Genetic Structure and Diversity in Oryza sativa L

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 diverge...

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Bibliographic Details
Published in:Genetics (Austin) 2005-03, Vol.169 (3), p.1631-1638
Main Authors: Garris, Amanda J, Tai, Thomas H, Coburn, Jason, Kresovich, Steve, McCouch, Susan
Format: Article
Language:English
Subjects:
Base Sequence
Breeding
Cell Nucleus - genetics
Chloroplasts - genetics
DNA Primers
Genetic Variation
Genome, Plant
Humans
Investigations
Oryza - classification
Oryza - genetics
Oryza sativa
Phylogeny
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Summary: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.
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1534/genetics.104.035642