Data from: Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)

Background: Domestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice. Results: We performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved ‘hotspots’ in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum. Conclusions: Intersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.

背景： 驯化在塑造栽培谷类作物的花序与株高性状方面发挥了关键作用。本研究借助数量性状基因座（Quantitative Trait Locus, QTL）元分析、对502份多样化高粱种质资源开展的系统发育分析、针对样本量为354的高粱关联作图群体开展的全基因组关联分析（Genome-Wide Association Study, GWAS），以及比较分析数据，解析了高粱与水稻驯化性状的遗传基础。
结果： 我们对高粱的6个花序形态相关性状与6个株高相关性状开展了全基因组关联分析，并分别对比了通过GWAS与QTL定位所鉴定到的性状关联基因组区域。在筛选选择信号的过程中，我们鉴定到了可能与高粱株高、开花期及果皮颜色驯化相关的基因组区域。跨类群比较研究显示，高粱与水稻在芒的有无与果皮颜色性状上存在功能保守的"热点区域"，这类区域并非由单个对应基因调控，而是可能代表了共调控基因簇。我们还发现，自谷类作物共同祖先约7000万年前及更早发生基因组复制事件以来，部分同源区域仍保留了株高与开花期的相似功能。在多数此类部分同源QTL区间对中，现代高粱仅单个QTL区间呈现出强烈的选择信号。
结论： QTL定位、全基因组关联分析与比较数据的整合分析，深化了我们对高粱花序与株高相关性状遗传决定因子的认知，并为高粱与水稻的比较研究拓展了新维度。