More than just a hill of beans: Phaseolus genome lends insights into nitrogen fixation

June 08, 2014

"It doesn't take much to see that the problems of three little people doesn't add up to a hill of beans in this crazy world," Humphrey Bogart famously said in the movie Casablanca. For the farmers and breeders around the world growing the common bean, however, ensuring that there is an abundant supply of this legume is crucial, both for its importance in cropping systems to ensure plant vitality and for food security. Moreover, the U.S. Department of Energy Office of Science has targeted research into the common bean because of its importance in enhancing nitrogen use efficiency for sustainability of bioenergy crops, and for increasing plant resilience and productivity with fewer inputs, on marginal lands, and in the face of the changing climate and environment.

All plants require nitrogen to thrive, and nitrogen fixation is the process by which atmospheric nitrogen is converted into ammonia. However, many agricultural lands are deficient in nitrogen, leading farmers to rely on fertilizers to supply the needed nutrient for their crops. According to the U.S. Department of Agriculture, the United States imports more than half of the nitrogen used as fertilizer, a total of nearly 11 million tons in 2012. Kidney beans, navy beans, string beans and pinto beans are all varieties of the common bean, which ranks as the 10th most cultivated food crop worldwide. Legumes such as the common bean and soybean, however, can form symbiotic relationships with nitrogen-fixing bacteria. Understanding how such symbiotic relationships are formed and sustained is a crucial to improving agricultural practices as increasing crop yields are desired both for fuel and food production.

To this end, a team of researchers led by Scott Jackson of the University of Georgia, Dan Rokhsar of the U.S. Department of Energy Joint Genome Institute, Jeremy Schmutz of the DOE JGI and the HudsonAlpha Institute for Biotechnology and Phil McClean of North Dakota State University sequenced and analyzed the genome of the common bean, Phaseolus vulgaris. The project was supported by the U.S. Department of Energy and the National Institute of Food and Agriculture, U.S. Department of Agriculture, and the work was published online June 8, 2014 in the journal Nature Genetics.

"Unlocking the genetic make-up of the common bean is a tremendous achievement that will lead to future advances in feeding the world's growing population through improved crop production," said Sonny Ramaswamy, director of USDA's National Institute of Food and Agriculture. "While we have much to learn about the application of genomics in agriculture, this study is groundbreaking. I applaud the work of this team of scientists and look forward to their continued work in this important area."

For the study, the team sequenced and assembled a 473-million basepair genome of the common bean. Though it is thought to have originated in Mexico, the common bean was domesticated separately at two different geographic locations in Mesoamerica and the Andes, diverging from a common ancestral wild population more than 100,000 years ago. The team then compared sequences from pooled populations representing these regions, finding only a small fraction of shared genes. This indicated that different events had been involved in the domestication process at each location.

The team looked for regions associated with traits such as low diversity, flowering time, and nitrogen metabolism. They found dense clusters of genes related to disease resistance within the chromosomes. They also identified a handful of genes involved in moving nitrogen around. This information could be beneficial for farmers practicing the intercropping system known as milpa, wherein beans and maize or, occasionally, squash, are planted either simultaneously or else in a relay system where the beans follow maize. The practice ensures that the land can continue to produce high-yield crops without resorting to adding fertilizers or other artificial methods of providing nutrients to the soil.

The team then compared the high quality common bean genome against the sequence of its most economically important relative, soybean. They found evidence of synteny, in which a gene in one species is present in another. They also noted that the common bean's genome had evolved more rapidly than soybean's since they diverged from the last common ancestor nearly 20 million years ago.

"Improvement of common bean will require a more fundamental understanding of the genetic basis of how it responds to biotic and abiotic stresses," the team concluded. "These findings provide information on regions of the genome that have been intensely selected either during domestication or early improvement and thus provide targets for future crop improvement efforts."
Phil McClean presented on the common bean genome project at the recent 9th Annual DOE JGI Genomics of Energy & Environment Meeting. Watch the video at

The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.

DOE's Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit

DOE/Joint Genome Institute

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