Genetic Structure and Diversity in Oryza sativa L.

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.

Phylogeography of Asian wild rice, Oryza rufipogon , reveals multiple independent domestications of cultivated rice, Oryza sativa

“…Comparison of levels of diversity between wild and cultivated rice indicate that cultivated rice has a reduced subset of the total genetic variation of O. rufipogon; these results are consistent with other genetic studies on rice diversity (19). O. sativa cultivars, whether elite or landrace, share only a subset of haplotypes with O. rufipogon and are most often associated with tip positions in the gene networks ( Figs.…”

“…With only a single sample of wild rice possessing haplotype C, the geographical origin of haplotype C is unclear. However, temperate japonica rice has been shown previously to be a subset of total japonica diversity and likely shares a common domestication event with the javanica rice sampled in haplotype B (19).…”

“…These two subspecies are commonly associated with differences in growth habitat as well, with indica rice usually found in the lowlands of tropical Asia and japonica rice typically found in the upland hills of southern China, southeast Asia, and Indonesia, as well as rice outside of Asia (Africa, North America, and South America) (13). O. sativa japonica can be further differentiated into tropical (javanica) and temperate (japonica) forms, with the temperate form appearing to be a derivative of tropical japonica (19). In addition to the two major races, several other minor rice types have been identified with genetic markers (19)(20)(21) and include the upland drought-tolerant Aus cultivars of India and Bangladesh, the deep-water Ashinas varieties of Bangladesh, and the aromatic basmati rice of India as well as many others.…”

“…O. sativa japonica can be further differentiated into tropical (javanica) and temperate (japonica) forms, with the temperate form appearing to be a derivative of tropical japonica (19). In addition to the two major races, several other minor rice types have been identified with genetic markers (19)(20)(21) and include the upland drought-tolerant Aus cultivars of India and Bangladesh, the deep-water Ashinas varieties of Bangladesh, and the aromatic basmati rice of India as well as many others. Whether all these different rice types have arisen from a single domestication event or are the result of multiple domestications remains unknown.…”

Molecular Characterization of Parental Lines of Rice Aiming to Address High Yield and Nutritional Quality Under Drought and Cold Stress Condition

“…On the other hand, monomorphism of the markers reflected genetic closeness of the cultivars. In closely related cultivars, these phenomena are frequent and are reported in many previous studies [22,[24][25][26]. However, comparatively high average PIC value (0.758) with a range from 0.511 to 0.861 that was calculated based on 51 polymorphic makers indicated that the cultivars are much diverged.…”