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United States Department of Agriculture

Agricultural Research Service


item Garris, Amanda
item Tai, Thomas
item Coburn, Jason
item Kresovich, Steve
item Mccouch, Susan

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/1/2005
Publication Date: 3/1/2005
Citation: Garris, A.J., Tai, T., Coburn, J., Kresovich, S., Mccouch, S.R. 2005. Genetic structure and diversity in oryza sativa l.. Genetics. 169: 1631-1638.

Interpretive Summary: The population structure of rice (Oryza sativa L.) was examined using molecular marker data (169 nuclear DNA microsatellite markers and two chloroplast DNA markers) from 232 accessions of rice. Five distinct groups were detected: indica, tropical japonica, temperate japonica, aus, and aromatics. Among these groups, the aus and indica are more closely related while the aromatics cluster with the tropical and temperate japonica groups. The framework developed here will facilitate studies to address the origin and diversity of genepools in cultivated Asian rice and provide a basis for characterizing the genes that distinguish them.

Technical Abstract: Characterization of population structure provides a framework for the interpretation of molecular diversity in an evolutionary context. The population structure of domesticated species is influenced by the natural history of the populations of pre-domesticated ancestors, as well as by the breeding system and complexity of the breeding practices used by humans. Within Oryza sativa, there is an ancient and well established divergence between the two major subspecies, indica and japonica, but finer levels of genetic structure are suggested by the breeding history. In this study, a sample of 232 accessions of rice was genotyped at 169 nuclear and two chloroplast loci. The data were analyzed to resolve the genetic structure and to interpret the evolutionary relationships between groups. Five distinct groups were detected, corresponding to indica, aus, aromatic, temperate japonica and tropical japonica rices. Nuclear and chloroplast data support a closer evolutionary relationship between the aus with indica and the aromatic with tropical and temperate japonica groups. Group differences can be explained through contrasting demographic histories. Given the availability of rice genome sequence and a large collection of publicly available genetic resources, it is of interest to develop a population-based framework for the molecular analysis of diversity in O. sativa.

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