The Color of Beans 5

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.

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.

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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.

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.

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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.

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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

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.

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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.

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.

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.

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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.

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.

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:

• Some seed sources:
• dualsnatural.com/products/ayocote-mexican-beans : P. coccineus "Ayacote Mexican".
• https://masienda.com/products/ayocote-beans : P. coccineus "Ayacote Pinto".
• www.nativeseeds.org/products/pl011: P. lunatus "Pima Orange"
• www.nativeseeds.org/collections/indigenous-seeds-bean-tepary: P. acutifolius varieties.

Potatoes

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.

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.

The two species (tomato, Solanum lysopersicum; potato, S. tuberosum) 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 purchased or made at home, but they are the result of actively grafting separate plants together and wouldn't accidentally form in the garden.

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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.

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.

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.

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.

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.

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I wouldn't advise eating the tomato-like berries to be found occasionally on potato plants, but they have other uses.

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.

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. 

A forum discussion about TPS about the likely results of growing seeds from Yukon Gold, written by Tom Wagner, a notable tomato and potato breeder:

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:

• whites with white flesh
• whites with light yellow flesh
• yellows with light yellow flesh
• yellows with medium yellow flesh
• yellows with deeper yellow flesh
• repeat of above but with either light pink eyes/red eye
• all of the above with templates of size, yield, shape, flavor, etc., differences.

Yukon Gold was selected from a cross between Norgleam (female) and W5279-4 (a yellow-fleshed diploid hybrid of S. phureja and haploid cv Katahdin). Yukon Gold is a tetraploid because of the unreduced gamete from it pollen parent.

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 look elsewhere.

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.

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A few years back I ordered some true potato seed from cultivariable.com to start experimenting with in my garden. Most of the seedlings each year have failed for one reason or another.

A few plants didn't produce a single tuber. Most of those that produced tubers got infected with what might have been late-blight (Phytophthora infestans). For my purposes, the specific disease didn't matter. Any with an obvious infection were discarded.

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.

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.

References:

• Grafted tomato/potato
• www.territorialseed.com/product/grafted-tomtato-ketchup-n-fries/new_for_spring_2015
• www.youtube.com/watch?v=6V_X77CeTcs
• Solanine
• www.food-info.net/uk/qa/qa-fp95.htm
• www.smithsonianmag.com/arts-culture/horrific-tales-of-potatoes-that-caused-mass-sickness-and-even-death-3162870/?no-ist
• Tom Wagner
• www.tomatoville.com/showthread.php?t=6761
• gardenrant.com/2012/01/an-interview-with-the-true-potato-seed-man.html
• Potato Seeds
• www.tom8toes.com/index.php/potatoes.html
• tatermaterseeds.com/shop/index.php?main_page=index&cPath=2&zenid=c96f378a548b3b7031d204e6f608f617 
• www.doublehelixfarms.com/true-potato-seed-TPS
• www.cultivariable.com/