Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31°N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non‐functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.
亚洲稻由籼稻和粳稻两个主要的亚种组成，两者具有显著的生理差异，分别适应于不同的纬度。光周期敏感性基因可能是受纬度选择的靶基因。通过对栽培稻和普通野生稻核苷酸多态模式的分析，我们对四个主要光周期途径基因PhyB、Hd1、Hd3a 和Ehd1 的自然和人工选择足迹进行了分析。根据北回归线（TOC）划分的光周期基因，在热带和亚热带普通野生稻中具有发现。除了PhyB，所有基因均存在很久之前就发生分化的进化枝，并且进化枝与根据纬度划分结果是一致的，基因可能受到歧化选择。籼稻表现出与热带野生稻基因更紧密的关系，粳稻分布更为广泛，因而表现出更为复杂的从野生稻分化的模式，这反应了不同农业需求与作物产量间的关系。粳稻中除了Hd3a 外，其他基因的遗传分化均发生在TOC，而Hd3a 的地理分化出现在31°N，这可能是光周期差异导致的。光周期基因的其他许多特征显示出受到驯化的迹象，包括基因内连锁不平衡（LD）增加，栽培水稻中Hd1 突变高频发生及重复发生，热带和亚热带Hd1 等位基因的交叉，以及粳稻和籼稻中Hd1 和Hd3a 间显著的LD。