="1500" data-original-width="1000" height="200" src="https://1.bp.blogspot.com/-nU9UpKzcYIM/XbkSJC-kawI/AAAAAAAAG5A/HNzBRbDLvh0QBwPFv_NvR20AAhFWGEN2ACLcBGAsYHQ/w133-h200/right_close.2.jpg" width="133" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #3, stem.</td></tr>
</tbody></table>
</td></tr>
</tbody></table>
I also like that it looks a bit more silvery than the other plants. A very close up view of some leaf tips shows that the second plant has much more prominent and branched trichomes. These photos were taken hand-held. I think I can probably do better and closer with some more technical preparation (tripod, lights, maybe focus stacking, etc.).<br />
<br />
<table align="center"><tbody>
<tr><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-Yvmn4zCuHjU/XbkUCSWln9I/AAAAAAAAG5g/e0b1M3YLXLENTttsiA_642-F1H9ktFcSQCLcBGAsYHQ/s1600/left_leaf.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Extreme close up of lavender leaf tip, showing tiny branched trichomes on leaf surface." border="0" data-original-height="1000" data-original-width="1500" height="133" src="https://1.bp.blogspot.com/-Yvmn4zCuHjU/XbkUCSWln9I/AAAAAAAAG5g/e0b1M3YLXLENTttsiA_642-F1H9ktFcSQCLcBGAsYHQ/w200-h133/left_leaf.2.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #1, leaf tip.</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-Gkjz8oL-Nw0/XbkUCMoY4EI/AAAAAAAAG5c/e8zFhvRkzrkw7evB0P3dRn0vP32zFJA7gCLcBGAsYHQ/s1600/middle_leaf.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Extreme close up of lavender leaf tip, showing tiny branched trichomes on leaf surface." border="0" data-original-height="1000" data-original-width="1500" height="133" src="https://1.bp.blogspot.com/-Gkjz8oL-Nw0/XbkUCMoY4EI/AAAAAAAAG5c/e8zFhvRkzrkw7evB0P3dRn0vP32zFJA7gCLcBGAsYHQ/w200-h133/middle_leaf.2.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #2, leaf tip.</td></tr>
</tbody></table>
</td><td><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-KURYEwW1MOo/XbkUCdhNF3I/AAAAAAAAG5k/nSmzJxapNrgcOC5SYZ4rBiMc-jqxnkQigCLcBGAsYHQ/s1600/right_leaf.2.jpg" style="margin-left: auto; margin-right: auto;"><img alt="Extreme close up of lavender leaf tip, showing tiny branched trichomes on leaf surface." border="0" data-original-height="1000" data-original-width="1500" height="133" src="https://1.bp.blogspot.com/-KURYEwW1MOo/XbkUCdhNF3I/AAAAAAAAG5k/nSmzJxapNrgcOC5SYZ4rBiMc-jqxnkQigCLcBGAsYHQ/w200-h133/right_leaf.2.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Lavender #3, leaf tip.</td></tr>
</tbody></table>
</td></tr>
</tbody></table>
<br />
<hr width="50%" />
<br />
<div style="text-align: center;">
<i>What lessons have I learned and how do they impact my longer term goals?</i></div>
<br />
Lavender varieties are propagated clonally, so there's no need for them to be homozygous for various alleles. As a result, lavender seeds would be expected to contain a surprising amount of genetic diversity compared to domesticated plants that are routinely grown from seed. The few plants I've grown have shown variations in ability to prosper in the temperature/water conditions I was growing them in, as well as having height and trichome differences.<br />
<br />
I have no reason not to expect variations in cold hardiness will also be manifest when I grow out a larger population, though I don't expect one of these three to be a winner in that regard. I'm also looking forward to what other interesting traits may turn up.<br />
<br />
The next steps are to acquire a larger number of seeds, grow more seedlings, then plant them out for winter. For initial hardiness trials, I can have many small plants in my back yard. If I find survivors, I'd want to collect seeds and begin the cycle again. Later I can plant seedlings or cuttings at a family property further north. Ideally, I would eventually find trial space in the far north of Minnesota, so the plants can be tested against the coldest that Minnesota winters can provide. That would be several years out, so I have some time yet to make arrangements if things develop such that they would be useful.<br />
<br />
<hr width="50%" />
<br />
<div style="text-align: center;">
<i>Why?</i></div>
<br />
Funny you should ask. In the medium-term, I'm simply motivated by the desire to play around with the plant and produce something I can grow in my yard without having to spend too much effort at keeping it alive. In the long-term, I want to produce varieties that can be farmed for fragrance production in Minnesota. (All current lavender farms in USA are a few growing zones warmer than is available here.) This would open up a new crop for local agriculture and help to diversify what is grown in the state. I don't know if this will come to pass, but that's the thing about long-term goals.<br />
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li>Lavender in zone 4:</li>
<ul>
<li><a href="https://www.gardeningknowhow.com/garden-how-to/gardening-by-zone/zone-4/lavender-in-zone-4-gardens.htm">https://www.gardeningknowhow.com/garden-how-to/gardening-by-zone/zone-4/lavender-in-zone-4-gardens.htm</a></li>
</ul>
<li>Lavender in zone 5:</li>
<ul>
