Common bean genome sequence provides powerful tools to improve critical food crop

June 08, 2014

Huntsville, Ala. - 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.

The researchers 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.

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.

"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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The HudsonAlpha Institute for Biotechnology is a nonprofit institute dedicated to innovating in the field of genomic technology and sciences across a spectrum of biological problems. Its mission is three-fold: sparking scientific discoveries that can impact human health and well being; fostering biotech entrepreneurship; and encouraging the creation of a genomics-literate workforce and society. The HudsonAlpha biotechnology campus consists of 152 acres within Cummings Research Park, the nation's second largest research park. Designed to be a hothouse of biotech economic development, HudsonAlpha's state-of-the-art facilities co-locate nonprofit scientific researchers with entrepreneurs and educators. These relationships formed on the HudsonAlpha campus encourage collaborations that yield results in medicine and agriculture. Since opening in 2008, HudsonAlpha, under the leadership of Dr. Richard M. Myers, has built a name for itself in genetics and genomics research and biotech education and includes 26 diverse biotech companies on campus.

HudsonAlpha Institute for Biotechnology

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