Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China.
Planta. 2018 Oct;248(4):947-962. doi: 10.1007/s00425-018-2952-4. Epub 2018 Jul 6.
RTM-GWAS identified 111 DT QTLs, 262 alleles with high proportion of QEI and genetic variation accounting for 88.55-95.92% PV in NAM, from which QTL-allele matrices were established and candidate genes annotated. Drought tolerance (DT) is one of the major challenges for world soybean production. A nested association mapping (NAM) population with 403 lines comprising two recombinant inbred line (RIL) populations: M8206 × TongShan and ZhengYang × M8206 was tested for DT using polyethylene-glycol (PEG) treatment under spring and summer environments. The population was sequenced using restriction-site-associated DNA sequencing (RAD-seq) filtered with minor allele frequency (MAF) ≥ 0.01, 55,936 single nucleotide polymorphisms (SNPs) were obtained and organized into 6137 SNP linkage disequilibrium blocks (SNPLDBs). The restricted two-stage multi-locus genome-wide association studies (RTM-GWAS) identified 73 and 38 QTLs with 174 and 88 alleles contributed main effect 40.43 and 26.11% to phenotypic variance (PV) and QTL-environment interaction (QEI) effect 24.64 and 10.35% to PV for relative root length (RRL) and relative shoot length (RSL), respectively. The DT traits were characterized with high proportion of QEI variation (37.52-41.65%), plus genetic variation (46.90-58.40%) in a total of 88.55-95.92% PV. The identified QTLs-alleles were organized into main-effect and QEI-effect QTL-allele matrices, showing the genetic and QEI architecture of the three parents/NAM population. From the matrices, the possible best genotype was predicted to have a weighted average value over two indicators (WAV) of 1.873, while the top ten optimal crosses among RILs with 95th percentile WAV 1.098-1.132, transgressive over the parents (0.651-0.773) but much less than 1.873, implying further pyramiding potential. From the matrices, 134 candidate genes were annotated involved in nine biological processes. The present results provide a novel way for molecular breeding in QTL-allele-based genomic selection for optimal cross selection.
RTM-GWAS 鉴定了 111 个 DT QTLs，262 个具有高比例 QEI 的等位基因，遗传变异占 NAM 中 88.55-95.92%的表型变异，建立了 QTL-等位基因矩阵并注释了候选基因。干旱耐受性 (DT) 是世界大豆生产面临的主要挑战之一。使用聚乙二醇 (PEG) 在春季和夏季环境下对包含两个重组自交系 (RIL) 群体 M8206×TongShan 和 ZhengYang×M8206 的嵌套关联作图 (NAM) 群体进行 DT 测试。该群体使用限制性位点相关 DNA 测序 (RAD-seq) 进行测序，过滤最小等位基因频率 (MAF)≥0.01，获得 55936 个单核苷酸多态性 (SNP)，并组织成 6137 个 SNP 连锁不平衡块 (SNPLDB)。限制两阶段多基因全基因组关联研究 (RTM-GWAS) 分别鉴定出与相对根长 (RRL) 和相对茎长 (RSL) 表型方差 (PV) 主效 40.43%和 26.11%、QTL-环境互作 (QEI) 效应 24.64%和 10.35%相关的 73 和 38 个 QTLs 及其 174 和 88 个等位基因。DT 性状的特点是 QEI 变异比例高 (37.52-41.65%)，加上遗传变异 (46.90-58.40%)，总变异比例为 88.55-95.92%。鉴定的 QTL-等位基因被组织成主效和 QEI 效应 QTL-等位基因矩阵，显示了三个亲本/NAM 群体的遗传和 QEI 结构。从矩阵中，可以预测最佳基因型的加权平均值 (WAV) 为 1.873，而 RIL 之间的前 10 个最佳杂交 WAV 为 1.098-1.132，超过亲本 (0.651-0.773)，但远低于 1.873，这意味着进一步的潜力。从矩阵中，注释了 134 个候选基因，涉及九个生物学过程。本研究结果为基于 QTL-等位基因的基因组选择最优杂交选择的分子育种提供了新途径。
