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

The Crop Journal 2023年第2期11卷 523-530页

作者： Shichao Sun Yumin Wang He Wei David E.Hufnagel Ya Wang Shiyu Guo Yinghui Li Li Wang Li-juan Qiu 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 SciencesShenzhen 518000GuangdongChina Soybean Research Institute Jilin Academy of Agricultural SciencesChangchun 130033JilinChina Henan Academy of Crops Molecular Breeding Henan Academy of Agricultural Sciences/National Centre for Plant BreedingZhengzhou 450002HenanChina Virus and Prion Research Unit National Animal Disease CenterThe Agricultural Research Service(ARS)of the United States Department of Agriculture(USDA)AmesIA 50010USA 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 SciencesChinese Academy of Agricultural SciencesBeijing 100081China Kunpeng Institute of Modern Agriculture at Foshan Foshan 528200GuangdongChina

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.

关键词： Deleterious mutations Domestication cost expansion load BAD_Mutations Soybean cyst nematode

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