Originally published as Genetics Published Articles Ahead of Print on January 16, 2005.

Genetics, Vol. 169, 1631-1638, March 2005, Copyright © 2005
doi:10.1534/genetics.104.035642

Genetic Structure and Diversity in Oryza sativa L.

Amanda J. Garris^*,1, Thomas H. Tai^,2, Jason Coburn^*, Steve Kresovich^* and Susan McCouch^*,3

^* Plant Breeding Department, Cornell University, Ithaca, New York 14853-1901
U.S. Department of Agriculture-Agricultural Research Service Dale Bumpers National Rice Research Center, Stuttgart, Arizona 72160

³ Corresponding author: 162 Emerson Hall, Cornell University, Ithaca, NY 14853.
E-mail: srm4{at}cornell.edu

The population structure of domesticated species is influenced by the natural history of the populations of predomesticated ancestors, as well as by the breeding system and complexity of the breeding practices exercised 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 234 accessions of rice was genotyped at 169 nuclear SSRs 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 indica and the aus and among the tropical japonica, temperate japonica, and aromatic groups. Group differences can be explained through contrasting demographic histories. With the availability of rice genome sequence, coupled with 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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