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PMID: 19674325 Published · ppublish English Historical Article Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Selection on grain shattering genes and rates of rice domestication.

The New phytologist ·Vol. 184 ·No. 3 ·2009-11-00 ·Pages 708-720

Zhang LB, Zhu Q, Wu ZQ, Ross-Ibarra J, Gaut BS, Ge S, Sang T

Abstract

Molecular cloning of major quantitative trait loci (QTLs) responsible for the reduction of rice grain shattering, a hallmark of cereal domestication, provided opportunities for in-depth investigation of domestication processes. Here, we studied nucleotide variation at the shattering loci, sh4 and qSH1, for cultivated rice, Oryza sativa ssp. indica and Oryza sativa ssp. japonica, and the wild progenitors, Oryza nivara andOryza rufipogon. The nonshattering sh4 allele was fixed in all rice cultivars, with levels of sequence polymorphism significantly reduced in both indica and japonica cultivars relative to the wild progenitors. The sh4 phylogeny together with the neutrality tests and coalescent simulations suggested that sh4 had a single origin and was fixed by artificial selection during the domestication of rice. Selection on qSH1 was not detected in indica and remained unclear in japonica. Selection on sh4 could be strong enough to have driven its fixation in a population of cultivated rice within a period of c. 100 yr. The slow fixation of the nonshattering phenotype observed at the archeological sites might be a result of relatively weak selection on mutations other than sh4 in early rice cultivation. The fixation of sh4 could have been achieved later through strong selection for the optimal phenotype.

MeSH Terms
Agriculture/history Base Sequence Breeding/history Cloning, Molecular DNA, Plant/genetics Genes, Plant Genetic Variation History, Ancient Models, Genetic Oryza/classification,genetics,growth & development,history Phenotype Phylogeny Polymorphism, Single Nucleotide Quantitative Trait Loci Selection, Genetic Time Factors
Chemicals
DNA, Plant
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Zhang Lin-Bin
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
Zhu Qihui
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
Wu Zhi-Qiang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
Ross-Ibarra Jeffrey
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
Gaut Brandon S
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
Ge Song
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
Sang Tao
Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
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Article Info
Journal
The New phytologist
Abbr.
New Phytol
ISSN
1469-8137
DOI
10.1111/j.1469-8137.2009.02984.x
Published
2009-11-00
Epub
2009-00-05
Pages
708-720
Language
English
Region
England
NLM ID
9882884
Subset
IM
External Links
PubMed source DOI: 10.1111/j.1469-8137.2009.02984.x View journal details
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