Common bean genome sequence to improve critical food crop

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String bean, snap bean, haricot bean, and pinto and navy bean. These are just a few members of the common bean family — scientifically called Phaseolus vulgaris. These beans are critically important to the global food supply. They provide up to 15 percent of calories and 36 percent of daily protein for parts of Africa and the Americas and serve as a daily staple for hundreds of millions of people.

Now, an international collaboration of researchers, led by Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology and Phillip McClean, of North Dakota State University (NDSU) have sequenced and analyzed the genome of the common bean to begin to identify genes involved in critical traits such as size, flavor, disease resistance and drought tolerance. The study was funded by the US Department of Agriculture, National Institute of Food and Agriculture and the US Department of Energy Office of Science.

They learned that, unlike most other food crops, the common bean was domesticated twice by humans about 8,000 years ago — once in Mexico and once in South America — through the selection of largely non-overlapping, unique subsets of genes.

“We found very little overlap, and very little mixing, among the two domesticated populations,” said Jeremy Schmutz, who co-directs the HudsonAlpha Institute’s Genome Sequencing Center and serves as the Plant Program Leader for the Department of Energy Joint Genome Institute. “Evolutionarily, this makes the common bean very unique and interesting.”

Schmutz shares lead authorship of the current study, which was published on June 8 in Nature Genetics, with Phillip McClean, director of the genomics and bioinformatics program at NDSU. Scott Jackson, from the University of Georgia, is the senior author.

The HudsonAlpha Genome Sequencing Center specializes in the production of reference plant genomes and genomic resources with a focus on improving agriculture and developing plant-based energy sources. In 2010, Schmutz led a team of researchers that used the Center’s unique facilities to be the first to sequence the genome of the soybean — another vital global crop.

Identifying genes involved in the domestication of the common bean, and comparing locally adapted domesticated bean groups (called landraces) to their wild counterparts throughout Mexico and South America will help researchers understand how beans evolved, and how modern breeding programs might be improved to yield tastier, more-easily harvested, and, yes, even more-nutrient-packed beans. It may also help scientists to develop bean varieties resistant to pests, or better able to grow in challenging environments.

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.

“We’re trying to understand what the common bean looked like before human intervention, to identify what occurred during early domestication and to apply that to modern bean breeding,” said Schmutz. “Modern beans have been bred to fill specific expectations with regard to color, size and shape, and as a consequence have very little diversity. Studies such as this are necessary to identify genes that could be used to improve traits such as ease of harvest, flavor, yield and disease resistance.”

Once genes are identified, they could be reintroduced into the population by selective breeding with wild populations, or careful breeding of existing landraces or even commercial beans. The Common Bean Coordinated Agricultural Project, or BeanCAP, launched in 2009 under the direction of study co-author McClean, is dedicated to the identification of gene markers that can be used in such breeding programs.

“The genome sequence has important implications for world-wide efforts to improve beans” said McClean. “The sequence will help breeders release varieties that are competitive with other crops and more climate resilient.” The sequence revealed that disease resistance genes are highly clustered in the genome, knowledge that will lead to better breeding strategies to combat the many diseases that challenge the bean crop. Data from the study is being actively used by the many international bean breeders and geneticists to develop the next generation of molecular markers to aid bean breeding efforts.

From a global perspective, this information could be beneficial to farmers in developing countries that practice the intercropping system known as “milpa”, where beans, corn, and occasionally squash, are planted together. The historical practice ensures that their land can continue to produce high-yield crops without resorting to adding fertilizers or other chemical methods of providing nutrients to the soil. McClean noted that “Breeders and genomic scientists in these countries are already working with the international bean community to utilize this important new genetic resource to address the production constraints unique to the “milpa” system.”


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