Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

P.E. Bayer; B. Valliyodan; H. Hu; J.I. Marsh; Y. Yuan; T.D. Vuong; G. Patil; Q. Song; J. Batley; R.K. Varshney; H‐M Lam; D. Edwards; H.T. Nguyen

doi:10.1002/tpg2.20109

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Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

Journal article

Peer reviewed

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding

P.E. Bayer, B. Valliyodan, H. Hu, J.I. Marsh, Y. Yuan, T.D. Vuong, G. Patil, Q. Song, J. Batley, R.K. Varshney, …

The Plant Genome, Vol.15(1), e20109

2022

DOI: https://doi.org/10.1002/tpg2.20109

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Abstract

The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.

Details

Title: Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding
Authors/Creators: P.E. Bayer (Author/Creator) - The University of Western Australia
B. Valliyodan (Author/Creator) - University of Missouri
H. Hu (Author/Creator) - The University of Western Australia
J.I. Marsh (Author/Creator) - The University of Western Australia
Y. Yuan (Author/Creator) - Chinese University of Hong Kong
T.D. Vuong (Author/Creator) - University of Missouri
G. Patil (Author/Creator) - Texas Tech University
Q. Song (Author/Creator) - Genomics (United Kingdom)
J. Batley (Author/Creator) - The University of Western Australia
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
H‐M Lam (Author/Creator)
D. Edwards (Author/Creator) - The University of Western Australia
H.T. Nguyen (Author/Creator) - University of Missouri
Publication Details: The Plant Genome, Vol.15(1), e20109
Publisher: Wiley Periodicals LLC on behalf of Crop Science Society of America
Identifiers: 991005543405807891
Copyright: © 2021 The Authors
Murdoch Affiliation: Centre for Crop and Food Innovation; Food Futures Institute; State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Genetics & Heredity; Plant Sciences
ESI research areas: Plant & Animal Science