Evolution and Association Analysis of <em>Ghd7</em> in Rice

Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise π and θ in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.株高、抽穗期与产量是水稻遗传改良的核心目标。Ghd7是一种可同时调控上述性状的多效基因。本研究利用104份栽培稻（Oryza sativa）种质材料与3份普通野生稻（Oryza rufipogon，缩写O.rufipogon）种质，分析了Ghd7的演化特征及其与株高、抽穗期和产量的关联。在104份栽培稻材料中，研究人员在Ghd7基因3932 bp的DNA片段内检测到76个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）与6个插入缺失变异。启动子区域的成对核苷酸多样性π与Wattersonθ值更高，表明Ghd7启动子具有高度多样化的序列特征。本研究共鉴定到16种单倍型与8种Ghd7蛋白质亚型。不同单倍型间的单核苷酸多态性差异显示，Ghd7起源于两个截然不同的祖先基因库，且籼稻与粳稻品种分别经历了独立的驯化进程。除此前已报道的、可引发多性状表型改变的Ghd7第一外显子提前终止突变外，本研究通过基于群体结构的关联分析，还发现了另一种功能型C/T突变（SNP S_555）。SNP S_555位于基因启动子区域，可能通过改变基因表达水平进而影响株高。此外，另有7个处于完全连锁状态的单核苷酸多态位点被发现与每穗小穗数显著相关，且该关联不受光周期条件影响。上述关联分析结果为Ghd7在水稻育种项目中的灵活应用提供了潜在可能。