Footprints of natural and artificial selection for photoperiod pathway genes in Oryza

Chao Li Huang, Cheng Yu Hung, Yu Chung Chiang, Chi Chuan Hwang, Tsai Wen Hsu, Chi Chun Huang, Kuo Hsiang Hung, Kun Chan Tsai, Kuo Hsiung Wang, Naoki Osada, Barbara Anna Schaal, Tzen Yuh Chiang

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)769-782
Number of pages14
JournalPlant Journal
Volume70
Issue number5
DOIs
Publication statusPublished - 2012 Jun

All Science Journal Classification (ASJC) codes

  • Genetics
  • Plant Science
  • Cell Biology

Fingerprint Dive into the research topics of 'Footprints of natural and artificial selection for photoperiod pathway genes in Oryza'. Together they form a unique fingerprint.

Cite this