Purging of deleterious mutations during domestication in the predominant selfing crop soybean

Abstract

As a predominant plant protein and oil source for both food and feed, soybean is unique in that both domesticated and wild types are predominantly selfing. Here we present a genome-wide variation map of 781 soybean accessions that include 418 domesticated (Glycine max) and 345 wild (Glycine soja) accessions and 18 of their natural hybrids. We identified 10.5 million single nucleotide polymorphisms and 5.7 million small indels that contribute to within-and between-population variations. We describe improved detection of domestication-selective sweeps and drastic reduction of overall deleterious alleles in domesticated soybean relative to wild soybean in contrast to the cost of domestication hypothesis. This resource enables the marker density of existing data sets to be increased to improve the resolution of association studies.

Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

“…Direct comparison between corresponding chromosome sequences of the Hwangkeum and Williams 82 assemblies identified 1,788,320 SNPs and 517,907 indels (< 50 bp) (Table S6 and File S2). Interestingly, the number of SNPs is similar to the combined number (1,678,164) of heterozygous (4,919), missing (713,953), and homozygous non-reference (959,292) SNPs for Hwangkeum in the 30,753,511 SNP set without the minor allele frequency filter detected in the 781 soybean haplotype map set (Kim et al 2021). The number of indels is also similar to the combined number (470,389) of heterozygous (28,639), missing (303,784), and homozygous non-reference (137,966) indels for Hwangkeum in the 5,717,052 indel set without the minor allele frequency filtration detected from the same set.…”

“…After three weeks' growth, a bulk of young trifoliolate leaf tissues was collected for genomic DNA extraction. Note that the seeds of Hwangkeum used in this study came from the line of Hwangkeum that had been subject to single plant selection at least twice during our recent 180K SoyaSNP array and genome resequencing studies (Lee et al 2015;Kim et al 2021). Genomic DNAs for the generation of Illumina short-read (Illumina, San Diego, CA, USA) and PacBio SMRT long-read sequences (Pacific Biosciences, Menlo Park, CA, USA) were extracted using the CTAB method, as described by Saghai-Maroof et al (1984).…”

The road to sorghum domestication: evidence from nucleotide diversity and gene expression patterns

“…2018), we didn’t find clear evidence of accumulation of deleterious load in the crop pool. Interestingly, a recent study in soybean found a genome wide reduction of the deleterious alleles in domesticated soybean relative to wild soybean (Kim et al . 2020).…”

“…However, in contrast with a previous work on sorghum (Smith et al, 2019), and evidence in other plant and animal domesticates (Liu et al, 2017; Moyers et al, 2018), we didn’t find clear evidence of accumulation of deleterious load in the domesticated pool. Interestingly, a recent study in soybean found a genome wide reduction of the deleterious alleles in domesticated soybean relative to wild soybean (Kim et al, 2020). These authors suggested that the increase of self crossing associated with domestication may have helped purging the deleterious load, partly by exposing to selection deleterious variants in homozygous state, a process suggested also in cassava (Ramu et al, 2017) and grape (Zhou et al, 2017).…”

“…Our estimate of nucleotide diversity loss was higher than previous estimates for domesticated sorghum based on nuclear microsatellite markers (14%, Casa et al 2005) , but lower than the loss recorded in other main crops with selfing or mixed mating systems. For instance, it was estimated a 62% nucleotide diversity reduction in rice (Caicedo et al 2007) , 72% in common beans (Bitocchi et al 2013) and 50% in soybean (Kim et al 2020) . The crop showed also lower expression variation than the wild accessions, a finding common to other crops such as maize (Lemmon et al 2014) and common bean (Bellucci et al 2014) but also animal domesticates (Liu et al 2019) .…”