<li><a href="https://www.gardeningknowhow.com/garden-how-to/gardening-by-zone/zone-5/zone-5-lavender-plants.htm">https://www.gardeningknowhow.com/garden-how-to/gardening-by-zone/zone-5/zone-5-lavender-plants.htm</a></li>
<li><a href="https://blog-yard-garden-news.extension.umn.edu/2019/02/good-lavenders-for-north.html">https://blog-yard-garden-news.extension.umn.edu/2019/02/good-lavenders-for-north.html</a></li>
</ul>
<li>Lavender varieties:</li>
<ul>
<li>"Munstead": <a href="http://plants.sargentsgardens.com/12080004/Plant/5429/Munstead_Lavender/">http://plants.sargentsgardens.com/12080004/Plant/5429/Munstead_Lavender/</a></li>
<li>"Hidcote": <a href="https://plants.gertens.com/12070009/Plant/7411/Hidcote_Blue_Lavender/">https://plants.gertens.com/12070009/Plant/7411/Hidcote_Blue_Lavender/</a></li>
<li>"Phenomenal": <a href="https://plants.gertens.com/12070009/Plant/16587/Phenomenal_Lavender">https://plants.gertens.com/12070009/Plant/16587/Phenomenal_Lavender</a></li>
</ul>
<li>Minnesota zones: <a href="https://www.gardeningknowhow.com/planting-zones/minnesota-planting-zones.htm">https://www.gardeningknowhow.com/planting-zones/minnesota-planting-zones.htm</a></li>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-28033716604871224082019-10-24T13:00:00.001-05:002023-02-07T18:02:25.815-06:00Botanizing in Alaska: Black Spruce<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-wrjqKiU5a3k/VbsSfCg6_2I/AAAAAAAABZc/0g6APPm8VcQ/s1600/blackSpruce.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Cluster of narrow black spruce trees growing alongside a road." border="0" height="400" src="https://3.bp.blogspot.com/-wrjqKiU5a3k/VbsSfCg6_2I/AAAAAAAABZc/0g6APPm8VcQ/w183-h400/blackSpruce.jpg" width="183" /></a></div>
Black spruce (<span class="ILfuVd"><span class="e24Kjd"><i>Picea mariana</i>) are a common forest tree up in central Alaska, ranging north until the tundra. The trees in the image at left are in Fairbanks, Alaska.</span></span><br />
<span class="ILfuVd"><span class="e24Kjd"><br /></span></span>
<span class="ILfuVd"><span class="e24Kjd">The trees grow slowly, eventually topping out at 20 meters in the southern parts of their range. The trees in Fairbanks are generally much shorter. The trees here are maybe 30 ft tall, growing less than a foot apart. They can get away with such crowding because those two trees are probably separate trunks growing from a unified root system. Large connecting roots grow horizontally just under the surface and graft together with their neighbors. The individual trunks share nutrients and carbohydrates and thus don't suffer from competitive shading as much as trees that don't cooperate in this manner.</span></span><br />
<span class="ILfuVd"><span class="e24Kjd"><br /></span></span>
<span class="ILfuVd"><span class="e24Kjd">This style of growth also potentially helps them stay upright in the swampy soils they're usually found in. The horizontal grafted root structure spans wider than the cluster of trunks, allowing the cluster to stay upright even if the ground beneath part of the cluster can't support their weight. This style of growth would help them grow horizontally out onto a bog, with some trees suspended over the lake hidden below.</span></span><br />
<br />
References:<br />
<ul style="text-align: left;">
<li>Black spruce: <a href="https://www.oecd-ilibrary.org/docserver/9789264095434-10-en.pdf?expires=1571892005&id=id&accname=guest&checksum=D3380DF0E335EC3E021633EB1523689A">https://www.oecd-ilibrary.org/docserver/9789264095434-10-en.pdf?expires=1571892005&id=id&accname=guest&checksum=D3380DF0E335EC3E021633EB1523689A</a></li>
<li>Root grafts:</li>
<ul>
<li><a href="https://www.nrcresearchpress.com/doi/pdf/10.1139/cjfr-2016-0121">https://www.nrcresearchpress.com/doi/pdf/10.1139/cjfr-2016-0121</a></li>
<li><a href="https://www.sciencedaily.com/releases/2011/06/110608141529.htm">https://www.sciencedaily.com/releases/2011/06/110608141529.htm</a></li>
</ul>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-22281523797583766702018-12-31T13:00:00.001-06:002023-02-07T18:03:12.318-06:00Biology of Fire<div dir="ltr" style="text-align: left;" trbidi="on">
<br />
Fire is a part of the natural world. Like everything else in the natural world, living systems have evolved to survive, use, or even require fire. We may have a special relationship with fire, but we're not the only ones with an important relationship with fire. When it's in our control, we see it as a constructive force. When
it's out of our control, we see it as a destructive force. And rightfully so, because it's both.<br />
<br />
<hr width="50%" />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-1GGpmXVTPBU/XBMwAch9-XI/AAAAAAAAGkY/Yttuqpl_askrXD7OT38--4wZkzw0RohVQCLcBGAs/s1600/camp-fire-crop.jpeg" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="View from above of neighborhood after a wildfire as burned through. Buildings are burned to ground, but taller coniferous trees remain intact." border="0" data-original-height="618" data-original-width="618" height="200" src="https://4.bp.blogspot.com/-1GGpmXVTPBU/XBMwAch9-XI/AAAAAAAAGkY/Yttuqpl_askrXD7OT38--4wZkzw0RohVQCLcBGAs/w200-h200/camp-fire-crop.jpeg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Cropped from image <a href="https://www.latimes.com/local/california/la-me-camp-fire-lessons-20181120-story.html">at article</a>.</td></tr>
