I just wanted to take a moment to highlight the key results and story behind the science of a recent collaborative study out of my lab that was published this past week on the evolution of seed dormancy in common bean. https://link.springer.com/epdf/10.1186/s12870-021-02837-6?sharing_token=HPbVJFeSFyE5C2IVOSOZiW_BpE1tBhCbnbw3BuzI2RM1CvoNZidBV97R4gIXddLITmJ5y2097dDgdZgKbJcq7fKLdAwmDU7F_XoarjGBOVQKfuwJj6ilFQy28Mp25GAyZotsB2rUOJ2-8sW1Ooj68gCCXTZjirXwBcTm1vZQIxQ%3D

The story starts when Ali Soltani joined my lab as part of the MSU Plant Resilience Institute ( @MSU_PRI) in 2016. Ali had previously conducted a lot of research on flooding tolerance in bean at North Dakota State University. Flooding is a huge problem for bean production in ND.

Ali ( @soltani61ali) had found multiple ways in which beans could be susceptible to flooding. They could be killed off as seedlings due to anoxic conditions as well as increased susceptibility to root pathogens.

But, there was another interesting way in which beans could be susceptible to flooding and that was that the seeds themselves could be killed before they had a chance to expand above the surface of the soil.

Ali toyed around with this idea some when he first arrived in the lab and soon realized that some beans indeed were more tolerant than others being submerged in water for an extended period of time.

As might be expected, the way in which bean seeds could prevent being killed by flooding would simply be to not take up water very quickly.

But, of course, not taking up water quickly is a bad thing for an agricultural variety, where rapid seed germination is important. Even more critically, not taking up water quickly slows down cooking time.

So, it seemed like we had an intriguing trade-off on our hands: Seed flooding tolerance vs. agriculturally desirable traits.

Things started to get more interesting when we realized that some varieties had bean seeds took up water really slowly. What the heck was going on here?

Ali then teamed up with @EndlessForms to track the entry of water into the bean seeds with a CT X-ray scanner. This imagining made it clear that the seeds which took up water quickly (top row) did so thorough the seed lens structure.

Ali then took it a step further and did some nice electron microscopy to show that the fast-imbibing varieties had more micro-cracks on the groove of the lens structure.

Ali and I are both geneticists at our core, so we had to map this thing. The strategy we took was to conduct a bulked-segregant analysis to conduct QTL mapping. This revealed a single QTL on chromosome 3 for seed water uptake.

Ali then screened hundreds of hybrids for recombination events within the QTL region. We then shipped DNA of those recombinant lines to Texas A&M for whole genome resequencing to identify breakpoints and fine-map the causative gene.

The fine-mapped region contained 11 genes. We surveyed all those genes for potential causative mutations and conducted gene expression studies to see which of those genes were actually expressed in bean seeds.

Only two of those 11 genes were expressed at high levels in the bean seed coat. Both of these genes were orthologs of pectin acetylesterase 8. Further, only 1 of 11 genes had a major mutation in it, and that was a frame-shift mutation in one of those pectin acetylesterase genes.

Now, comes a limitation to our study. We ran out of time to conduct a transformation experiment to confirm this gene's function. Transformation is hard in bean to start with, so this will have to wait for a future collaborator.

While we could not do the transgenic study, we could still do some population genetics with this gene. Very interestingly, the functional allele of this gene is found in all 25 wild bean populations we surveyed and almost never found in highly domesticated US bean varieties.

Ali has put together a nice hypothesis of how breaking a pectin acetylesterase gene could result in micro-cracks in the lens and in turn a faster uptake of water into the seed. Still needs to be tested.

So, some time in the past, it seems likely that indigenous peoples in the Andes selected upon this non-function copy of this gene to increase seed water uptake to either speed up cooking time, increase germination rate, or both.

While this seems like a likely hypothesis, it begs the question as to why the functional copy of this gene has been maintained in some domesticated lines, especially in Latin America and Africa.

We don't know the answer to this question, but it is possible that having higher seed dormancy through this mechanism could be better for storage in more humid conditions or could be beneficial for flooding tolerance.

As for the bean line that Ali discovered the high seed dormancy in the first place, we found out later that it was originally bred to be a green shelled-bean for consumption in the Caribbean. These beans are consumed before hardening and thus, cooking time doesn’t matter.

So, it may be that variation in human food preferences and dominant market classes around the world could also maintain variation in this gene (and likely many others).