| 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 <i>Oryza sativa</i>, there is an ancient and well-established divergence between the two major subspecies, <i>indica</i> and <i>japonica</i>, 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 <i>indica</i>, <i>aus</i>, <i>aromatic</i>, <i>temperate japonica</i>, and <i>tropical japonica</i> rices. Nuclear and chloroplast data support a closer evolutionary relationship between the <i>indica</i> and the <i>aus</i> and among the <i>tropical japonica</i>, <i>temperate japonica</i>, and <i>aromatic</i> 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 <i>O. sativa</i>.
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