</tbody></table>
The recent <a href="https://en.wikipedia.org/wiki/Camp_Fire_(2018)">Camp Fire</a> in California was dramatically destructive, turning much of the community of Paradise into ash. The scale and speed of the destruction was greater than anything in living memory. Over a pair of days, the fire jumped from one building to the next like a living thing. It raced throughout the city, destroying everything as it went. Thousands of people were displaced. There are numerous harrowing tales of narrow escape. Far too many people suffered horrific deaths. In another place and another time, the stories would be handed down through the ages until they became epic sagas.<br />
<br />
The trees didn't notice.<br />
<br />
<hr width="50%" />
<br />
The trees remaining standing among all the destruction led some to believe in conspiracy theories. That the buildings were intentionally burned down. That the horrors and escapes were all fiction. That some hidden government agency murdered all those who died. How could all those buildings have burned and missed burning the trees?<br />
<br />
Animals can run or hide. Plants have to deal with what comes there way. So. How did they do it?<br />
<br />
The trees that so clearly survived this horrific fire had evolved in an environment that included fire. They have thick fire-resistant bark and they shed their lower branches once they get tall enough. They're adapted to survive the sort of ground fire that destroyed Paradise-CA. (Well, the adults are adapted to survive. Any juvenile trees would have been taken out, but the adults will make more.) The structures we built there were not adapted to survive such a fire. Maybe in the future we'll have building codes appropriate to environments where such fires are possible.<br />
<br />
<hr width="50%" />
<br />
So. The trees are adapted to survive fire. Do any plants -use- fire?<br />
<br />
I'd have to travel a bit to see a really good example of this. In Australia there is a type of grass in the genus <i>Triodia</i> that is called <a href="https://theconversation.com/spinifex-grass-would-like-us-to-stop-putting-out-bushfires-please-105651">Spinifex</a>. (There is a different genus of grass with the name Spinifex, so... I got nothing.) During the dry season the grass become so incredibly flammable that it is almost guaranteed that any large area of the grass will burn every few years. The fires burn hot enough to kill off trees and many other plants. The Spinifex survives and readily regrows from underground stems and seeds resting in the soil. Effectively, the grass uses fire to kill off its competition.<br />
<br />
Many other grasses seem to have adapted to use this strategy to greater or lesser degrees, but the evidence isn't always so clear-cut.<br />
<br />
<hr width="50%" />
<br />
Ok. The trees survive fire. The grass uses fire. Do any plants -need- fire?<br />
<br />
Another tree, the Jack Pine, often definitely needs fire. Its cones are gummed up with so much hard resin that they can't open to release their seeds until they've been burned by a fast, hot fire. After a fire the seeds are able to rapidly germinate into an environment with much less competition. As well, with the reduced level of fuel, the seedlings will likely be protected from another fire until they're large enough to survive it like the adults do. Without fire, the Jack Pine (and other species with <a href="https://en.wikipedia.org/wiki/Serotiny">serotinous</a> cones/fruit) cannot reproduce. In the absence of some helpful humans who might crack open the cones with power tools, the trees absolutely need fire.<br />
<br />
<hr width="50%" />
<br />
There are numerous fire-adapted ecosystems around the world, with amazing and diverse species that survive, use, and/or need fire for their continued existence. Though plants can't get out of the way of a fire, they're not the only ones with such intricate relationships with it. Animals and fungi deal with fire too. Those sound like later blog posts. Stay tuned.<br />
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li><a href="https://en.wikipedia.org/wiki/Camp_Fire_(2018)">https://en.wikipedia.org/wiki/Camp_Fire_(2018)</a></li>
<li><a href="https://www.latimes.com/local/california/la-me-camp-fire-lessons-20181120-story.html">https://www.latimes.com/local/california/la-me-camp-fire-lessons-20181120-story.html</a></li>
<li><a href="https://www.agric.wa.gov.au/rangelands/spinifex-rangeland-pastures-and-fire">https://www.agric.wa.gov.au/rangelands/spinifex-rangeland-pastures-and-fire</a></li>
<li><a href="https://theconversation.com/spinifex-grass-would-like-us-to-stop-putting-out-bushfires-please-105651">https://theconversation.com/spinifex-grass-would-like-us-to-stop-putting-out-bushfires-please-105651</a></li>
