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

OAR@ICRISAT

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Relation http://oar.icrisat.org/11882/
https://doi.org/10.1002/tpg2.20109
doi:10.1002/tpg2.20109
 
Title Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding
 
Creator Bayer, P E
Valliyodan, B
Hu, H
Marsh, J I
Yuan, Y
Vuong, T D
Patil, G
Song, Q
Batley, J
Varshney, R K
Lam, H M
Edwards, D
Nguyen, H T
 
Subject Plant Breeding
Genetics and Genomics
 
Description 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 representingmore
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.
 
Publisher Wiley
 
Date 2021-04
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11882/1/USDA%20core.pdf
Bayer, P E and Valliyodan, B and Hu, H and Marsh, J I and Yuan, Y and Vuong, T D and Patil, G and Song, Q and Batley, J and Varshney, R K and Lam, H M and Edwards, D and Nguyen, H T (2021) Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome (TSI). pp. 1-12. ISSN 1940-3372