Legumes—such as the common bean and soybean—form symbiotic relationships with nitrogen-fixing bacteria, which maximize the amount of useable nitrogen plants can extract from the soil. Understanding how such symbiotic relationships are formed and sustained is crucial to improving agricultural practices, as increasing crop yields are desired both for fuel and food production.

For the study, the team sequenced and assembled a 473-million basepair genome of the common bean. Thought to have originated in Mexico more than 100,000 years ago, the common bean was domesticated separately at two different geographic locations in Mesoamerica and the Andes. The team 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 nitrogen fixing.

This information could be beneficial for farmers practicing the intercropping system known as milpa, in which beans and maize or, occasionally, squash are planted either simultaneously or in a relay system where the beans follow maize. The practice ensures the land can continue to produce high-yield crops without resorting to fertilizer inputs 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, the 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 the soybean’s once they diverged from the last common ancestor nearly 20 million years ago.