<li><a href="https://en.wikipedia.org/wiki/Serotiny">https://en.wikipedia.org/wiki/Serotiny</a> </li>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com2tag:blogger.com,1999:blog-2660869052224924549.post-36746882818939339732018-12-24T13:00:00.000-06:002018-12-24T13:00:09.078-06:00Mathematical Recreations : Ramanujan's Nested Radical 4<div dir="ltr" style="text-align: left;" trbidi="on">
I've previously discussed an interesting math problem posed by <a href="http://www.thefamouspeople.com/profiles/srinivasa-ramanujan-503.php">Srinivasa Ramanujan</a> way back in 1911. <br />
<br />
<ul>
<li><a href="http://the-biologist-is-in.blogspot.ca/2014/12/mathematical-recreations-ramanujans.html">the-biologist-is-in.blogspot.ca/2014/12/mathematical-recreations-ramanujans.html</a></li>
<li><a href="http://the-biologist-is-in.blogspot.com/2016/08/mathematical-recreations-ramanujans-2.html">the-biologist-is-in.blogspot.com/2016/08/mathematical-recreations-ramanujans-2.html</a></li>
<li><a href="http://the-biologist-is-in.blogspot.com/2016/08/mathematical-recreations-ramanujans-3.html">the-biologist-is-in.blogspot.com/2016/08/mathematical-recreations-ramanujans-3.html</a> </li>
</ul>
Over the last three posts on the topic, I've explored my thoughts about this problem and then proved there are an infinite number of valid solutions (any value greater than three).<br />
<br />
Since then I've been trying to figure out how to prove all values less than three are not valid solutions. I haven't figured out how to do this yet, but I have figured out how to prove a subset of values are not valid solutions. Any trajectory which reaches zero will then pass to less than zero and be invalid. I might formalize this statement once I've figured out if it can help me finish the overall solution. It might just be a blind alley...<br />
<br />
<hr width="50%" />
<br />
I haven't found anyone else working this problem in the way I have been. The closest I've found has been some comments below <a href="https://www.youtube.com/watch?v=r5BGIi84arY">a YouTube video</a> where a user talked about calculating through trajectories like I have been. They didn't suggest any sort of general solution to the problem, however.<br />
<br />
I did find a mathematical paper using Ramanujan's solution to the problem as part of the title. The authors and reviewers of the paper assumed Ramanujan was correct and didn't test their assumption. I'm considering writing them a letter...<br />
<br />
<br />
References:<br />
<ul>
<li><a href="http://www.thefamouspeople.com/profiles/srinivasa-ramanujan-503.php">www.thefamouspeople.com/profiles/srinivasa-ramanujan-503.php</a></li>
<li>My posts: </li>
<ul>
<li><a href="http://the-biologist-is-in.blogspot.ca/2014/12/mathematical-recreations-ramanujans.html">the-biologist-is-in.blogspot.ca/2014/12/mathematical-recreations-ramanujans.html</a></li>
<li><a href="http://the-biologist-is-in.blogspot.com/2016/08/mathematical-recreations-ramanujans-2.html">the-biologist-is-in.blogspot.com/2016/08/mathematical-recreations-ramanujans-2.html</a></li>
<li><a href="http://the-biologist-is-in.blogspot.com/2016/08/mathematical-recreations-ramanujans-3.html">the-biologist-is-in.blogspot.com/2016/08/mathematical-recreations-ramanujans-3.html</a></li>
</ul>
<li><a href="https://www.youtube.com/watch?v=r5BGIi84arY">https://www.youtube.com/watch?v=r5BGIi84arY</a></li>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-90355026922990154012018-12-17T13:00:00.000-06:002018-12-17T13:00:02.924-06:00Seed Banks<div dir="ltr" style="text-align: left;" trbidi="on">
The largest seed collections are multi-national affairs, backing up national seed collections for large numbers of crop varieties and wild species.<br />
<blockquote>
<b>Svalbard Global Seed Vault.</b> The Svalbard global seed vault is designed as a backup for national seed banks. It protects crop biodiversity against regional (and potential global) catastrophes of natural or man-made origin. The facility is protected from many problems that can impact national seed banks by its extreme isolation. Dug into a mountain on an island well north of the Arctic circle, the extreme persistent cold helps to preserve the seeds stored there even with complete power failure. Nations retain ownership of the seeds they store in the global vault. After some event has damaged their local seed banks (or whenever they choose), they can request their seeds back from the vault. Nobody else is given access to the seeds unless the owning nation allows it.</blockquote>
<blockquote>
<b>Millennium Seed Bank Partnership.</b> This organization has the goal of banking seeds from 25% of the world's bankable wild species. (Some plant species produce seeds that can't be preserved in a dry state. These have to be preserved through active growth instead of banking.) They focus on species from mountain, dryland, coastal, and island environments that are the most vulnerable to climate change. They also focus on wild relatives of crop species. Their seed collection is used for research, for conservation/restoration projects, and as a back-up for local seed banks (much like Svalbard).
