NDSU scientists central to nationwide genome sequencing
FARGO, N.D. — Several North Dakota State University scientists are close to the center of a national project that completed the sequence of the common bean genome. It will greatly speed up the search for genes controlling different traits of interest in dry edible beans and snap beans around the world.
Five individuals from NDSU’s Plant Sciences Department in Fargo were among 20 authors on the project. In addition, three former graduate students from NDSU participated elsewhere in the country.
Phil McClean, a professor and director of NDSU’s Genomics and Bioinformatics Program, and NDSU bean breeder Juan Osorno, helped lead the project, which cataloged 27,000 genes in the bean genome. The next effort is to develop markers near or in those traits to control important agricultural traits.
Common beans include kidney beans, navy beans, string beans and pinto beans. Combined, the bean crops rank as the 10th most cultivated crop worldwide.
The project was co-directed at the University of Georgia, the U.S. Department of Energy Joint Genome Institute, and the HudsonAlpha Institute of Biotechnology in Huntsville, Ala.
The project was supported by a $3 million, four-year DOE grant, and by the National Institute of Food and Agriculture, an office of the U.S. Department of Agriculture. The work was published June 8 in the journal Nature Genetics. NDSU provided all the material that was sequenced for DNA and RNA for different growth stages in the project.
A co-lead investigator in the overall project, McClean presented the work at the 9th Annual DOE JGI Genomics and Energy & Environment Meeting in March 2014, in Walnut Creek, Calif. For the project, he guided data analysis of common bean domestication, which occurred separately in Mexico and the Andes about 100,000 years ago, diverging from an ancestral wild population.
‘The big leagues’
For his part, Osorno organized national field trials that identified regions of the genome associated with seed size and other traits.
“I think it’s going to boost a lot of the research we have on common bean — dry bean, especially,” Osorno says of the completed genome sequence. “It’s mostly because we will not only be able to know the location of the genes responsible for many traits of agricultural importance — the ones that give us money — but we’ll be able to understand how those genes work.”
It’s a first step, Osorno says. “It doesn’t mean you know all of the answers, but that’s the initial stage of how you need to get to the answers.”
Young scientists often go into corn or soybean research because companies and institutions are investing a lot of money into research in those crops. The effect of “opening the library” to answers on the common bean will encourage people to participate in breeding projects because it allows them to skip the baseline research, McClean says.
“It puts us at another level,” Osorno says. “Now we are in the big leagues of crops. We have a genome sequence available. I think it has a lot of benefits in the short, medium and long term. We’re already finding genes related to disease resistance, and it will be a lot easier to work with them from now on.”
The team looked for regions associated with traits such as low diversity, flowering time and nitrogen metabolism. It found dense clusters of genes related to disease resistance within chromosomes. The researchers also identified nitrogen transport and metabolism genes within plants.
The published paper focused on both sequencing and analyzing the domestication of the beans. The scientists assembled a 473-million base pair genome series of the common bean, comparing sequences from both Mexico and the Andes, and found only a small fraction of shared genes.
“We knew they had separate domestication, this is the first time we knew how few were shared,” McClean says.
The scientists also compared the high-quality common bean genome against the soybean genome sequence — its most economically important relative. They found evidence of genes common to both, and that the common bean had evolved more rapidly since they’d both diverged from a common ancestor, thought to be about 19.3 million years old.
The researchers took particular interest in the transition from prostrate to a standing crop, which has dramatically changed the bean industry in the past 20 years.
“Before that, the beans were swathed,” McClean says. “With the advance of upright beans, you could come in with combines and harvest it right away.”
He says that characteristic might be increased in pinto beans, which are upright but not as upright as navy beans. He also sees better diagnostic markers for diseases, including white mold, common bacterial blight, anthracnose and bean rust.
“Bean production is much more affected by diseases than any other production constraints,” McClean says. “We’re also working on drought tolerance. Related to that, high-value corn, soybeans and canola take over the prime ground, the specialty crops are often moved to less-productive land. We’re working to develop (bean) productivity on those more marginal lands.”
Besides helping farmers in this part of the world, the research also helps people in the developing world. Many farmers employ “milpa,” a technique where beans and corn or squash are planted simultaneously or in a relay system to maximize production in a year.
Desirable traits, no GMOs
One of the DOE’s interests in the project is the production of crops that require less nitrogen fertilizer. The U.S. imports more than half of its nitrogen as fertilizer — 11 million tons in 2012. As the world population advances to 9 billion by 2050, beans that are heavy in nutrition and require less supplemental nitrogen fertilizer will become more important.
Common bean research is a standard genetic project — no genetically modified organisms. Genetically modified bean research is only available in Brazil, and only for one disease present there.