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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #380153

Research Project: Characterization of Genetic Diversity in Soybean and Common Bean, and Its Application toward Improving Crop Traits and Sustainable Production

Location: Soybean Genomics & Improvement Laboratory

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

item BAYER, PHILIPP - University Of Western Australia
item VALLIYODARI, BABU - Lincoln University Of Missouri
item HU, HAIFEI - University Of Western Australia
item MARSH, JACOB - University Of Western Australia
item YUAN, YUXUAN - University Of Western Australia
item VUONG, TRI - University Of Missouri
item PATIL, GUNVANT - University Of Missouri
item Song, Qijian
item BATLEY, JACQUELINE - University Of Western Australia
item VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item LAM, HON-MING - The Chinese University Of Hong Kong (CUHK)
item EDWARDS, DAVID - University Of Western Australia
item NGUYEN, HENRY - University Of Missouri

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/26/2021
Publication Date: 6/24/2021
Citation: Bayer, P.E., Valliyodari, B., Hu, H., Marsh, J., Yuan, Y., Vuong, T.D., Patil, G., Song, Q., Batley, J., Varshney, R.K., Lam, H., Edwards, D., Nguyen, H.T. 2021. Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding. The Plant Genome. 15(1):e20109.

Interpretive Summary: Cultivated soybean is a staple crop which was domesticated 6,000–9,000 years ago in East Asia from the wild soybean. Scientists know that domestication can lead to gene variation between individuals of the same species as well as a change of frequency of specific genes in a population, but they do not know exactly all of the genes affected. Now with 1,110 genome sequences available for different soybeans, we studied the effect of domestication and breeding on the soybean genome. We found an overall decrease in the number of genes after domestication and a reduced amount of genetic diversity. Further analysis revealed an increase in some genes with functions for responses to environmental stress and pathogen defense. These results provide a valuable resource to study gene-trait association which may help scientists in industry, government agencies, and universities breed better soybeans. The data also will help researchers better understand the positive and negative consequences of domestication.

Technical 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, for example by a loss of genetic diversity. Here we have assembled and analyzed a soybean pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genome-wide 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.