Genetic structure of Oryza rufipogon Griff. in China

Abstract

Oryza rufipogon Griff. (common wild rice; CWR) is the ancestor of Asian cultivated rice (Oryza sativa L.). Investigation of the genetic structure and diversity of CWR in China will provide information about the origin of cultivated rice and the grain quality and yield. In this study, we used 36 simple sequence repeat (SSR) markers to assay 889 accessions, which were highly representative of whole germplasm in China. The analysis revealed a hierarchical genetic structure within CWR. First, CWR has diverged into two ecotypic populations, a south subtropical population (SSP) and a middle subtropical population (MSP), probably owing to natural selection by the different climates. The distribution of specific alleles and haplotypes indicated that Chinese CWR had both indica-like and japonica-like variations; the SSP was an indica-like type, whereas the MSP was more japonica-like. The SSP and MSP further diverged into five (HN, GD-GX1, GX2, FJ and YN) and two (JX-HuN1 and HuN2) geographical populations, respectively. The genetic data suggest the isolation by distance, although water systems also appear to play an important role in the formation of homogenous populations, and occasionally landscape was also involved. The population GD-GX1, which grew widely in Guangdong and Guangxi provinces, was the largest geographical population in China. It had a high level of genetic diversity (GD) and the closest genetic relationship with other inferred populations. The population HN, with the smallest SSR molecular weights and the highest level of GD, may be the most ancestral population.

Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon

“…; Wang et al . ). SNPs and indels have also been used in the rice genetic diversity researches recently (Yamanaka et al .…”

Origin of Oryza sativa in China Inferred by Nucleotide Polymorphisms of Organelle DNA

“…sativa and O . rufipogon has been investigated based on molecular markers, SNPs and indels [33], [34], [35], [36], [37]. These researches had suggested that there was a bottleneck in the domestication of O .…”

Landscape-Scale Genetic Structure of Wild Rice Zizania latifolia: The Roles of Rivers, Mountains and Fragmentation

“…However, the fragmented nature of wetlands in this area has resulted in the hydrological disconnectivity between ponds or marshes and the arteries of rivers, which could have hindered the dispersal via seeds or propagules of the plant. Although episodic floods can result in temporary hydrological connectivity and facilitate the gene exchange, as suggested in O. rufipogon populations (Wang et al, 2008), high values of F ST and D est among pairs of populations along the same river indicate that episodic floods were not an effective path of dispersal for Z. latifolia.…”