Impacts of Nucleotide Fixation during Soybean Domestication and Intensive Breeding

In the course of soybean domestication and intensive breeding, artificial selection resulted in substantial phenotypic divergence and the origin of modern cultivars from their wild ancestors. In our project, population analysis of available sequencing accessions estimated that ∼9.8 million single nucleotide polymorphisms reach saturation in soybean germplasm, and then ∼5.3 million in cultivars. We observed a severe reduction of genetic diversity in the switch from wild soybeans to landraces and to elite cultivars. Selective sweeps defined by neutrality tests reveal that 2,255 and 1,051 genes were affected in early domestication and intensive breeding, respectively. It corresponds to 3% of genome sequences and 4% of all the genes that were affected by artificial selection.;Strong selective pressure on favorite phenotypes could cause nucleotide fixations in soybean cultivars in quite a short time. Artificial selection generated ∼0.1 million nucleotide fixations in cultivated soybeans, which promoted to the soybean divergence. Meta-analysis of reported quantitative trait and selective signals with nucleotide fixation identified a list of candidate genes for 13 agriculturally important traits. Nucleotide fixations introduced by artificial selection were involved in diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes, including plant-pathogen interactions.;Our analysis provides comprehensive insights into the impacts of soybean nucleotide fixations introduced by artificial selection, which would facilitate future gene mapping and molecular breeding practice.