Phylogenetic analysis and sequence alignment of <i>Arabidopsis DREB1</i>s and their homologs in rice using ClustalW2.

<p>A: The phylogenetic analysis was carried out by the neighbour-joining method of ClustalW2, and the tree was edited and viewed by TreeView software. SD: segmental duplication; TD: tandem duplication; Transposition: single gene duplication by transposition. Bootstrap values from 1000 replicates were indicated at each node. Scale bar represented 0.1 amino acid substitution per site. B: The NLS (nuclear localization signal), ERF/AP2 domain, DSAW motif, and LWSY motif are shown. The alignment of the 141–171 region of <i>CBF1</i> and the corresponding regions of its rice and <i>Arabidopsis</i> homologs has been omitted due to the absence of conserved motif.</p

Colinearity and Similar Expression Pattern of Rice <em>DREB1s</em> Reveal Their Functional Conservation in the Cold-Responsive Pathway

<div><p>The clustered genes <u>C</u>-repeat (CRT) <u>b</u>inding <u>f</u>actor (<em>CBF)1/</em><u>d</u>ehydration-<u>r</u>esponsive <u>e</u>lement <u>b</u>inding protein <em>(DREB)1B</em>, <em>CBF2/DREB1C</em>, and <em>CBF3/DREB1A</em> play a central role in cold acclimation and facilitate plant resistance to freezing in <em>Arabidopsis thaliana</em>. Rice (<em>Oryza sativa</em> L.) is very sensitive to low temperatures; enhancing the cold stress tolerance of rice is a key challenge to increasing its yield. In this study, we demonstrate chilling acclimation, a phenomenon similar to <em>Arabidopsis</em> cold acclimation, in rice. To determine whether rice <em>CBF/DREB1</em> genes participate in this cold-responsive pathway, all putative homologs of <em>Arabidopsis DREB1</em> genes were filtered from the complete rice genome through a BLASTP search, followed by phylogenetic, colinearity and expression analysis. We thereby identified 10 rice genes as putative <em>DREB1</em> homologs: nine of these were located in rice genomic regions with some colinearity to the <em>Arabidopsis CBF1</em>–<em>CBF4</em> region. Expression profiling revealed that six of these genes (Os01g73770, Os02g45450, Os04g48350, Os06g03670, Os09g35010, and Os09g35030) were similarly expressed in response to chilling acclimation and cold stress and were co-expressed with genes involved in cold signalling, suggesting that these <em>DREB1</em> homologs may be involved in the cold response in rice. The results presented here serve as a prelude towards understanding the function of rice homologs of <em>DREB1</em> genes in cold-sensitive crops.</p> </div

GO enrichment analysis of co-expressed genes of rice <i>DREB1</i> homologs using agriGO software.

<p>GO enrichment analysis of co-expressed genes of rice <i>DREB1</i> homologs using agriGO software.</p

Survival rate of 7-day-old rice seedlings after the low temperature stress with or without chilling acclimation.

<p>Cold treatment (CT): 7-day-old seedlings were first maintained for 4 days (for indica rice: 9311 and Kasalath) or 7 days (for japonica rice: Nipponbare and TP309) at a low temperature of 4°C, then restored for 10 days to normal growth temperature. Chilling acclimation treatment (CA): 7-day-old seedlings were first maintained for 2 days at a mild temperature of 12°C, then 4 days (for indica rice: 9311 and Kasalath) or 7 days (for japonica rice: Nipponbare and TP309) at a low temperature of 4°C, and finally restored for 10 days to normal growth temperature. Each rice varieties were treated with four times of independent experiments and the bars represent the standard deviation. P values of T-test for difference between CT and CA treatments of each variety were shown in Fig. 1.</p

Expression of rice <i>DREB1s</i> under drought, salt, and cold stresses in rice seedlings from the SALK RiceGE database.

<p>X axis: different stresses; Y axis: total RNA expression level of seven-day-old seedlings.</p

Colinearity among regions containing either <i>Arabidopsis CBF1–3</i> or their orthologs in rice.

<p>The dotted box indicates that the pairs of regions of chromosomes 2 and 4 contain lots of pairs of paralogs as showed by the dotted lines. The solid lines indicate that the genes are orthlogous to each other as they possess the highest E value or identities from reciprocal blast analyses.</p

The messages of relative genes in the study.

a<p>KOME FL-cDNA;</p>b<p>Community cDNA;</p>c<p>NCBI-EST;</p>d<p>No EST or FL-cDNA found.</p

Expression pattern of rice <i>DREB1</i> genes in the ZS97 cultivar during the entire life cycle of the plant.

<p>Expression pattern of rice <i>DREB1</i> genes in the ZS97 cultivar during the entire life cycle of the plant.</p