</blockquote>
Their overall goal is preservation. Stored crop varieties and species will be maintained (usually in cold storage) in their current form, skipping through time without experiencing any evolutionary changes.<br />
<br />
<hr width="50%" />
<br />
On a smaller scale are local seed lending libraries. Such a library operates by providing seed to members of their local community at the start of the year, then receiving seeds back from those gardeners (that had success) for distribution in the next year. Some growers will ensure their plants are isolated and produce "pure" selfed seed to return to the library. Other growers won't realize they might need to do anything and will occasionally produce hybridized seed to return to the library. Over the scale of many years, the plants that grow from these seeds will be continuously changing. They will be adapting to the local environment and the tastes/favors of the growers contributing seeds back to the library.<br />
<br />
Though such a localized variety may have always had the (hypothetical) name "Tomato Alpha", it will be a distinct variety from the "Tomato Alpha" that has been preserved in the seed banks. The common name being applied to what have become multiple different localized varieties will lead to confusion that makes it difficult for people to know what seeds they've received. (This sort of confusion is now seen in tomatoes called "Brandywine".)<br />
<br />
Seed lending libraries can't effectively keep an eye out for hybrids (or mistaken identity) in their seeds (nor should they, as this is necessary for developing localized varieties), but they can minimize confusion by ensuring their name is attached to every seed they distribute. "Tomato Alpha, library #1 strain" will be distinct from "Tomato Alpha, library #2 strain" or "Tomato Alpha" (from a seed bank).<br />
<br />
<hr width="50%" />
<br />
Part of my seed-saving philosophy says it is very important for people to save seeds from the plants they grow because it will put incorporate their goals and desires into the future of the plant. This is well captured by the seed lending libraries. I also appreciate the importance of preserving varieties the way the seed banks do because it maintains genetic diversity which can otherwise be easily lost. So, what should we do about the issue of single names coming to refer to multiple varieties?<br />
<br />
My personal seed library includes seeds from a variety of sources. I record the variety names for seed that I buy and I'll continue to use the name for seeds I've saved as long as the plants match what the variety is supposed to be. I actively look for hybrids in my garden. If they're interesting, I'll save seeds from them, and then from some of their progeny (etc.). None of these seeds belong to the starting variety, so they get labeled with a description of what the mother plant looked like (since I don't know the daddy) as well as if I know they're F1, F2, etc. Eventually over a several seasons I'll get a better idea of what I want them to be. At the same time their genetics will be stabilizing as they get a better idea of what they want themselves to be. Eventually we'll come to some sort of agreement. I might give them a name at that point, or I might just wait until they tell me what their name is. It might take a while.<br />
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li>Svalbard Global Seed Vault </li>
<ul>
<li><a href="http://www.croptrust.org/what-we-do/svalbard-global-seed-vault/">www.croptrust.org/what-we-do/svalbard-global-seed-vault/</a></li>
<li><a href="http://en.wikipedia.org/wiki/Svalbard_Global_Seed_Vault">en.wikipedia.org/wiki/Svalbard_Global_Seed_Vault</a></li>
</ul>
<li>Millennium Seed Bank Partnership</li>
<ul>
<li><a href="http://en.wikipedia.org/wiki/Millennium_Seed_Bank_Partnership">en.wikipedia.org/wiki/Millennium_Seed_Bank_Partnership</a></li>
<li><a href="http://www.kew.org/science-conservation/collections/millennium-seed-bank/about-millennium-seed-bank">www.kew.org/science-conservation/collections/millennium-seed-bank/about-millennium-seed-bank</a></li>
</ul>
<li>Seed Lending Libraries</li>
<ul>
<li><a href="http://www.richmondgrowsseeds.org/">www.richmondgrowsseeds.org/</a></li>
</ul>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-39942232989692674092018-10-29T13:00:00.001-05:002023-02-07T18:04:53.792-06:00Domestication of Yeasts<div dir="ltr" style="text-align: left;" trbidi="on">
<i>Saccharomyces cerevisiae</i> is known as the Baker's Yeast. It has helped us make bread, beer, and wine since before recorded history. These days we also use it to make fuel, pharmaceuticals, and for basic biology research. With the innumerable industrial, food, and research purposes we use it for, it is a thoroughly domesticated organism.<br />
<br />
