Soybean Pangenome Project Uncovers Hidden Genetic Diversity

Soybeans, serving as a significant global source of protein and cleaner, renewable biodiesel energy, play a vital role. However, is soybean reaching its utmost potential? A pioneering endeavor, spearheaded by the University of Illinois Urbana-Champaign and the US Department of Energy Joint Genome Institute (JGI), aims to sequence 400 soybean genomes to construct a “pangenome.”

This initiative seeks to comprehensively depict all valuable genetic diversity within the genome, ultimately fostering the development of a more robust and resilient crop.

The soybean pangenome project aims to sequence and analyze a minimum of 50 soybean genomes, including both cultivated varieties and wild counterparts, to reference quality standards, representing the highest modern sequencing standard. Additionally, the JGI will produce 350 genomes as high-quality drafts.

The project's scope encompasses a diverse array of soybean lines, encompassing perennial relatives and those specially chosen for their resilience in challenging environments, ultimately paving the way for the industry to transition towards 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."

Matt Hudson, Project Leader and Professor, Department of Crop Sciences, Part of the College of Agricultural, Consumer and Environmental Sciences, University of Illinois Urbana-Champaign

He serves as the co-director of the Center for Digital Agriculture, holds the position of science integration chair at the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), and is a faculty affiliate at the Carl R. Woese Institute for Genomic Biology.

Hudson, in collaboration with multiple institutions, will be responsible for the selection and cultivation of soybean lines. The extracted DNA will then be sent to the JGI for long-read sequencing, as part of the JGI’s Community Science Program. The analysis of the results will be led by Hudson's team in conjunction with partners from U. of I.’s AIFARMS.

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

Matt Hudson, Project Leader and Professor, Department of Crop Sciences, Part of the College of Agricultural, Consumer and Environmental Sciences, University of Illinois Urbana-Champaign

By encompassing wild relatives and an extensive range of reference and high-quality draft genomes for sequencing, this project is poised to bring about a significant enhancement to the existing soybean reference genome.

Hudson elucidates that genetic diversity serves as the fundamental foundation for crop enhancement, and the reference genome currently in use does not adequately represent the crop's diversity. He draws a parallel to the initial human genome, which was assembled solely from individuals of Caucasian descent.

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. But it’s hard to locate the missing diversity by any other means than sequencing more genomes.”

Matt Hudson, Project Leader and Professor, Department of Crop Sciences, Part of the College of Agricultural, Consumer and Environmental Sciences, University of Illinois Urbana-Champaign

The team intends to engage with the worldwide soybean breeding community, which includes industry collaborators, to collectively determine the priority lines for inclusion in the project.

Hudson adds 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.”