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

Abstract

China is rich of germplasm resources of common wild rice (Oryza rufipogon Griff.) and Asian cultivated rice (O. sativa L.) which consists of two subspecies, indica and japonica. Previous studies have shown that China is one of the domestication centers of O. sativa. However, the geographic origin and the domestication times of O. sativa in China are still under debate. To settle these disputes, six chloroplast loci and four mitochondrial loci were selected to examine the relationships between 50 accessions of Asian cultivated rice and 119 accessions of common wild rice from China based on DNA sequence analysis in the present study. The results indicated that Southern China is the genetic diversity center of O. rufipogon and it might be the primary domestication region of O. sativa. Molecular dating suggested that the two subspecies had diverged 0.1 million years ago, much earlier than the beginning of rice domestication. Genetic differentiations and phylogeography analyses indicated that indica was domesticated from tropical O. rufipogon while japonica was domesticated from O. rufipogon which located in higher latitude. These results provided molecular evidences for the hypotheses of (i) Southern China is the origin center of O. sativa in China and (ii) the two subspecies of O. sativa were domesticated multiple times.

Domestication and association analysis of Hd1 in Chinese mini-core collections of rice

“…5, O. rufipogon samples from the same region tended to be in neighboring haplotypes. The phenomenon of geographical difference in O. rufipogon was also detected in previous research (Wang et al 2008;Wei et al 2012b). However, obvious association between the distribution of cultivated accessions and the haplotypes had not been observed.…”

Development of Simple Sequence Repeat (SSR) Markers of Sesame (Sesamum indicum) from a Genome Survey

“…Thirty-one accessions of sesame collected from worldwide (Table S3), were used to evaluate the SSR suitability for genetic distance analysis. Young leaves were collected and frozen in liquid nitrogen prior to genomic DNA extraction using CTAB methods [37]. DNA concentrations were measured spectrophotometrically at 260 nm, and the extracts were electrophoresed on 1% agarose to confirm the quality.…”

Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats

“…Molecular phylogenetic and phylogenomic studies in this genus have well-resolved evolutionary relationships and reconstructed the phylogeny of different rice genome types and species 10,12–18 . Besides cpDNA sequences that have been applied to determining phylogenetic relationships among Oryza species 12,19–23 , the completion of 10 Oryza plastomes ( O. australiensis , O. barthii , O. glaberrima , O. glumaepatula , O. longistaminata , O. meridionalis , O. nivara , O. officinalis , O. rufipogon , and O. sativa ) 24–30 , and for example, the fully sequenced rice chloroplast genomes 24,31 have been extensively used to phylogenetic and population genetic studies in cultivated rice and wild relatives 32–34 . The genus Oryza particularly becomes an unparalleled system for studying comparative and evolutionary genomics in plants owning to available nuclear genomes of the two cultivated rice subspecies 35–37 and the other six Oryza species having been sequenced recently 18,38 .…”