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

文献类型： 外文期刊

作者： Sun, Shichao 1 ; Wang, Yumin 2 ; Wei, He 3 ; Hufnagel, David E. 4 ; Wang, Ya 5 ; Guo, Shiyu 5 ; Li, Yinghui 5 ; Wang, Li 1 ; Qiu, Li-juan 5 ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Genome Anal Lab,Minist Agr,Shenzhen Branch, Shenzhen 518000, Guangdong, Peoples R China

2.Jilin Acad Agr Sci, Soybean Res Inst, Changchun 130033, Jilin, Peoples R China

3.Henan Acad Agr Sci, Henan Acad Crops Mol Breeding, Natl Ctr Plant Breeding, Zhengzhou 450002, Henan, Peoples R China

4.ARS, Virus & Pr Res Unit, Natl Anim Dis Ctr, USDA, Ames, IA 50010 USA

5.Chinese Acad Agr Sci, Key Lab Crop Gene Resource & Germplasm Enhancement, Key Lab Soybean Biol Beijing MOA, Inst Crop Sci,Natl Key Facil Crop Gene Resources &, Beijing 100081, Peoples R China

6.Kunpeng Inst Modern Agr Foshan, Foshan 528200, Guangdong, Peoples R China

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

期刊名称：CROP JOURNAL （ 影响因子：6.6； 五年影响因子：6.5 ）

ISSN： 2095-5421

年卷期： 2023 年 11 卷 2 期

页码：

收录情况： SCI

摘要： Soybean (Glycine max L.) is a protein and oil crop grown worldwide. Its fitness may be reduced by dele-terious 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 lan-drace 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 pheno-typic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2 (SCN2), soy-bean 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 can-didate 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.(c) 2022 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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