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Gene-allele system of shade tolerance in southern China soybean germplasm revealed by genome-wide association study using gene-allele sequence as markers

文献类型： 外文期刊

作者： Su, Yanzhu 1 ; Zhang, Zhipeng 1 ; He, Jianbo 1 ; Zeng, Weiying 7 ; Cai, Zhaoyan 7 ; Lai, Zhenguang 7 ; Pan, Yongpeng 1 ; Hao, Xiaoshuai 1 ; Xing, Guangnan 1 ; Wang, Wubin 1 ; Zhang, Jiaoping 1 ; Li, Yan 1 ; Sun, Zudong 7 ; Gai, Junyi 1 ;

作者机构： 1.Nanjing Agr Univ, Soybean Res Inst, Nanjing 210095, Jiangsu, Peoples R China

2.Nanjing Agr Univ, MARA Natl Ctr Soybean Improvement, Nanjing 210095, Jiangsu, Peoples R China

3.Nanjing Agr Univ, MARA Key Lab Biol & Genet Improvement Soybean, Nanjing 210095, Jiangsu, Peoples R China

4.Nanjing Agr Univ, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Jiangsu, Peoples R China

5.Nanjing Agr Univ, State Innovat Platform Integrated Prod & Educ Soyb, Nanjing 210095, Jiangsu, Peoples R China

6.Nanjing Agr Univ, Jiangsu Collaborat Innovat Ctr Modern Crop Prod, Nanjing 210095, Jiangsu, Peoples R China

7.Guangxi Acad Agr Sci, Inst Econ Crops, 5300007, Nanning, Guangxi, Peoples R China

期刊名称：THEORETICAL AND APPLIED GENETICS （ 影响因子：5.4； 五年影响因子：5.7 ）

ISSN： 0040-5752

年卷期： 2023 年 136 卷 7 期

页码：

收录情况： SCI

摘要： Key messageFifty-three shade tolerance genes with 281 alleles in the SCSGP were identified directly using gene-allele sequence as markers in RTM GWAS, from which optimized crosses, evolutionary motivators, and gene-allele networks were explored.Shade tolerance is a key for optimal cultivation of soybean inter/relay-cropped with corn. To explore the shade tolerance gene-allele system in the southern China soybean germplasm, we proposed using gene-allele sequence markers (GASMs) in a restricted two-stage multi-locus model genome-wide association study (GASM-RTM-GWAS). A representative sample with 394 accessions was tested for their shade tolerance index (STI), in Nanning, China. Through whole-genome re-sequencing, 47,586 GASMs were assembled. From GASM-RTM-GWAS, 53 main-effect STI genes with 281 alleles (2-13 alleles/gene) (totally 63 genes with 308 alleles, including 38 G x E genes with 191 alleles) were identified and then organized into a gene-allele matrix composed of eight submatrices corresponding to geo-seasonal subpopulations. The population featured mild STI changes (1.69 -> 1.56-1.82) and mild gene-allele changes (92.5% alleles inherited, 0% alleles excluded, 7.5% alleles emerged) from the primitive (SA(III)) to the derived seven subpopulations, but large transgressive recombination potentials and optimal crosses were predicted. The 63 STI genes were annotated into six biological categories (metabolic process, catalytic activity, response to stresses, transcription and translation, signal transduction and transport and unknown functions), interacted as gene networks. From the STI gene-allele system, 38 important alleles of 22 genes were nominated for further in-depth study. GASM-RTM-GWAS performed powerful and efficient in germplasm population genetic study comparing to other procedures through facilitating direct and thorough identification of its gene-allele system, from which genome-wide breeding by design could be achieved, and evolutionary motivators and gene-allele networks could be explored.

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