soybeans in hand University of Missouri
The soybean can used in a variety of ways, from cooking oil to animal feed. The seed has a high oil content and plays a big role in biofuels and biodiesels.

Scientists develop additional soybean reference genomes

Having several reference genomes will allow breeders to develop and deliver new varieties more quickly and efficiently.

When the Human Genome Project began in 1990, the goal was to sequence and map all of the genes that make up human DNA. That project was completed in 2003, and genome projects on many other species followed in subsequent years.

Several crops grown in Missouri soon underwent genetic sequencing and mapping, including soybeans. The first soybean cultivar to be sequenced, “Williams 82,” was published in 2010. This widely grown cultivar was chosen to represent the northern U.S. soybean germplasm. For nearly a decade, this cultivar has served as the main soybean reference genome — the sequence that gives scientists a baseline of a species’ set of genes.

A few years later, Henry Nguyen, a Curators’ distinguished professor of plant sciences in the University of Missouri College of Agriculture, Food & Natural Resources, wanted to develop additional reference genomes, this time focusing on soybeans grown in the southern U.S. as well as a wild ancestor of soybean. These two reference genomes -- soybean cultivar “Lee” and wild type PI 483463 -- are now available at GenBank and SoyBase.

Nguyen, who led the research effort, worked with a group of scientists from the University of Missouri, the U.S. Department of Agriculture's Agricultural Research Service (ARS), the HudsonAlpha Institute for Biotechnology, Pacific Biosciences, Bionano Genomics and Washington University, in addition to international collaborations with the University of Western Australia and the Chinese University of Hong Kong.

“The significance here is that we now have three reference genomes for soybeans,” Nguyen said. “Having those reference genomes gives us a solid foundation to build on and allows us to continue to understand the genetic diversity of soybeans. If we want to increase yields, improve disease resistance and seed composition quality and allow for better stress adaptation and resilience, we have to understand how the genetics work.”

Having a map of soybean genes is key for breeders, who work to develop varieties farmers can use to help battle crop diseases and other environmental factors. The soybean is an extremely important crop on a worldwide level: Approximately 340 million metric tons of soybeans are produced globally each year. The annual market for soybeans is worth $40 billion in the U.S. alone, the announcement said.

Soybeans are extremely common in the Midwest. The crop is grown as far north as Minnesota and North Dakota and as far south as Georgia and Florida.

“Soybean cultivars differ by their genetic background and environmental adaptation,” Nguyen said. “Williams 82 is considered a northern germplasm. I thought that it was important to have a southern germplasm as well.

“Genetically, it makes sense to select another diverse cultivar," he added. "We feel like with these two varieties, we have a good representation of U.S. soybean germplasms that we utilize in the breeding and genetics world. Moreover, genome sequence of a wild soybean will help identify untapped genetic diversity.”

Having several reference genomes will allow breeders to develop and deliver new varieties more quickly and efficiently. The purpose of this sequencing project, “Better Soybean, Better Life,” is to assist molecular breeding and genome editing in order to enhance the productivity, biotic and abiotic stress tolerance and nutritional quality of soybeans around the world.

In a statement, the United Soybean Board said it "is pleased to note the release of two key reference genomes for soybean. This represents fruition of a collaborative effort led by the University of Missouri, as partially funded by the United Soybean Board.”

Soybeans originated in Asia, with China serving as a center of diversity and domestication. Wild soybeans (Glycine soja) were most common in those times. Soybeans were later domesticated and cultivated (Glycine max). While the soybean was introduced to the U.S.more than 250 years ago, a complete realization of its value really took shape after World War II.

Soybeans can used in a variety of ways, from cooking oil to animal feed. The seed has a high oil content and plays a large role in biofuels and biodiesel.

“The new genome assemblies will be important for several reasons,” ARS research geneticist (plants) Steven Cannon said. “The Lee cultivar is an important variety in the southern U.S. and has been used as a parent of many other commercial soybean lines. The other new genome sequence is from a close wild relative of soybeans and will give a picture of how the soybean was domesticated, starting several-thousand years ago in Asia. These high-quality assemblies are also being used to improve the first soybean to have been sequenced -- for the northern cultivar Williams 82. Together, these genome assemblies should help researchers more rapidly identify important genes and to efficiently produce improved soybean varieties.”

Funding for the sequencing project was provided by the soybean board and three private companies: Bayer CropScience, Dow AgroSciences and Monsanto.

Besides Nguyen, other project contributors included Babu Valliyodan, Gunvant Patil, Steven Cannon, Hon Ming Lam, Dave Edwards, Philipp Bayer, Jacqueline Campbell, Ting-Fung Chan and Qijian Song.

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