Scientists Trace Footprints of Photoperiod Pathway Genes in Oryza

Asian rice (Oryza sativa) has two known subspecies, indica and japonica, which have different physiological characteristics and are adapted to different latitudes. Genes for photoperiod sensitivity are usual targets of selection along latitude. National Cheng Kung University scientist Chao-Li Huang and a team of researchers assessed 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 studying the patterns of nucleotide polymorphisms in cultivated and wild rice.

Geographical subdivision between tropical and subtropical O. rufipogon was present for all othe genes in plants divided by the Tropic of Cancer (TOC). All the genes except for PhyB were characterized by the presence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. O. indica exhibited a linkage with the tropical O. rufipogon for all genes. On the other hand, O. japonica, which has a much wider range of distribution, showed complicated patterns of differentiation from O. rufipogon, which exhibited different agricultural needs for crop yield. In O. japonica, all genes except Hd3a were genetically differentiated at the TOC, while geographical subdivision occurred in Hd3a, probably due to different photoperiods.

Other characteristics of the photoperiod genes also revealed differences due to domestication such as high linkage disequilibrium (LV) 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 O. japonica and indica.

Read more details about the study at http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2012.04915.x/abstract