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12 results for “Oryza rufipogon”
SNP data for F2 population derived from Oryza rufipogon and O. nivara
<p>To elucidate the genetic architecture underlying phenotypic divergence is essential to the understanding of ecological adaptation and speciation. Two wild rice species (<em>O. rufipogon</em> and <em>O. nivara</em>) are a progenitor-daughter species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolved linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F<sub>2</sub> population generated from a cross between the perennial <em>O. rufipogon</em> and annual <em>O. nivara</em>. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots), with each involving multiple adaptive traits, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and <em>v</em>-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits.</p>
Study on the mating systems of wild rice Oryza rufipogon and O. nivara and their effects on population genetic variation
<p>As the wild ancestors of Asian cultivated rice,<em> Oryza rufipogon</em> Griff. and <em>O. nivara</em> Sharma et Shastry serve as valuable germplasms for rice breeding. Mating systems are important in shaping the level and pattern of population genetic variation, and are crucial for germplasm conservation. We genotyped 12 simple sequence repeats (SSR) markers for a large number of maternal plants and seeds collected from <em>O</em>.<em> rufipogon</em> and <em>O. nivara</em> populations distributed in Southeast Aisa and South China. Based on the 12 SSR markers, we estimated the outcrossing rates and other parameters of the mixed-mating model for the two wild rice species. We also assessed the level of genetic diversity and population structure for parental populations of <em>O</em>.<em> rufipogon</em> and <em>O. nivara</em>. Our study could facilitate <em>in situ</em> and <em>ex situ</em> conservation, and the utilization of these valuable germplasm resources.</p>
SNP data for F2 population derived from Oryza rufipogon and O. nivara
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Study on the mating systems of wild rice Oryza rufipogon and O. nivara and their effects on population genetic variation
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Data from: Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view
Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration–drift balance in creating this clinal variation pattern is also discussed.
Data from: Population genetic structure of Oryza rufipogon and O. nivara: implications for the origin of O. nivara
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Data from: Are habitat fragmentation, local adaptation and isolation by distance driving population divergence in wild rice Oryza rufipogon?
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Data from: Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view
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Data from: Domestication and geographic origin of Oryza sativa in China: insights from multilocus analyses of nucleotide variation of O. sativa and O. rufipogon
Previous studies have indicated that China is one of the domestication centres of Asian cultivated rice (Oryza sativa), and common wild rice (O. rufipogon) is the progenitor of O. sativa. However, the number of domestication times and the geographic origin of Asian cultivated rice in China are still under debate. In this study, 100 accessions of Asian cultivated rice and 111 accessions of common wild rice in China were selected to examine the relationship between O. sativa and O. rufipogon and thereby infer the domestication and evolution of O. sativa in China through sequence analyses of six gene regions, trnC-ycf6 in chloroplast genomes, cox3 in mitochondrial genomes and ITS, Ehd1, Waxy, Hd1 in nuclear genomes. The results indicated that the two subspecies of O. sativa (indica and japonica) were domesticated independently from different populations of O. rufipogon with gene flow occurring later from japonica to indica; Southern China was the genetic diversity centre of O. rufipogon, and the Pearl River basin near the Tropic of Cancer was the domestication centre of O. sativa in China.
Data from: Domestication and geographic origin of Oryza sativa in China: insights from multilocus analyses of nucleotide variation of O. sativa and O. rufipogon
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Comparative transcriptomic analysis of iron deficiency response in roots of Oryza sativa and O. rufipogon
GEO Series GSE131238. Oryza sativa; Oryza rufipogon. 8 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis of salt stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.)
GEO Series GSE73181. Oryza rufipogon. 4 samples. Type: Expression profiling by high throughput sequencing.
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