The patterns of deleterious mutations during the domestication of soybean.

Kim, Myung-Shin; Lozano, Roberto; Kim, Ji Hong; Bae, Dong Nyuk; Kim, Sang-Tae; Park, Jung-Ho; Choi, Man Soo; Kim, Jaehyun; Ok, Hyun-Choong; Park, Soo-Kwon; Gore, Michael A; Moon, Jung-Kyung; Jeong, Soon-Chun

Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel.