title: Footprints of natural and artificial selection for photoperiod pathway genes in Oryza.
abstract: 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.
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Chao-Li
authors.initials: CL
authors.lastname: Huang
authors.forename: Cheng-Yu
authors.initials: CY
authors.lastname: Hung
authors.forename: Yu-Chung
authors.initials: YC
authors.lastname: Chiang
authors.forename: Chi-Chuan
authors.initials: CC
authors.lastname: Hwang
authors.forename: Tsai-Wen
authors.initials: TW
authors.lastname: Hsu
authors.forename: Chi-Chun
authors.initials: CC
authors.lastname: Huang
authors.forename: Kuo-Hsiang
authors.initials: KH
authors.lastname: Hung
authors.forename: Kun-Chan
authors.initials: KC
authors.lastname: Tsai
authors.forename: Kuo-Hsiung
authors.initials: KH
authors.lastname: Wang
authors.forename: Naoki
authors.initials: N
authors.lastname: Osada
authors.forename: Barbara Anna
authors.initials: BA
authors.lastname: Schaal
authors.forename: Tzen-Yuh
authors.initials: TY
authors.lastname: Chiang
mesh_terms: D000483:Alleles; D018556:Crops, Agricultural / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D003434:Crossing Over, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056426:Genetic Loci; D014644:Genetic Variation; D005843:Geography; D015810:Linkage Disequilibrium; D012275:Oryza / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D017440:Photoperiod; D051939:Phytochrome B / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012641:Selection, Genetic
chemical_list: D010940:Plant Proteins; D051939:Phytochrome B