Characterizing the whole genetic architecture of drought tolerance (DT) is a persistent challenge for the breeders. Here we developed a half-sib population comprising of 404 lines of two recombinant inbred line (RIL) populations with M8206 as the joint parent (M8206 × TongShan and ZhengYang × M8206) and tested for its DT under sand culture. The population was sequenced using restriction-site-associated DNA sequencing filtered with minor allele frequency ≥0.01; 55,936 single nucleotide polymorphisms (SNPs) were obtained and assembled into 6137 SNPLDBs (SNP linkage disequilibrium blocks). The restricted two-stage multi-locus genome-wide association analysis characterized with error and false-positive control identified 40 QTLs with 93 alleles on an average of 34.75% of the phenotypic variance (PV) collectively for relative root length (RRL) and relative shoot length (RSL) that served as potential DT indicators. Among these, eight loci corresponded to previously reported QTLs, whereas 32 loci were therefore novel. The identified QTLs with their corresponding alleles for RRL and RSL were organized into QTL-allele matrices, depicting the comprehensive DT genetic architecture of the three parents/half-sib population. From the matrices, we predicted the possible best/optimal genotype with weighted average value (WAV) 1.553 over two indicators, while for the top 10 single crosses among RILs with 95th percentile WAV was 1.218–1.257, transgressive over the parents (0.693–0.794) yet much less than 1.553. From the detected QTL-allele system, 65 potential candidate genes collectively for both indicators explaining on an average of 24.41% PV were annotated and χ2-tested as a DT candidate gene system involving nine biological processes.

中文翻译：

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使用大豆半同胞群体（Glycine max (L.) Merr.）中的多位点多等位基因全基因组关联分析对苗期耐旱性的 QTL 等位基因系统进行分子表征和优化基因型设计

对耐旱性 (DT) 的整个遗传结构进行表征是育种者面临的一个长期挑战。在这里，我们开发了一个半同胞群体，由两个重组近交系（RIL）群体的 404 个品系组成，M8206 作为联合亲本（M8206 × TongShan 和正阳 × M8206），并在沙培养下测试其 DT。使用以 ≥0.01 次要等位基因频率过滤的限制性位点相关 DNA 测序对该群体进行测序；获得了 55,936 个单核苷酸多态性 (SNP)，并组装成 6137 个 SNPLDB (SNP 连锁不平衡块)。以错误和假阳性对照为特征的受限两阶段多位点全基因组关联分析确定了 40 个 QTL，平均有 34 个等位基因 93 个。75% 的表型变异 (PV) 共同用于作为潜在 DT 指标的相对根长 (RRL) 和相对芽长 (RSL)。其中，8 个位点对应于先前报道的 QTL，而 32 个位点因此是新的。已鉴定的 QTL 及其对应的 RRL 和 RSL 等位基因被组织成 QTL 等位基因矩阵，描绘了三个亲本/半同胞群体的综合 DT 遗传结构。从矩阵中，我们预测了两个指标的加权平均值（WAV）为 1.553 的可能的最佳/最佳基因型，而对于 RIL 中的前 10 个单交，有 95 个 已鉴定的 QTL 及其对应的 RRL 和 RSL 等位基因被组织成 QTL 等位基因矩阵，描绘了三个亲本/半同胞群体的综合 DT 遗传结构。从矩阵中，我们预测了两个指标的加权平均值（WAV）为 1.553 的可能的最佳/最佳基因型，而对于 RIL 中的前 10 个单交，有 95 个 已鉴定的 QTL 及其对应的 RRL 和 RSL 等位基因被组织成 QTL 等位基因矩阵，描绘了三个亲本/半同胞群体的综合 DT 遗传结构。从矩阵中，我们预测了两个指标的加权平均值（WAV）为 1.553 的可能的最佳/最佳基因型，而对于 RIL 中的前 10 个单交，有 95 个th百分位 WAV 为 1.218–1.257，超过父母 (0.693–0.794) 但远低于 1.553。从检测到的 QTL 等位基因系统中，注释了两个指标的 65 个潜在候选基因，平均解释了 24.41% PV。χ2-作为涉及九个生物过程的 DT 候选基因系统进行测试。