MBE Advance Access published online on January 11, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm005
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Research Article |
Multilocus Analysis of Nucleotide Variation of Oryza sativa and Its Wild relatives: Severe Bottleneck During Domestication of Rice
1 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
2 Center for Bioinformatics, State Key Laboratory of Plant Genetic Engineering and Protein Engineering and College of Life Sciences, Peking University, Beijing 100871, China
3 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA
Corresponding author: Song Ge, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China, E-mail: gesong{at}ibcas.ac.cn, Tel: +86-10-62836097, Fax: +86-10-62590843
Accepted for publication January 4, 2007.
Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationship and demographic history of O. sativa and its close relatives (O. rufipogon and O. nivara), we investigated nucleotide diversity data from 10 unlinked nuclear loci in species-wide samples of these species. The results indicated that O. rufipogon and O. nivara possessed comparable levels of nucleotide variation (
sil = 0.0077
0.0095) compared to the relatives of other crops. In contrast, nucleotide diversity of O. sativa was as low as sil = 0.0024 and even lower (sil = 0.0021 for indica and 0.0011 for japonica) if we consider the two subspecies separately. Overall, only 20% to 10% of the diversity in the wild species was retained in two subspecies of the cultivated rice (indica and japonica), respectively. Because statistic tests did not reject the assumption of neutrality for all ten loci, we further used coalescent to simulate bottlenecks under various lengths and population sizes to better understand the domestication process. Consistent with the dramatic reduction in nucleotide diversity, we detected a severe domestication bottleneck and demonstrated that the sequence diversity currently found in the rice genome could be explained by a founding population of 1500 individuals if the initial domestication event occurred over a 3000-year period. Phylogenetic analyses revealed close genetic relationships and ambiguous species boundary of O. rufipogon and O. nivara, providing additional evidence to treat them as two ecotypes of a single species. Lowest linkage disequilibrium (LD) was found in the perennial O. rufipogon where the r2 value dropped to a negligible level within 400 bp, and the highest in the japonica rice where LD extended to the entirely sequenced region ( 900 bp), implying that LD mapping by genome scans may not be feasible in wild rice due to the high density of markers needed.
Key Words: Nucleotide diversity • domestication • bottleneck • linkage disequilibrium • Oryza sativa • O. rufipogon
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