With the various mammals we've domesticated, researchers have identified a "<a href="http://www.genetics.org/content/197/3/795">domestication syndrome</a>"; a set of features common across domesticated animals. They have shorter faces, milder temperaments, reduced weaponry (teeth, horns, claws), and color changes. In short, they've become cuter. To some degree these are traits that could have been actively selected for, but it turns out that if we only select on temperament, all of the other traits <a href="https://blogs.scientificamerican.com/guest-blog/mans-new-best-friend-a-forgotten-russian-experiment-in-fox-domestication/">come along for free</a> because all those traits are mediated by the action of neural crest cells throughout the body.<br />
<br />
Now, yeast don't have neural crest cells, but they're still domesticated. It didn't evolve to have a more amenable temperament, but it did evolve to grow rapidly in the amenable conditions we provide for them. There's a different sort of "domestication syndrome" that it would have developed along the way. Any trait or ability it needed to live as a wild yeast, but did not need to live under our care, would be lost. This would happen because any lineage that dispensed with those traits would be able to grow faster without the energy drain they represent.<br />
<br />
So. What traits would yeast lose under domestication? It's not entirely clear. We can't just look at the cells and see a difference. Nor do we exactly have the wild progenitor yeast around to make comparisons with.<br />
<br />
<hr width="50%" />
<br />
Here we're going to take a bit of diversion. <br />
<br />
<div style="text-align: right;">
</div>
My first major project in grad school was to figure out how to use flow cytometry to determine the genome size of a different yeast called <i>Candida albicans</i>. In the past, This analysis had proven difficult to do with this yeast for others. This difficulty had been generally blamed on the organism's ability to grow either as independent yeast cells or as elongated hyphal cells that get all tangled up in each other.<br />
<a href="https://1.bp.blogspot.com/-dqkrAU2yp_o/W9F0sDeNSDI/AAAAAAAAGi4/StZyUj9ROhYiddsR4mdKInbuD1t-_iU6wCLcBGAs/s1600/Figure_2-2A__diploid.png" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Figure showing genome content size of a population of yeast cells. One large peak near the left edge, with a smaller peak at twice the distance along the x-axis. Smaller peaks at 3x and 4x locations." border="0" data-original-height="401" data-original-width="495" height="161" src="https://1.bp.blogspot.com/-dqkrAU2yp_o/W9F0sDeNSDI/AAAAAAAAGi4/StZyUj9ROhYiddsR4mdKInbuD1t-_iU6wCLcBGAs/w200-h161/Figure_2-2A__diploid.png" width="200" /></a> <br />
<br />
I started with protocols developed for <i>S. cerevisiae</i>. At three months in, I was testing yet another protocol variation and the data that came out of the experiment looked like the figure at right. Previous data had much broader,
indistinct peaks. (I'm sure I have some of those early figures around somewhere, but I'm not going to spend a bunch of time digging for them.) I was amazed and quickly set up a repeat of the exact same experiment. It failed miserably.<br />
<br />
I had made a mistake somewhere in the protocol which made things work. Because it was a mistake, it wasn't written down in my lab notes. You can only write down what you know you're doing.<br />
<br />
It took me another frustrating month to figure out what it was I had done wrong. I had used way too much EDTA in the buffers for processing the cells. With this improved protocol, I could get good flow cytometry data from even the most difficult hyphal-growing strains of <i>C. albicans</i>. This disproved the previous theory as to why this species was difficult to work with while doing this assay.<br />
<br />
Subsequently, the protocol proved effective with every random yeast species I was able to acquire for testing. I never tested them with the original <i>S. cerevisiae</i> protocol for comparison. In retrospect, I consider this to be an oversight.<br />
<br />
<div style="text-align: center;">
<i>The flow cytometry protocol has since then been used in numerous papers from several separate labs. The flow cytometry protocol and analysis tools I developed become the second chapter in <a href="https://conservancy.umn.edu/handle/11299/185630">my thesis</a>. The idea of wrapping up the material into a paper did come up after I graduated, but I really didn't have the time/energy to dedicate to the process. Researchers should probably cite that chapter, but I know that thesis chapters tend to only get cited rarely. If you are interested in all the details, you are welcome to <a href="https://conservancy.umn.edu/handle/11299/185630">have a read</a>.</i></div>
<br />
<hr width="50%" />
<br />
