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

The clustered genes C-repeat (CRT) binding factor (CBF)1/ dehydration-responsive element binding protein (DREB)1B, CBF2/DREB1C, and CBF3/DREB1A play a central role in cold acclimation and facilitate plant resistance to freezing in Arabidopsis thaliana. Rice (Oryza sativa 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 Arabidopsis cold acclimation, in rice. To determine whether rice CBF/DREB1 genes participate in this cold-responsive pathway, all putative homologs of Arabidopsis DREB1 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 DREB1 homologs: nine of these were located in rice genomic regions with some colinearity to the Arabidopsis CBF1–CBF4 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 DREB1 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 DREB1 genes in cold-sensitive crops.     

Complexity of rice Hsp100 gene family: lessons from rice genome sequence data

Elucidation of genome sequence provides an excellent platform to understand detailed complexity of the various gene families. Hsp100 is an important family of chaperones in diverse living systems. There are eight putative gene loci encoding for Hsp100 proteins in Arabidopsis genome. In rice, two full-length Hsp100 cDNAs have been isolated and sequenced so far. Analysis of rice genomic sequence by in silico approach showed that two isolated rice Hsp100 cDNAs correspond to Os05g44340 and Os02g32520 genes in the rice genome database. There appears to be three additional proteins (encoded by Os03g31300, Os04g32560 and Os04g33210 gene loci) that are variably homologous to Os05g44340 and Os02g32520 throughout the entire amino acid sequence. The above five rice Hsp100 genes show significant similarities in the signature sequences known to be conserved among Hsp100 proteins. While Os05g44340 encodes cytoplasmic Hsp100 protein, those encoded by the other four genes are predicted to have chloroplast transit peptides.     

Differential Drought Responses in F-box Gene Expression and Grain Yield Between Two Rice Groups with Contrasting Drought Tolerance

Understanding the molecular mechanisms regulating rice’s response to drought stress is important for cereal crop development. We investigated the physiological and gene expression responses of three drought-tolerant and two drought-sensitive unrelated rice cultivars at the reproductive stage. Leaf water loss and leaf rolling tests distinguished these two groups from each other. Both 7 and 14 days of drought stress affected most of the tested agronomic traits including grain yield, and the effects were stronger in the drought-sensitive cultivars. Fourteen days of drought stress severely reduced grain yield in the sensitive cultivars. Expression levels of 50 genes previously published were examined in panicles. Of these, 25 genes were expressed in panicles and could be classified into 6 groups. LOC_Os02g51350, a Kelch domain-containing F-box gene, was selected for further studies including expression analysis in panicles during the 14-day drought stress, domain analysis, and analysis of cis-acting elements in the promoters. All three drought-resistant cultivars possessed the F-box domain, which was absent in the two drought-sensitive cultivars. In addition, drought-related ABRE and DRE/CRT cis-acting elements were more abundant in Os02g51350 promoters of cultivars with good grain yield under drought stress than in promoters of cultivars with severe yield reduction. Our results suggest that the F-box version of Os02g51350 is important for maintenance of grain yield under drought.     

Identification of a drought-induced rice gene, OsSAP, that suppresses Bax-induced cell death in yeast

We identified rice genes that might be involved in drought stress tolerance by virtue of their anti-apoptotic activity. Potential anti-apoptosis related genes were identified by screening an Oryza sativa cDNA library derived from drought stressed tissues in a yeast functional assay. About 28 O. sativa cDNAs promoted yeast survival following engagement of Bax-induced apoptosis. An O. sativa cDNA encoding R12H780 was a highly conserved putative senescence-associated-protein (OsSAP). OsSAP was both highly and rapidly expressed in response to drought stress. Additionally, OsSAP was found to be localized to the mitochondria. Overall, OsSAP represents a new type of Bax suppressor related gene and endows multiple stress tolerance in yeast.     

Nucleotide variability and gene expression reveal new putative genes related to seed shattering in weedy rice

Seed shattering is one of the main traits related with the domestication of cultivated rice and with the invasiveness and persistence of weedy rice. Two independent studies in 2006 have indicated that qSH1 in Japonica and Sh4 in Indica rice are major genes governing this trait. However, a wide variation of seed shattering occurs in weedy rice ecotypes from the same geographic region and even within the same ecotype. The aim of this study was to evaluate the nucleotide variability of known and putative genes related to seed shattering in cultivated rice and to identify and validate new genes related to this trait in weedy rice. The qSH1 gene was not associated with seed shattering in the evaluated genotypes. The nucleotide variability of the genes Os01g0849100 and Os08g0512400, previously identified based on a genome‐wide resequencing study, was related to seed shattering in rice. The nucleotide variability of three single nucleotide polymorphisms (SNPs) of the OsXTH8 gene, which is related to cell wall biosynthesis, was not associated with seed shattering. However, the high expression of this gene was related to the occurrence of this trait. This study evaluated jointly a series of genes involved in rice seed shattering and indicated that the genes OsXTH8, Os08g0512400 and Os01g0849100 are important for the regulation of this trait in weedy rice in addition to previously described genes. Seed shattering in weedy rice has a more complex regulation than in cultivated rice where few major genes were identified.     

Structural characterization and promoter activity analysis of the γ-kafirin gene from sorghum

A genomic clone encoding the γ-kafirin gene from sorghum was isolated and sequenced. A 2938 bp sequenced fragment includes an intronless open reading frame of 636 nucleotides encoding a putative polypeptide of 212 amino acids. Comparison of the deduced amino acid sequence of γ-kafirin with the published sequences of γ-prolamins of maize, and Coix revealed highly conserved domains. The N-terminal region of these proteins contains the conserved hexapeptide PPPVHL, which is repeated eight times in γ-zein, four times in γ-kafirin and three times in γ-coixin. The number of PPPVHL repeats accounts predominantly for the differences in the molecular weights of γ-prolamins. Several putative regulatory sequences common to the γ-kafirin and γ-zein genes were identified in both the 5′ and the 3′ flanking regions. Putative GCN4-like regulatory sequences were found at positions ?192 and ?476 in the 5′ flanking region of γ-kafirin. In the 3′ noncoding region, three putative polyadenylation signals, two AATAAT and one AATGAA, were found at positions + 658, + 716, and + 785, respectively. In order to investigate the role of the putative GCN4-like motifs and other possible cis-acting element(s) of the γ-kafirin promoter, a series of deleted and chimeric promoter constructs were introduced into maize, Coix and sorghum tissues by particle bombardment. Histochemical analysis of β-glucuronidase (GUS) activity in different tissues indicated that the element(s) responsible for tissue specificity is probably located in the 285-bp proximal region of the promoter, while the remaining promoter sequence seems to carry the element(s) responsible for the quantitative response.