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Showing posts with label beans. Show all posts
Showing posts with label beans. Show all posts

Tuesday, August 29, 2023

The Color of Beans 6

Cluster of bright red bean flowers.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.

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.

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.

I did have one red-flowered Phaseolus coccineus (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 P. vulgaris x P. coccineus hybrid for years.

Dry beans. Most are tan with dark brown streaks, but a few are solid blue.

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 P. coccineus parent and the blue color came from the P. vulgaris parent (the blue seeds here for comparison purposes).

Hybrids between P. vulgaris and P. coccinues 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.




Because the P. coccineus 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.

I have read from a few references that the P. coccineus chromosomes are preferentially lost vs the P. vulgaris 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 P. vulgaris, 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.

References:

  1. Interspecific hybridization between cultivated american species of the genus Phaseolus.
  2. Embryo development in reciprocal cross of Phaseolus vulgaris L. and P. coccineus Lam.

Friday, February 24, 2023

The Color of Beans 5

Pile of blue dry beans.

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.

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.

Anthocyanin pathway diagram, emphasizing red and blue anthocyanins, as well as yellow astragalin.

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.


The initial random hybrid was between a black variety (Haudenosaunee Skunk) and a yellow-tan variety (Arikara Yellow). 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.

The color of black beans is caused by a combination of red, blue, and yellow-brown pigments at high intensity. In Phaseolus vulgaris, 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.

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.

At left, purple dry beans. At right, yellow dry beans.
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 P. coccineus (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.

While I was waiting for those to arrive, I was also looking for P. lunatus (lima) beans with the same colors. The yellow-brown variety I found is called Pima Orange. I ordered the purple variety from someone on Ebay and am still waiting for them to arrive.

I wasn't able to find any sign of a purple version of P. acutifolius (tepary) beans. I did find black and yellow 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.


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.

  • 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.
  • 2024 : Plant yellow seeds only. Save harvested seeds by color.
    • Yellow seeds : mother plant wasn't hybrid.
    • Purple seeds : mother plant was a hybrid between purple & yellow plants. These seeds will grow into F2 plants.
  • 2025 : Plant purple seeds only. Save harvested seeds by color.
    • 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.

P. coccineus and P. lunatus 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.

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.


This plan assumes the genes driving F3'H (red anthocyanins) and F3'5'H (blue anthocyanins) are unlinked in these species. I know in P. vulgaris 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 is possible to make hybrids between P. vulgaris and P. coccineus tells us their genomes are organized in largely the same fashion, so the two genes should be similarly not tightly linked in P. coccineus. Making hybrids with P. lunatus is harder, but still possible, so similarly I don't expect the two genes to be tightly linked.

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 P. vulgaris 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.


References:
  1. Bean varieties:
    1. Haudenosaunee Skunk: https://exchange.seedsavers.org/page/variety/id/193592
    2. Arikara Yellow: https://www.seedsavers.org/arikara-yellow-bean
    3. Pima Orange : https://www.nativeseeds.org/products/pl011
    4. Black Tepary : https://www.nativeseeds.org/collections/tepary-beans/products/pt082
    5. S'oam Baw Tepary : https://www.nativeseeds.org/collections/tepary-beans/products/pt120
  2. Blog posts:
    1. https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html
    2. https://the-biologist-is-in.blogspot.com/2022/12/the-color-of-beans-2.html
    3. https://the-biologist-is-in.blogspot.com/2023/01/the-color-of-beans-3.html
    4. https://the-biologist-is-in.blogspot.com/2023/02/the-color-of-beans-4.html
  3. Bean species hybrds:
    1. https://link.springer.com/article/10.1007/BF01902923
    2. https://www.semanticscholar.org/paper/Hybrid-plant-of-Phaseolus-vulgaris-L.-and-P.-L.-by-Kuboyama-Shintaku/c20048408e38632b8ae8fe45d234e967ad57df2d

Friday, February 10, 2023

The Color of Beans 4

In my last post (https://the-biologist-is-in.blogspot.com/2023/01/the-color-of-beans-3.html), I shared a couple figures illustrating the flavonoid/anthocyanin pigment pathway in plants and in common beans (Phaseolus vulgaris) specifically. A couple days later, I found some additional evidence which led me to feel the need to update my figures somewhat.



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.
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).

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.

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.
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.

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.

pale tan beans with orange-toned eyes.
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.

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. @g3netic_lottery on Instagram 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.


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.

  • Runner beans (P. coccineus): This photo of "Ayacote Mexican" beans includes some very orange looking seeds, but I have no idea how much that reflects reality.
  • Lima beans (P. lunatus): "Pima Orange" has seeds that look yellow-brown or orange depending on the photo. Again, it is hard to say what they really look like.
  • Tepary beans (P. acutifolius) : There are some photos around of very orange tepary beans, but I can't find any varieties available for sale that look anything near orange.
  • Year-long beans (P. dumosus) : 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.
Mix of dark purple and black beans.
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.

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 different vendor 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.

Mix of orange colored beans with variable dark markings.
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.

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.

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.

References:

Friday, January 20, 2023

The Color of Beans 3

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.
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 tomatoes [1] and peppers [2], 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.

