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. 2005 Mar;169(3):1631-8.
doi: 10.1534/genetics.104.035642. Epub 2005 Jan 16.

Genetic structure and diversity in Oryza sativa L

Amanda J Garris  1 , Thomas H Tai, Jason Coburn, Steve Kresovich, Susan McCouch
Affiliations

Genetic structure and diversity in Oryza sativa L

Amanda J Garris et al. Genetics. 2005 Mar.

Abstract

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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Figures

F<sc>igure</sc> 1.—
Figure 1.—
Unrooted neighbor-joining tree based on C.S. Chord (Cavalli-Sforza and Edwards 1967) based on 169 nuclear SSRs. The key relates the color of the line to the chloroplast haplotype based on ORF100 and PS-ID sequences. Admixed individuals are identified with an asterisk. Bootstrap values (out of 100) are indicated at the branch points.
F<sc>igure</sc> 2.—
Figure 2.—
Model-based ancestry for each accession. Color codes are as follows: aromatic, purple; aus, orange; indica, yellow; temperate japonica, dark blue; and tropical japonica, light blue.
See this image and copyright information in PMC

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