Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, 29634, USA.
Advanced Plant Technology, Clemson University, Clemson, South Carolina, 29634, USA.
Plant J. 2022 Aug;111(3):888-904. doi: 10.1111/tpj.15853. Epub 2022 Jul 5.
Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole-genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25-72×), enabling the development of a high-density genomic marker set of 43 983 694 variants including single-nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5-kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six F peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.
关联作图面板是理解表型多样性遗传基础的基础资源，通过探索不同材料的遗传变异来推进植物育种。我们报告了来自 Sorghum Association Panel（SAP）的 400 个高粱（Sorghum bicolor（L.）Moench）品系的全基因组测序（WGS），平均覆盖度为 38×（25-72×），从而开发了一个包含 43983694 个变体的高密度基因组标记集，包括单核苷酸多态性（约 3800 万）、插入/缺失（约 500 万）和拷贝数变异（CNV）（约 170000）。我们观察到插入缺失中缺失略多，而 CNV 中缺失的发生率远高于插入缺失。与以前的低密度标记集相比，这个新的标记集能够识别出几个新的植物高度和单宁含量的假定基因组关联。WGS 鉴定和评分了可用测序（GBS）数据未捕获变体的 5-kb -bin 中的变体，基因组中有一半的-bin 属于这一类。与使用 GBS 标记相比，WGS 标记平均将基因组最佳无偏线性预测器（GBLUP）模型的预测能力提高了 30%。我们在驯化过程中由于进化分歧而形成的亚群中鉴定出了 18 个选择峰，并且在 SAP 内的转化系和选育系之间发现了 6 个 F 峰，它们与与历史选择相关的峰不同。这个群体已经并将继续作为高粱研究的重要公共资源，证明了改进现有基因组资源的价值。
