Common bean genome sequence to improve critical food crop
Although the specific genes involved in domestication were mostly unique between the two groups, the researchers found that they tended to affect the same traits. For example, each group displayed evidence of positive selection for genes involved in common molecular pathways governing flowering and plant size — but the genes themselves differed. In contrast, although they found clear evidence for positive selection for genes involved in seed size in the Mesoamerican population, there were no clear candidates from the Andean population.
“Imagine you’re picking through your beans, trying to decide which ones to hold on to and plant next year,” said Schmutz. “You’re exerting selective pressure for those traits you feel are valuable—size, yield, or taste, for example. It’s apparent that the people of the Andes selected for things that were of interest to them, but the Mesoamericans had their own set of criteria. There wasn’t much back and forth between the two populations until more modern times.”
The common bean originated from a wild bean population in Mexico, and shares a common ancestor with the soybean. In addition to its role as a critical food crop, it serves as a partner in a symbiotic relationship with nitrogen-fixing bacteria to improve the soil in which it is planted.
Schmutz and his colleagues sequenced 473 million of the 587 million base pairs in the genome of a particular landrace from Peru to come up with a standard reference sequence for the common bean. They then compared this reference genome with that of soybean and with the sequences of wild beans from Mesoamerica and the Andes. The researchers found that, although the common bean evolved more rapidly than the soybean after their split from their common ancestor, the two bean types still share many of their genes, organized in roughly the same way.
The researchers next analyzed the two wild common bean populations. They estimated that, although the two wild pools diverged from one another about 165,000 years ago, the Andean pool at first comprised only a few thousand individual plants — contributing to a population bottleneck that lasted for about 76,000 years. About 8,000 years ago, humans in Mexico and South America began breeding them as a food source, eventually forming many specialized landraces.
Schmutz and his colleagues sequenced pools of 100 landraces representing distinct, geographically isolated subpopulations in Mexico, Central America and South America to identify genes that may have been involved in domestication. Surprisingly, only 59 genes were shared among the 1,835 genes in the Mesoamerican common bean and the 748 of the Andean common bean that exhibited the low-diversity and high-differentiation associated with positive selective pressure.
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