Mining crop genomic variation can facilitate the genetic research of complex traits and molecular breeding. In sorghum [Sorghum bicolor L. (Moench)], several large‐scale single nucleotide polymorphism (SNP) datasets have been generated using genotyping‐by‐sequencing of ApeKI reduced representation libraries. However, data reuse has been impeded by differences in reference genome coordinates among datasets. To facilitate reuse of these data, we constructed and characterized an integrated 459,304‐SNP dataset for 10,323 sorghum genotypes on the version 3.1 reference genome. The SNP distribution showed high enrichment in subtelomeric chromosome arms and in genic regions (48% of SNPs) and was highly correlated (r = 0.82) to the distribution of ApeKI restriction sites. The genetic structure reflected population differences by botanical race, as well as familial structure among recombinant inbred lines (RILs). Faster linkage disequilibrium decay was observed in the diversity panel than in the RILs, as expected, given the greater opportunity for recombination in diverse populations. To validate the quality and utility of the integrated SNP dataset, we used genome‐wide association studies (GWAS) of genebank phenotype data, precisely mapping several known genes (e.g Y1 and Z) and identifying novel associations for other traits. We further validated the dataset with GWAS of new and published plant height and flowering time data in a nested association mapping population, precisely mapping known genes and identifying epistatic interactions underlying both traits. These findings validate this integrated SNP dataset as a useful genomics resource for sorghum genetics and breeding.

中文翻译：

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超过10,000个高粱基因型的按测序综合基因分型多态性图。

挖掘农作物基因组变异可以促进复杂性状和分子育种的遗传研究。在高粱[ Sorghum bicolor L.（Moench）]中，使用Ape KI简化表征库的基因分型序列，已经生成了几个大规模的单核苷酸多态性（SNP）数据集。但是，数据重用已受到数据集之间参考基因组坐标差异的阻碍。为了促进这些数据的重用，我们为3.1版参考基因组上的10,323个高粱基因型构建了459,304-SNP集成数据集并对其进行了特征化。SNP分布在亚端粒染色体臂和基因区域（占SNP的48％）中高度富集，与Ape的分布高度相关（r = 0.82）。KI限制位点。遗传结构反映了植物种族之间的种群差异，以及重组近交系（RIL）之间的家族结构。鉴于预期，鉴于多样性群体中重组的机会更大，因此在多样性面板中观察到的连锁不平衡衰减更快。为了验证整合的SNP数据集的质量和实用性，我们使用了种质库表型数据的全基因组关联研究（GWAS），精确定位了多个已知基因（例如Y1和Z），并找出其他特质的新颖联想。我们使用嵌套关联映射种群中新的和已发布的植物高度和开花时间数据的GWAS进一步验证了数据集，精确地映射了已知基因并确定了这两个性状的上位相互作用。这些发现证实了该整合的SNP数据集是高粱遗传和育种的有用的基因组资源。