I pretty quickly developed a working theory about what was going on. EDTA binds to divalent cations (Ca<sup>2+</sup> and Mg<sup>2+</sup>) in solution, locking them up so other enzymes don't have access to them. Many enzymes require certain levels of these ions to function normally. For whatever reason, the endogenous nucleases of <i>C. albicans</i> were much less sensitive to low levels of divalent cations than those found in <i>S. cerevisiae</i>. Now, I couldn't think of any way to test this theory. I wasn't in a biochemistry or structural biology lab, so the techniques that would have been useful were well outside our wheelhouse.<br />
<br />
This uncertainty has stuck with me for the roughly seven years since then. Just a couple days ago, I developed an idea that in some sense explains the results. Domestication.<br />
<br />
<i>S. cerevisiae</i> is a thoroughly domesticated species. It hasn't had to fight for what it needs, so it could very well have evolved enzymes that are used to easier environments with more consistent levels of necessary ions. I strongly suspect the flow cytometry protocol for <i>S. cerevisiae</i> only works because of the domestication syndrome of traits found in <i>S. cerevisiae</i>.<br />
<br />
I'm not sure how one would test this theory, but it sure seems to make sense of the observations so far.<br />
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li>Domestication Syndrome: <a href="http://www.genetics.org/content/197/3/795">http://www.genetics.org/content/197/3/795</a></li>
<li>Fox domestication: <a href="https://blogs.scientificamerican.com/guest-blog/mans-new-best-friend-a-forgotten-russian-experiment-in-fox-domestication/">https://blogs.scientificamerican.com/guest-blog/mans-new-best-friend-a-forgotten-russian-experiment-in-fox-domestication/</a></li>
<li>PhD thesis of Darren Abbey: <a href="https://conservancy.umn.edu/handle/11299/185630">https://conservancy.umn.edu/handle/11299/185630</a></li>
<li>Papers with <i>C. albicans</i> flow cytometry analysis:</li>
<ul>
<li><a href="https://www.nature.com/articles/nature11865">https://www.nature.com/articles/nature11865</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5908203/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5908203/</a></li>
<li><a href="http://www.genetics.org/content/209/3/725.long">http://www.genetics.org/content/209/3/725.long</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/pubmed/28195309">https://www.ncbi.nlm.nih.gov/pubmed/28195309</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/pubmed/28543785">https://www.ncbi.nlm.nih.gov/pubmed/28543785</a></li>
<li><a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001815">https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001815</a></li>
<li>... probably many others.</li>
</ul>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com0tag:blogger.com,1999:blog-2660869052224924549.post-3194720007840261502018-10-01T13:00:00.006-05:002023-02-07T18:07:01.756-06:00The Color of Beans<div dir="ltr" style="text-align: left;" trbidi="on">
I've been looking for some blue-colored beans for several years. Its easy to find beans in a range of colors (red, pink, white, yellow, green, black), but blues are a rarity in beans. Early on I found an Italian bean called "<i>Nonna Agne's Blue Bean</i>", but the only <a href="https://www.rareseeds.com/nonna-agnes-s-blue-bean/reviews/">seller in my country</a> was out of stock. Sometime
along the way I received an offer of some French heirloom blue beans via
a facebook connection, but no seeds ever appeared. (She offered them
for free, so I can't complain too much.) Blue beans are around, but they're rare.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://2.bp.blogspot.com/-hFpzQbq-uOc/W623O_si6OI/AAAAAAAAGhc/TnMz8MOh4MQRTdXxrRKMSPVhbQpHBMeLQCEwYBhgL/s1600/pic_01.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Three black dry beans, with an almost bluish shine in the light." border="0" data-original-height="800" data-original-width="800" height="200" src="https://2.bp.blogspot.com/-hFpzQbq-uOc/W623O_si6OI/AAAAAAAAGhc/TnMz8MOh4MQRTdXxrRKMSPVhbQpHBMeLQCEwYBhgL/w200-h200/pic_01.jpg" width="200" /></a></div>
Last year I received some beans from an online collaborator after I had mentioned my interest in blue beans. She said one of her plants that season had turned out to be an unexpected hybrid that produced blueish seeds. The three seeds that arrived are shown at left. To my eye they were basically black, but with maybe the slightest blue cast. I wasn't optimistic, but after the difficulty I'd had finding blue beans I was going to give them a try.<br />
<br />
<a href="https://4.bp.blogspot.com/-nT86Ce6z18I/W623O5Y78nI/AAAAAAAAGhg/_4uTJrGokWU5IRXbiTyd9Ks6A-TV-aY0QCEwYBhgL/s1600/pic_02.jpg" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img alt="Square plastic pot with two bean seedlings." border="0" data-original-height="800" data-original-width="800" height="200" src="https://4.bp.blogspot.com/-nT86Ce6z18I/W623O5Y78nI/AAAAAAAAGhg/_4uTJrGokWU5IRXbiTyd9Ks6A-TV-aY0QCEwYBhgL/w200-h200/pic_02.jpg" width="200" /></a>Two of those three beans sprouted. This was kinda a dramatic time, as those two sprouts could easily have died and then another possible blue bean lead would have gone nowhere. Fortunately, both plants thrived.<br />
