Impact of multiple selective breeding programs on genetic diversity in soybean germplasm

Key message Independent soybean breeding programs shape genetic diversity from unimproved germplasm to modern cultivars in similar ways, but distinct breeding populations retain unique genetic variation, preserving additional diversity. From the domestication of wild soybean ( Glycine soja Sieb. & Zucc.), over 3,000 years ago, to the modern soybean ( Glycine max L. Merr) cultivars that provide much of the world’s oil and protein, soybean populations have undergone fundamental changes. We evaluated the molecular impact of breeding and selection using 391 soybean accessions including US cultivars and their progenitors from the USDA Soybean Germplasm Collection (CGP), plus two new populations specifically developed to increase genetic diversity and high yield in two alternative gene pools: one derived from exotic G. max germplasm (AGP) and one derived from G. soja (SGP). Reduction in nucleotide genetic diversity ( π ) was observed with selection within gene pools, but artificial selection in the AGP maintained more diversity than in the CGP. The highest F ST levels were seen between ancestral and elite lines in all gene pools, but specific nucleotide-level patterns varied between gene pools. Population structure analyses support that independent selection resulted in high-yielding elite lines with similar allelic compositions in the AGP and CGP. SGP, however, produced elite progeny that were well differentiated from, but lower yielding than, CGP elites. Both the AGP and SGP retained a significant number of private alleles that are absent in CGP. We conclude that the genomic diversity shaped by multiple selective breeding programs can result in gene pools of highly productive elite lines with similar allelic compositions in a genome-wide perspective. Breeding programs with different ancestral lines, however, can retain private alleles representing unique genetic diversity.