Illinois-Led Project to Sequence 400 Soybean Genomes, Improve Future Crops

By Lauren Quinn

As a source of protein and biodiesel for cleaner renewable energy, soybean is an important crop worldwide. But is it performing to its full potential? An ambitious effort led by the University of Illinois Urbana-Champaign and the U.S. Department of Energy Joint Genome Institute (JGI) will sequence 400 soybean genomes to develop a “pangenome” — an attempt to characterize all the useful diversity in the genome to create an even more robust and resilient crop.

The soybean pangenome project will sequence and analyze at least 50 soybean genomes from cultivated lines and wild relatives at reference quality, the gold standard of modern sequencing. A further 350 genomes will be sequenced as high-quality drafts by the JGI. The plan is to include a diverse set of soybean lines, including perennial relatives and lines selected to yield in harsh conditions, preparing the industry to move toward a climate-resilient future.    

“There have been soybean pangenome efforts before, but this will be a big step forward. We want to identify all of the variation present within this diverse set of cultivated soybeans. Knowing details of all of the genetic variation should very much enhance and speed up the ability of crop breeders and biotechnology experts to identify important genes and incorporate them into better crops,” said project leader Matt Hudson, professor in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences (ACES) at U. of I. He is also co-director of the Center for Digital Agriculture, science integration chair for the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), and faculty affiliate at the Carl R. Woese Institute for Genomic Biology.

 Hudson and his multi-institution collaborators will select and grow soybean lines, shipping extracted DNA to the JGI for long-read sequencing as part of the JGI’s Community Science Program. Hudson’s team, along with partners at U. of I.’s AIFARMS, will take the lead in analyzing the output. 

“AIFARMS was designed to deal with large datasets coming out of agriculture projects,” Hudson said. “Having this dataset is going to be a boost for our other digital ag activities.”

With its inclusion of wild relatives and the sheer number of reference and high-quality draft genomes set for sequencing, the project will drastically improve the current soybean reference genome. Hudson explains that genetic diversity is the raw material for crop improvement, but the crop’s diversity is not reflected in the reference genome. He likens it to the first human genome, which was pieced together only from Caucasian individuals. 

“There’s an increasing effort to have the reference human genome reflect all of the variation in people. We think there are equally big reasons to do the same thing in crops,” Hudson said. “But it’s hard to locate the missing diversity by any other means than sequencing more genomes.”

The team plans to consult the global soybean breeding community, including industry partners, in deciding priority lines to include. 

Ultimately, Hudson said, the project will “enable deep analysis of the evolution and domestication of modern soybean and empower soybean researchers and breeders to directly select for otherwise hidden genetic variation in genes that can be targeted for variety development. As soybean is becoming increasingly important as a worldwide crop, as well as being a key bioenergy crop, this project will have global impact and be particularly relevant to U.S. agriculture."