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

Citations Over TimeTop 1% of 2021 papers

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.

Related Papers

• → Genetic Diversity and Core Germplasm Research of 144 Munake Grape Resources Using 22 Pairs of SSR Markers(2023)8 cited
• Genetic diversity and construction of primary core germplasm in Cornus officinalis by ISSR marker.(2009)
• Research Progress of Genetic Diversity of Forage Germplasm Resources in China(2015)
• → RAPD MARKERS BASED GENETIC DIVERSITY ANALYSIS OF ONION (ALLIUM CEPA) GERMPLASM(2023)1 cited
• → 552 Comparison of Genetic Diversity in between Two Germplasm Banks Containing Lycopersicon esculentum Accessions(2000)