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Plant and Cell Physiology Advance Access originally published online on August 12, 2008
Plant and Cell Physiology 2008 49(9):1283-1293; doi:10.1093/pcp/pcn118
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© The Author 2008. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Rapid Paper

Inference of the japonica Rice Domestication Process from the Distribution of Six Functional Nucleotide Polymorphisms of Domestication-Related Genes in Various Landraces and Modern Cultivars

Saeko Konishi1, Kaworu Ebana2 and Takeshi Izawa1,*

1 Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
2 QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan

*Corresponding author: E-mail, tizawa{at}nias.affrc.go.jp. Fax, +81-29-838-7446


  Abstract

Crop domestication can serve as a model of plant evolutionary processes. It involves a series of selection events from standing natural variation and newly occurring mutations and combinations of mutations as a result of natural crossings in populations during local adaptation and propagation of plant lines to other cultivation areas. Our earlier identification of three functional nucleotide polymorphisms (FNPs) of distinct genes involved in the rice domestication process led us to propose a model of the japonica rice domestication process. Here, we examined three more FNPs in two domestication-related genes involved in pigment synthesis during the development of seed pericarp color (Rc and Rd) in 91 landraces (and some modern cultivars) of japonica rice collected from throughout the area of distribution of rice. These polymorphisms were assigned by using genome-wide patterns of restriction fragment length polymorphisms (RFLPs) and the local origins of the landraces. The results led us to infer the process of japonica rice domestication in more detail and propose a more refined model of the japonica domestication process. In this model, the critical role of the Rc FNP at an early step of the domestication process was highlighted. Independent artificial selections of two defective Rd alleles were found, suggesting a role for Rd other than in pigment synthesis during rice domestication.

Keywords: Domestication - Evolution - Genome - RFLP - Rice (Oryza sativa)

Abbreviations: bHLH, basic helix–loop–helix; DFR, dihydroflavonol-4-reductase; FNP, funcional nucleotide polymorphism; ORF, open reading frame; RFLP, restriction fragment length polymorphism; SINE, short interspersed element

(Received July 17, 2008; Accepted August 8, 2008)
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