Bean genome sequencing yields uncommon findings

A newly reported genome sequence for the common bean — which includes a number of varieties that together rank as the world’s 10th most widely grown food crop — has been released by a research team including a UC Davis plant scientist. The results shed light on nitrogen fixation, how beans were domesticated and disease resistance.

The sequencing effort is key to helping boost production of this vitally important global food source, improving competitive production of the $1.2 billion U.S. crop and better understanding the genetic makeup of the broader group of related legume plants.

“The availability of this new whole-genome sequence for beans is already paying off,” said Professor Paul Gepts, a UC Davis plant scientist and co-author on the new sequencing study.

Gepts noted that the new sequence is already being used to confirm many of the findings made earlier by his UC Davis research group, including identification of the common bean’s two points of origin and domestication — one in the Andes and the other in the Mesoamerican area of Central America.

Gepts leads the UC Davis bean-breeding program, with responsibility for producing new varieties of common beans, as well as lima and garbanzo beans.

The new whole-genome sequencing is also helping to identify genetic “markers” that can be used to speed up breeding of new bean varieties in the United States, East Africa and other countries, Gepts said.

The nitrogen connection

The common bean, Phaseolus vulgaris, includes kidney, navy, string and pinto beans. All of these well-known bean varieties share with the closely related soy bean the highly valued ability to form symbiotic relationships with “nitrogen-fixing” bacteria in the soil.

Working together, the plants and bacteria convert nitrogen in the atmosphere into ammonia — which includes nitrogen in a form that enriches the soil and feeds crops. Nitrogen-fixing crop plants can actually reduce or eliminate the need for farmers to apply expensive fertilizers.

One of the goals of the sequencing project was to better understand the genetic basis for how such symbiotic relationships between nitrogen-fixing plants and bacteria are formed and sustained. This will be critically important for increasing crop yields for both fuel and food production.

The new sequencing identified a handful of genes involved with moving nitrogen around, which could be helpful to farmers who intercrop beans with other crops that don’t fix nitrogen.

Sequencing and bean ancestry

The common bean is thought to have originated in Mexico more than 100,000 years ago, but — as the Gepts group earlier discovered — was domesticated separately at two different geographic locations in Mesoamerica and the southern Andes.

“This finding makes the common bean an unusually interesting experimental system because the domestication process has been replicated in this crop,” Gepts said.

The sequencing team compared gene sequences from pooled populations of plants representing these two regions and found that only a small fraction of the genes are shared between common bean species from the two locations. This supports the earlier finding that the common bean was domesticated in two separate events, one at each location, but distinct genes were involved in each event.

Other important findings

The researchers also discovered:
• dense clusters of genes related to disease resistance within the common bean’s chromosomes;
• certain genes that are shared by both the common bean and the soybean, its most economically important relative; and
• evidence that the common bean’s genome evolved more rapidly than did the soybean genome, after the two species parted ways on the evolutionary pathway nearly 20 million years ago.

The project was led by researchers at the University of Georgia, U.S. Department of Energy Joint Genome Institute, Hudson Alpha Institute for Biotechnology and North Dakota State University. Findings from the study are reported this week online in the journal Nature Genetics.
Funding for the genome sequencing study was provided by the U.S. Department of Energy and the U.S. Department of Agriculture.