Table_1.DOC

<p>Seed germination plays important roles in the establishment of seedlings and their subsequent growth; however, seed germination is inhibited by salinity, and the inhibitory mechanism remains elusive. Our results indicate that NaCl treatment inhibits rice seed germination by decreasing the contents of bioactive gibberellins (GAs), such as GA₁ and GA_4, and that this inhibition can be rescued by exogenous bioactive GA application. To explore the mechanism of bioactive GA deficiency, the effect of NaCl on GA metabolic gene expression was investigated, revealing that expression of both GA biosynthetic genes and GA-inactivated genes was up-regulated by NaCl treatment. These results suggest that NaCl-induced bioactive GA deficiency is caused by up-regulated expression of GA-inactivated genes, and the up-regulated expression of GA biosynthetic genes might be a consequence of negative feedback regulation of the bioactive GA deficiency. Moreover, we provide evidence that NaCl-induced bioactive GA deficiency inhibits rice seed germination by decreasing α-amylase activity via down-regulation of α-amylase gene expression. Additionally, exogenous bioactive GA rescues NaCl-inhibited seed germination by enhancing α-amylase activity. Thus, NaCl treatment reduces bioactive GA content through promotion of bioactive GA inactivation, which in turn inhibits rice seed germination by decreasing α-amylase activity via down-regulation of α-amylase gene expression.</p

A map showing the sampled populations of <i>O</i>.

<p><b><i>rufipogon</i></b><b> and the distribution of haplotypes.</b> Detailed information of the samples is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049546#pone.0049546.s005" target="_blank">Table S1</a>. Phylogenetic relationship of the haplotype based on the NJ analysis is indicated below the map. Pie charts show the proportions of the haplotypes within each population. Haplotypes are indicated by different colors. The Tropical of Cancer is indicated by the green dotted line. Codes: CL, Chaling; DX, Dongxiang; JH, Jinghong; JY, Jiangyong; YJ, Yuanjiang; ZP, Zhangpu;</p

Longitude and latitude of the <i>O</i>.

<p><b><i>rufipogon</i></b><b> from H1, H2 and H3.</b> Accessions from H2 and H3 are indicated by circles and accessions from H1 are indicated by triangles. The horizontal ordinate origins from 23.5° (N) which is the Tropical of Cancer located in.</p

Origin of <em>Oryza sativa</em> in China Inferred by Nucleotide Polymorphisms of Organelle DNA

<div><p>China is rich of germplasm resources of common wild rice (<em>Oryza rufipogon</em> Griff.) and Asian cultivated rice (<em>O. sativa</em> L.) which consists of two subspecies, indica and japonica. Previous studies have shown that China is one of the domestication centers of <em>O</em>. <em>sativa</em>. However, the geographic origin and the domestication times of <em>O</em>. <em>sativa</em> 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 <em>O</em>. <em>rufipogon</em> and it might be the primary domestication region of <em>O</em>. <em>sativa</em>. 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 <em>O</em>. <em>rufipogon</em> while japonica was domesticated from <em>O</em>. <em>rufipogon</em> which located in higher latitude. These results provided molecular evidences for the hypotheses of (i) Southern China is the origin center of <em>O</em>. <em>sativa</em> in China and (ii) the two subspecies of <em>O</em>. <em>sativa</em> were domesticated multiple times.</p> </div

Population structuring of <i>O</i>.

<p><b><i>sativa</i></b><b> and </b><b><i>O</i></b>. <b><i>rufipogon</i></b><b>.</b> STRUCTURE was constructed by all loci. K = 5. Clusters are indicated by different colors. Samples included in all clusters are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049546#pone.0049546.s005" target="_blank">Table S1</a>.</p

Summary statistic of pairwise divergence (F_ST) between groups.

<p>Summary statistic of pairwise divergence (F_ST) between groups.</p

Summary of nucleotide polymorphisms.

<p>S: number of segregating sites; h: number of haplotypes; Hd: haplotype diversity; π: nucleotide diversity; θ_w: Watterson’s parameter for silent sites.</p

Phylogenetic tree of combined chloroplastic and mitochondrial loci.

<p>Bootstrap values above 50% are shown on the trees. The accessions contained in the branches were indicated by different symbols: <i>O</i>. <i>rufipogon</i> alleles by open squares, indica alleles by filled triangles and japonica by inverted filled triangles. The tree was rooted with <i>O</i>. <i>barthii</i> allele which is indicated by solid circles.</p