The prevalence of deleterious mutations during the domestication and improvement of soybean
Shichao Sun,
Yumin Wang,
He Wei,
David E. Hufnagel,
Ya Wang,
Shiyu Guo,
Yinghui Li,
Li Wang,
Li-juan Qiu
Affiliations
Shichao Sun
Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, Guangdong, China
Yumin Wang
Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 130033, Jilin, China
He Wei
Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding, Zhengzhou 450002, Henan, China
David E. Hufnagel
Virus and Prion Research Unit, National Animal Disease Center, The Agricultural Research Service (ARS) of the United States Department of Agriculture (USDA), Ames, IA 50010, USA
Ya Wang
The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Shiyu Guo
The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Yinghui Li
The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Corresponding authors.
Li Wang
Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, Guangdong, China; Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528200, Guangdong, China; Corresponding authors.
Li-juan Qiu
The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Corresponding authors.
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.
