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Plant and Cell Physiology Advance Access published online on August 12, 2008
Plant and Cell Physiology, 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 e-mail: journals.permissions@oxfordjournals.org

Abduction of 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: Dr. Takeshi Izawa, Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan, TEL.: +81-29-838-7446, FAX: none, E-mail: tizawa{at}nias.affrc.go.jp


  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 or 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 distribution of rice. These polymorphisms were assigned by using genome-wide patterns of restriction fragment length polymorphisms (RFLP) and the local origins of the landraces. The results led us to abduct 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 the beginning of the domestication process was highlighted. Independent artificial selections of two defective Rd alleles were abducted, suggesting a role of Rd other than in pigment synthesis during rice domestication.

Keywords: abduction - domestication - evolution - genome - RFLP - rice (Oryza sativa)

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