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

• Published in: The Plant journal : for cell and molecular biology Vol. 70; no. 5; pp. 769 - 782
• Main Authors: Huang, Chao‐Li, Hung, Cheng‐Yu, Chiang, Yu‐Chung, Hwang, Chi‐Chuan, Hsu, Tsai‐Wen, Huang, Chi‐Chun, Hung, Kuo‐Hsiang, Tsai, Kun‐Chan, Wang, Kuo‐Hsiung, Osada, Naoki, Schaal, Barbara Anna, Chiang, Tzen‐Yuh
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.06.2012; Blackwell
• Subjects: Alleles; Biological and medical sciences; Crops, Agricultural - genetics; Crops, Agricultural - metabolism; Crops, Agricultural - physiology; Crossing Over, Genetic; diversifying selection; domestication; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Regulation, Plant; Genes, Plant; Genetic linkage; Genetic Loci; Genetic Variation; geographical subdivision; Geography; Linkage Disequilibrium; Oryza - genetics; Oryza - metabolism; Oryza - physiology; Photoperiod; photoperiod pathway genes; Phytochrome B - genetics; Phytochrome B - metabolism; Plant biology; Plant physiology and development; Plant Proteins - genetics; Plant Proteins - metabolism; Polymorphism; Rice; Selection, Genetic; Monocotyledones; diversifying selection; Domestication; Artificial selection; Photoperiod; Linkage equilibrium; rice; Natural selection; Oryza sativa; photoperiod pathway genes; geographical subdivision; Gene; Gramineae; Angiospermae; Spermatophyta; linkage disequilibrium
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313X.2012.04915.x

Summary 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.