The patterns of deleterious mutations during the domestication of soybean

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

Nat. Commun. 2021 Jan 4;12(1):97.  doi: 10.1038/s41467-020-20337-3.

Abstract

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.

See: https://pubmed.ncbi.nlm.nih.gov/33397978/

Figure 2: Genomic landscape of soybean.

a Chromosomes based on the Williams 82 reference genome sequence v. Wm82.a2.v1 (a). Centromere repeat regions are indicated by gray bands. Gene density heatmap (b). SNP density (c). Indel density (d). Population recombination rates calculated in 1 Mb windows (blue = historical recombination rate and red = estimates of recombination rate from mapping populations (e). SV density (f). Average GERP score density (>0), with dark blue of high GERP score (g). All window sizes are 100 kb except recombination rates. b Mean LD scores estimated with a 1 Mb window.