The prevalence of deleterious mutations during the domestication and improvement of soybean

作者：Shichao Sun, Yu‐Min Wang, Wei He, David E. Hufnagel, Ya Wang, Shiyu Guo, Yinghui Li, Li Wang, Lijuan Qiu · 发表于：The Crop Journal · 年份：2022 · DOI：10.1016/j.cj.2022.10.008 · 被引用次数：7 · 研究领域：Soybean genetics and cultivation、Legume Nitrogen Fixing Symbiosis、Nematode management and characterization studies

Soybean (Glycine max L.) is a protein and oil crop grown worldwide. Its fitness may be reduced by deleterious mutations, whose identification and purging is desirable for crop breeding. In the published whole-genome re-sequenced data of 2214 soybean accessions, including 221 wild soybean, 1132 landrace cultivars and 861 improved soybean lines, we identified 115,275 deleterious single-nucleotide polymorphisms (SNPs). Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved lines. Genes in selective-sweep regions showed fewer deleterious mutations than the remaining genes. Deleterious mutations explained 4.3%–48% more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2 (SCN2), soybean cyst nematode race 3 (SCN3) and soybean mosaic virus race 3 (SMV3). These findings illustrate how mutation load has shifted during soybean domestication, expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.