Soybean Research Institute and MARA National Center for Soybean Improvement and MARA Key Laboratory of Biology and Genetic Improvement of Soybean and State Key Laboratory for Crop Genetics and Germplasm Enhancement and State Innovation Platform for Integrated Production and Education in Soybean Bio-Breeding and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
Institute of Economic Crops, Guangxi Academy of Agricultural Sciences, Nanning, 5300007, Guangxi, China.
Theor Appl Genet. 2023 Jun 13;136(7):152. doi: 10.1007/s00122-023-04390-2.
Fifty-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 × 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) 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.
利用基因-等位基因序列作为 RTM-GWAS 中的标记，直接在 SCSGP 中鉴定了 53 个具有 281 个等位基因的品种耐荫性基因，从中探索了优化杂交、进化驱动力和基因-等位基因网络。耐荫性是大豆与玉米间/套作优化栽培的关键。为了探索中国南方大豆种质资源的耐荫性基因-等位基因系统，我们提出在受限两阶段多基因座模型全基因组关联研究（GASM-RTM-GWAS）中使用基因-等位基因序列标记（GASM）。在中国南宁对 394 个样本进行了耐荫性指数（STI）测试。通过全基因组重测序，共组装了 47586 个 GASM。通过 GASM-RTM-GWAS，鉴定出 53 个主要效应 STI 基因，具有 281 个等位基因（2-13 个等位基因/基因）（共计 63 个基因，308 个等位基因，包括 38 个 G × E 基因，191 个等位基因），然后将其组织成一个由八个子矩阵组成的基因-等位基因矩阵，分别对应于地理季节亚群。该群体表现出轻微的 STI 变化（1.69→1.56-1.82）和轻微的基因-等位基因变化（92.5%的等位基因遗传，0%的等位基因排除，7.5%的等位基因出现），从原始（SA）到衍生的七个亚群，但预测存在较大的超越重组潜力和最佳杂交。这 63 个 STI 基因被注释到六个生物学类别（代谢过程、催化活性、应激反应、转录和翻译、信号转导和运输和未知功能），相互作用形成基因网络。从 STI 基因-等位基因系统中，选出了 22 个基因的 38 个重要等位基因，供进一步深入研究。与其他程序相比，GASM-RTM-GWAS 在种质群体遗传研究中表现出强大而有效的功能，通过直接和彻底地识别其基因-等位基因系统，实现了全基因组设计育种，并可以探索进化驱动力和基因-等位基因网络。
