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ARS Home » Southeast Area » Baton Rouge, Louisiana » Honey Bee Lab » Research » Publications at this Location » Publication #387874

Research Project: Using Genetics to Improve the Breeding and Health of Honey Bees

Location: Honey Bee Breeding, Genetics, and Physiology Research

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

item GOMES VIANA, JOAO - University Of Illinois
item FANG, YUANJIN - University Of Illinois
item Avalos, Arian
item Song, Qijian
item NELSON, RANDALL - University Of Illinois
item HUDSON, MATTHEW - University Of Illinois

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2022
Publication Date: 2/27/2022
Citation: Gomes Viana, J.P., Fang, Y., Avalos, A., Song, Q., Nelson, R., Hudson, M.E. 2022. Impact of multiple selective breeding programs on genetic diversity in soybean germplasm. Theoretical and Applied Genetics. 135(5):1591–1602.

Interpretive Summary: Modern soybean is a cultivar of critical economic significance as a major source of oil and protein across the globe. The present work examines artificial selection of modern soybean lines in the USDA Soybean Germplasm Collection, their progenitors (CGP), and also two novel populations (AGP, SGP) independently bred in an effort to increase genetic diversity and high yield. Across all populations there was reduced genetic diversity due to selection, but novel populations (specifically AGP) retained greater variation than CGP. A high degree of convergence between CGP and AGP lines was also observed, though each line retained significant numbers of population-specific alleles and resulting elite crosses produced well differentiated, yield comparable progeny. Together, these characteristics point at possible mechanisms for developing populations with unique genetic diversity to be explored in further breeding.

Technical Abstract: 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 (AGP, SGP). Reduction in nucleotide genetic diversity (p) was observed with selection within gene pools, but artificial selection in the AGP maintained more diversity than in the CGP. The highest FST levels were seen between ancestral and elite lines in both gene pools, but specific nucleotide-level patterns varied between gene pools. Population structure analyses support independent, convergent selection in the AGP and CGP, both of which developed high-yielding elite lines with similar allelic compositions. Glycine soja parents in crosses with elite lines (SGP), however, produced elite progeny that were well differentiated from 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 in highly productive elite lines originating from multiple selective breeding programs can converge to gene pools with similar allelic compositions in a genome-wide perspective. However, independently, different selective breeding programs can retain private alleles that represents a unique genetic diversity that could be explored in soybean genetic breeding.