<br />
<a href="https://2.bp.blogspot.com/-pyWz9ndvvvs/W6285Aeq_DI/AAAAAAAAGh0/OY7o7Xkj4lYKZwcpQLSYrTxGDbvtU1bRgCLcBGAs/s1600/pic_04.jpg" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img alt="Mixed dry beans in shades of dark blue, brown, and a color in between that looks like a dark grey.." border="0" data-original-height="800" data-original-width="800" height="200" src="https://2.bp.blogspot.com/-pyWz9ndvvvs/W6285Aeq_DI/AAAAAAAAGh0/OY7o7Xkj4lYKZwcpQLSYrTxGDbvtU1bRgCLcBGAs/w200-h200/pic_04.jpg" width="200" /></a>A few months later I had a small pile of new beans. When I started shelling them I was very pleased to see some distinctive blue color. As the beans age and dry down, they start to produce some tan pigment which muddies up the pretty blue.<br />
<br />
Next spring I'll plant enough of the more blue beans so I can grow enough to make a few meals of them. Right now I have too few to make a meal and have enough for planting.<br />
<br />
<hr width="50%" />
<br />
How did I know that the biology of bean color should be able to produce a blue bean? The red color of beans is due to a group of biological pigments called <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613902/">anthocyanins</a>. This same group of compounds is also responsible for the rare blue pigments we see in biology.<br />
<br />
An <a href="https://pubs.acs.org/doi/abs/10.1021/jf970264d?journalCode=jafcau">analysis of black beans</a> showed most of the anthocyanins to be delphinidin (at 56%), with lesser amounts of petunidin and malvidin (26% and 18%, respectively). <a href="https://en.wikipedia.org/wiki/Delphinidin">Delphinidin</a> and <a href="https://en.wikipedia.org/wiki/Malvidin">malvidin</a> are responsible for blue color in various flowers. The <a href="https://en.wikipedia.org/wiki/Petunidin">petunidin</a> is described as having a dark-red/purple color. All together, this suggests that black beans really are just super-dark blue beans. This is corroborated by references I've heard of black beans crossed to white beans sometimes producing distinctly blue beans in among the progeny.<br />
<br />
So, why are blue beans so rare? I got nothing that explains it. Blue is such a lovely and generally rare color that I would have thought people would have been growing blue beans as much or more than the now-common red beans. Maybe I can help rectify the situation in time.<br />
<br />
<hr width="50%" />
<br />
As I was writing this post I decided to look around again for vendors selling blue bean varieties. I found a <a href="http://oroseeds.com/index.php?route=product/product&product_id=1289">European vendor</a> that seems to have stock of the Italian "<i>Nonna Agne's Blue Bean</i>". I also found another unrelated blue variety called "<a href="https://stores.southgaseedco.com/blue-shackamaxon-pole-bean-seeds-qty-20-very-rare-bean/"><i>Blue Shackamaxon Pole Bean</i></a>". I might think about ordering some of each, but it'd be more fun to make my own now that I've got a start at it.<br />
<br />
<br />
References:<br />
<ul style="text-align: left;">
<li>Nonna Agne's Blue Bean: </li>
<ul>
<li><a href="https://www.rareseeds.com/nonna-agnes-s-blue-bean/reviews/">https://www.rareseeds.com/nonna-agnes-s-blue-bean/reviews/</a></li>
<li><a href="http://oroseeds.com/index.php?route=product/product&product_id=1289">http://oroseeds.com/index.php?route=product/product&product_id=1289</a></li>
</ul>
<li> Blue Shackamaxon Bean:</li>
<ul>
<li><a href="https://stores.southgaseedco.com/blue-shackamaxon-pole-bean-seeds-qty-20-very-rare-bean/">https://stores.southgaseedco.com/blue-shackamaxon-pole-bean-seeds-qty-20-very-rare-bean/</a></li>
</ul>
<li>Anthocyanins:</li>
<ul>
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613902/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613902/</a> </li>
<li><a href="https://www.frontiersin.org/articles/10.3389/fchem.2018.00052/full">https://www.frontiersin.org/articles/10.3389/fchem.2018.00052/full</a></li>
<li>Petunidin: <a href="https://en.wikipedia.org/wiki/Petunidin">https://en.wikipedia.org/wiki/Petunidin</a></li>
<li>Delphinidin: <a href="https://en.wikipedia.org/wiki/Delphinidin">https://en.wikipedia.org/wiki/Delphinidin</a></li>
<li>Malvidin: <a href="https://en.wikipedia.org/wiki/Malvidin">https://en.wikipedia.org/wiki/Malvidin</a></li>
</ul>
<li>Anthocyanins in beans: </li>
<ul>
<li><a href="https://pubs.acs.org/doi/abs/10.1021/jf970264d?journalCode=jafcau">https://pubs.acs.org/doi/abs/10.1021/jf970264d?journalCode=jafcau</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/pubmed/14611168">https://www.ncbi.nlm.nih.gov/pubmed/14611168</a> </li>
</ul>
</ul>
</div>
Darren Abbey, PhDhttp://www.blogger.com/profile/08452703848133489576noreply@blogger.com11