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

Authors: BAYER, PHILIPP - University Of Western Australia; VALLIYODARI, BABU - Lincoln University Of Missouri; HU, HAIFEI - University Of Western Australia; MARSH, JACOB - University Of Western Australia; YUAN, YUXUAN - University Of Western Australia; VUONG, TRI - University Of Missouri; PATIL, GUNVANT - University Of Missouri; Song, Qijian; BATLEY, JACQUELINE - University Of Western Australia; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; LAM, HON-MING - The Chinese University Of Hong Kong (CUHK); EDWARDS, DAVID - University Of Western Australia; 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. https://doi.org/10.1002/tpg2.20109.
DOI: https://doi.org/10.1002/tpg2.20109

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.