Genetic Structure and Diversity in Oryza sativa L.

TLDR

The population structure of domesticated rice is shaped by the natural history of its ancestors and human breeding practices, with a well‑established divergence between indica and japonica and evidence of finer genetic substructure. The study aims to resolve rice genetic structure and evolutionary relationships and to develop a population‑based framework for molecular diversity analysis using the genome sequence and extensive genetic resources. The authors genotyped 234 rice accessions at 169 nuclear SSRs and two chloroplast loci and analyzed the data to resolve genetic structure and evolutionary relationships. Five distinct groups were identified—indica, aus, aromatic, temperate japonica, and tropical japonica—showing closer evolutionary relationships between indica and aus and among tropical, temperate, and aromatic groups, with group differences attributable to contrasting demographic histories.

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.