Academic journal article Genetics

Genetic Structure and Diversity in Oryza Sativa L

Academic journal article Genetics

Genetic Structure and Diversity in Oryza Sativa L

Article excerpt

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.

ASIAN cultivated rice ( Oryza saliva L.) holds a unique position among domesticated crop species in that it is both a critical food staple and the first fully sequenced crop genome. Rice is consumed as a grain almost exclusively by humans, supplying 20% of daily calories for the world population (World Rice Statistics, http:/ywww.irri.org; FAOSTAT, http://apps.fao.org). As a model organism with a fully sequenced genome, rice affords unique opportunities to use genomic approaches to study its domestication, adaptive diversity, and the history of crop improvement.

Archeological evidence supports a similar time of domestication for rice, wheat (Triticum aestivum), and maize (Zea mays ssp. mays), 5-10,000 years ago, but the evolutionary histories of these cereals differ in several significant ways (SOLHEIM 1972; SHARMA and MANDA 1980; ZOHARY and HOPF 2000; PIPERNO and FLANNERY 2001). Recent studies tracing the molecular evolution of maize offer several points of comparison that help illuminate the genetic history of rice. Unlike maize, rice is predominantly autogamous and, hence, gene flow is restricted. As a result, geographically or ecologically distinct groups of rice are expected to show greater genetic differentiation than would be the case in an outcrossing species. Because of fewer opportunities for cross-pollination, the structure of landraces in rice and maize is also predicted to be fundamentally different. A greater proportion of diversity is expected to reside in differences between homozygous lines within a heterogenous landrace in rice (OLUFOWOTE et al. 1997) compared to the distribution of diversity among heterozygous individuals within a landrace of maize (LABATE et al. 2003). In addition, evidence suggests that the two primary subspecies of rice, indica and japonica, are the products of separate domestication events from the ancestral species, O. rufipogon, a hypothesis initially based on studies of biochemical traits (secOND 1982) and hybrid sterility (KATO et al. 1928) and subsequently supported by molecular analyses (Doi et al. 2002; CHENG et al 2003). This is in contrast to the single domestication event that led to the evolution of modern maize (MATSUOKA et al. 2002).

At all levels of analysis, the differences between the indica and japonica subspecies are very apparent. Differences between nonsticky (indica) and sticky (japonica) rices are documented in Chinese literature as early as 100 AD (MATSUO etal. 1997). In ecogeographical terms, indica are primarily known as lowland rices that are grown throughout tropical Asia, while japonica are typically found in temperate East Asia, upland areas of Southeast Asia, and high elevations in South Asia. …

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