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.)

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.
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 (Phaseolus vulgaris). 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.
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 P. coccineus, the scarlet runner bean, but I'm still investigating this.



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.

  • 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.
  • V [violet] : Enzyme F3'5'H. This one isn't as important as F3'H and is entirely absent in many plants.
  • J : Pretty solidly identified as the enzyme DFR.
  • 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.
  • B : A transcription factor driving expression of chalcone synthase (CHS) and/or chalcone isomerase (CHI).
  • 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.

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 paper identifying V as being the gene for the enzyme F3'5'H 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.

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.


References
  1. Related blog posts:
    1. https://the-biologist-is-in.blogspot.com/2014/04/the-color-of-tomatoes.html
      • Carotenoid pigments in tomatoes.
    2. https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html
      • Carotenoid pigments in peppers.
    3. https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html
      • Introduction of my #BlueBeanProject.
    4. https://the-biologist-is-in.blogspot.com/2022/12/the-color-of-beans-2.html
      • Status update of my #BlueBeanProject.
    5. https://the-biologist-is-in.blogspot.com/2019/11/biology-of-blue.html
      • Discussions around the chemistry of blue in biology.
  2. Papers related to anthocyanin pathway in bean, cotton, etc:
    1. http://arsftfbean.uprm.edu/bic/wp-content/uploads/2018/04/ChemistrySeedCoatColor.pdf
    2. https://nph.onlinelibrary.wiley.com/doi/full/10.1002/ppp3.10132
    3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602603/
    4. https://link.springer.com/article/10.1007/s11738-011-0858-x
    5. https://pubmed.ncbi.nlm.nih.gov/28981784/
    6. https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-2065-7
    7. https://pubmed.ncbi.nlm.nih.gov/35289870/
    8. https://squashpractice.com/2011/10/08/bean-genes/
    9. https://journals.ashs.org/jashs/view/journals/jashs/124/5/article-p514.xml
    10. https://www.frontiersin.org/articles/10.3389/fpls.2022.869582/full#ref33
    11. https://journals.ashs.org/downloadpdf/journals/jashs/120/6/article-p896.pdf
    12. https://journals.ashs.org/downloadpdf/journals/jashs/125/1/article-p52.pdf
    13. https://www.semanticscholar.org/paper/Allelism-Found-between-Two-Common-Bean-Genes%2C-Hilum-Bassett-Shearon/f9cef3175289b7d2822461b9d495d8885bb67a48
    14. https://www.semanticscholar.org/paper/Inheritance-of-Reverse-Margo-Seedcoat-Pattern-and-J-Bassett-Lee/7557538290b700d1fd980a24fba3148846861690
    15. https://www.semanticscholar.org/paper/The-Margo-%28mar%29-Seedcoat-Color-Gene-Is-a-Synonym-%28-Bassett/d1c58ec1fa0bf9e500d8bd48364a61568b0b7a11
    16. https://naldc.nal.usda.gov/catalog/IND92036951

Friday, December 30, 2022

The Color of Beans 2

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. 

https://the-biologist-is-in.blogspot.com/2018/10/the-color-of-beans-1.html

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.

Dry beans in mixed colors. Browns, blues, and dark greys.
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.

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.

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.

Dark blue dry beans.
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.

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.

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.



Eleven pale blue bean seeds, each with a black ring around the hilium.Five dark blue bean seeds with tan speckles.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.

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!

References:

Thursday, November 28, 2019

Fava Beans

Cluster of brown/purple flowers on a fava bean plant.
[Photo from link.]
I've eaten fava beans (Vicia faba) from time to time, but I've never grown them. I was recently perusing some postings from blogs I occasion and found an interesting post. 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 forum discussion revealed that these variations were the result of crossing the varieties "Crimson Flowered" and "Red Epicure". 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.

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.
  1. Hybridize F. faba with related species with different flower colors.
  2. Find rare varieties of F. faba with different colors.
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 V. faba. There is some research looking into why crosses don't work. F. faba as seed parent crossed with V. galilaea and V. johannis both appear to result in fertilized eggs. F. faba as pollen parent crossed with V. bithynica 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.

Variously colored fava means laid out in a grid, 11 beans wide and 6 beans tall.
[Photo from link.]
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.


References:

Monday, October 1, 2018

The Color of Beans

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 "Nonna Agne's Blue Bean", but the only seller in my country 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.

Three black dry beans, with an almost bluish shine in the light.
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.

Square plastic pot with two bean seedlings.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.

Mixed dry beans in shades of dark blue, brown, and a color in between that looks like a dark grey..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.

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.



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 anthocyanins. This same group of compounds is also responsible for the rare blue pigments we see in biology.

An analysis of black beans showed most of the anthocyanins to be delphinidin (at 56%), with lesser amounts of petunidin and malvidin (26% and 18%, respectively). Delphinidin and malvidin are responsible for blue color in various flowers. The petunidin 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.

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.



As I was writing this post I decided to look around again for vendors selling blue bean varieties. I found a European vendor that seems to have stock of the Italian "Nonna Agne's Blue Bean". I also found another unrelated blue variety called "Blue Shackamaxon Pole Bean". 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.


References: