Development of user-selectable diverse sets of cultivated and wild soybean germplasm for genetic and breeding applications

Authors: Song, Qijian; Araya Salas, Susan; Quigley, Charles; Elia, Patrick

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/6/2026
Publication Date: 3/9/2026
Citation: Song, Q., Araya Salas, S.I., Quigley, C.V., Elia, P.E. 2026. Development of user-selectable diverse sets of cultivated and wild soybean germplasm for genetic and breeding applications. The Plant Genome. 19(1). Article e70216. https://doi.org/10.1002/tpg2.70216.
DOI: https://doi.org/10.1002/tpg2.70216

Interpretive Summary: Over many decades, U.S. soybean breeding has made the crop higher-yielding, better quality, and more resistant to pests and harsh conditions. However, this progress came with a hidden cost: today’s soybeans are much more genetically uniform. More than 95% of modern soybeans can be traced back to only 28 ancestors, meaning many valuable rare genes have been lost in the commercial soybeans. To address this, scientists at USDA-ARS in Beltsville, Maryland studied about 20,000 soybean accessions from both cultivated and wild soybeans in the USDA-ARS Soybean Germplasm Collection. Using about 50,000 genetic markers, they measured how different each soybean accession was from the others. Then they created special “diversity sets”—groups of soybeans that together capture the widest possible range of genetic differences. They found that instead of needing all 20,000 samples, choosing just 300–400 carefully selected soybean types can preserve majority of the important genetic diversity in the entire collection. To help breeders and geneticists make the best use of soybean germplasm, the team further developed an easy-to-use method called “I-select”, it allows users to build their own custom mini-collection of soybeans based on specific needs—such as where the plants will be grown, which varieties they prefer, or which seeds are available. The information from this work gives soybean breeders and researchers a smart, efficient method and tool to use germplasm collection and improve soybean crop.

Technical Abstract: After decades of intensive breeding, modern U.S. soybean varieties have achieved significant improvements in yield, quality, and stress tolerance, but these gains have come at the cost of severely reduced genetic diversity. To reduce vulnerability and promote efficient use of germplasm, diversity sets (DS) of varying sample sizes were defined for the entire USDA-ARS Soybean Germplasm Collection and 13 maturity groups using the SoySNP50K SNP profile, and the average retained genetic diversity of the 50K SNPs was compared between 10 DS and 10 random sets (RS) at different sizes. DS consistently outperformed random sampling: in cultivated soybean, DS captured 94.9–98.4% of SNP diversity compared with 73.1–93.9% for RS; in wild soybean, DS captured 92.8–97.9% compared with 83.4–97.7% for RS. The performance of DS was further validated using whole-genome sequences from 1,511 accessions, demonstrating that DS could retain the same diversity predicted by the 42k SNP subset across 1,308 cultivated soybean genomes and 203 wild soybean genomes of different sample sizes. DS had also been shown to be effective in capturing genetic diversity across different traits. To allow users to select DS, an “I-select” approach was proposed and a table containing germplasm clusters across the USDA collection and different maturity groups was created. This resource enables researchers to tailor combinations based on maturity groups, accession and sample size preferences, and seed availability. The study provides both methodology and resources that can streamline germplasm evaluation, maximize resource utilization, and enhance future soybean genetic improvement. Several DS have already been used by U.S. soybean breeders in their programs.