Genetic structure and diversity in Oryza sativa L

¹ Cornell University
² USDA-ARS DBNRRC

^* To whom correspondence should be addressed. E-mail: srm4{at}cornell.edu.

Submitted on September 2, 2004
Revised on October 6, 2004
Accepted on 30 November 2004

	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 exercised by humans. Within Oryza sativa, there is an ancient and well-established divergence between the two major sub-species, 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 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. 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.

Key Words: diversity, population genetics, rice

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