Population structure analysis and association mapping of blast resistance in indica rice (Oryza sativa L.) landraces.

Rice blast caused by Magnaporthe oryzae is one of the most devastating rice diseases worldwide. To understand the genetic diversity of indica landrace accessions and identify simple sequence repeat (SSR) markers that are associated with blast resistance, a population of 276 indica landraces from across the world was constructed. This population was then used to evaluate the blast-resistance phenotype through artificial inoculation under controlled conditions in 2012 and 2013. The genetic diversity and association of the population with resistance were analyzed by examining the phenotype for 160 SSR markers distributed on 12 rice chromosomes. The 276 accessions were classified into seven groups using model- and distance-based cluster analyses. Associations between SSR markers and blast resistance showed that 26 SSR markers were significantly associated with blast resistance in 2012 and 2013 (P < 0.01) and that the phenotypic variation ranged from 2.68 to 13.11%. Nineteen of the markers associated with blast resistance were located in regions where genes or quantitative trait loci (QTLs) have been previously reported, and seven were newly identified in this study. These results indicate that marker-trait association has potential advantages over classical linkage analysis and QTL mapping, and that these markers could be used for marker-assisted selection in rice blast-resistance-breeding programs.

OsMYB511 encodes a MYB domain transcription activator early regulated by abiotic stress in rice.

The MYB-domain proteins exist universally across diverse organisms and regulate numerous processes during the plant life cycle. In the present research, a full-length MYB gene OsMYB511 was identified from rice seedlings through microarray data. Induction of OsMYB511 by cold stress was dramatic in japonica cultivar Jiucaiqing as compared to indica IR26. In addition to cold, OsMYB511 was also markedly induced by osmotic stress, high temperature, and exogenous ABA, suggesting that OsMYB511 is a multiple-stress responsive gene in rice. Tissue-specific expression analysis indicated that OsMYB511 was highly expressed in rice panicles at earlier development stage. Interestingly, OsMYB511 expression is fully subjected to circadian rhythm regulation. The subcellular localization and yeast hybrid assay suggested that OsMYB511 is nucleus-localized transcription activator. Deletion analysis suggested that trans-activation activity of OsMYB511 relied on its C-terminus. Co-expression analysis revealed additional 2 MYB genes co-expressed with OsMYB511, implying that these MYB genes might coordinately regulate stress responses in rice.

Identification of quantitative trait loci conferring blast resistance in Bodao, a japonica rice landrace.

Bodao, a japonica landrace from the Taihu Lake region of China, is highly resistant to most Chinese isolates of Magnaporthe oryzea, a form of rice blast. To effectively dissect the influence of genetics on this blast resistance, a population of 155 recombinant inbred lines (F2:8) derived from a cross of Bodao x Suyunuo was inoculated with 12 blast isolates. Using a quantitative trait locus (QTL) mapping approach, 13 QTL on chromosomes 1, 2, 9, 11, and 12 were detected from Bodao. Five QTL, including qtl11-1-1, qtl11-3-7, qtl11-4-9, qtl12-1-1, and qtl12-2-3, have not been previously reported. The qtl11-3-7 and qtl11-4-9 may be the two main effective QTL and resistant to 7 and 9 isolates, respectively. The results of the present study will be valuable for the fine mapping and cloning of these two new resistance genes.

Comprehensive gene expression analysis of the DNA (cytosine-5) methyltransferase family in rice (Oryza sativa L.).

Cytosine DNA methylation is a conserved epigenetic regulatory mechanism in both plants and animals. DNA methyltransferases (DNA MTases) not only initiate (de novo) but also maintain the process of DNA methylation. Here, we characterized the genome-wide expression profiles of 10 cytosine DNA MTase genes belonging to 4 subfamilies, MET1, CMT, DNMT2, and DRM, in rice. Tissue-specific gene expression analysis showed that all family members varied widely in their expression and specificities and might be involved in some basic metabolic pathways. Similarly, the expression of all rice cytosine DNA MTase genes was not regulated by plant hormones except OsDRM1a and OsDRM1b, which were downregulated by jasmonic acid. The transcription level of 10 genes in rice shoots and roots was also measured under salt and osmotic stress. Meanwhile, quantitative polymerase chain reaction data of the japonica and indica rice cultivars revealed that there is large variation in the expression activities of all genes. The results provide a foundation to further explore the roles of DNA MTases and the epigenetic regulation of abiotic stress responses in rice.

Regulation of ATG6/Beclin-1 homologs by abiotic stresses and hormones in rice (Oryza sativa L.).

Autophagy, a complex and conserved mechanism, serving as a defense response in all eukaryotic organisms, is regulated by several proteins, among which ATG proteins are the most important due to their involvement in autophagosome formation. ATG6/Beclin-1 proteins, reported to be essential for autophagosome formation and assigned as a conserved domain, were subjected to database searches. We found three homologs in the rice (Oryza sativa) genome. A phylogeny tree was constructed to establish their across species relationship, which divided them into three distinct groups; two for plants, i.e., monocots and dicots, and one for animals. Evolutionary study of this family by critical amino acid conservation analysis revealed significant functional divergence. The finding of important stress-related cis-acting elements in the promoter region of rice ATG6 genes demonstrated their involvement in abiotic stress responses. Furthermore, expression profiling of rice ATG6 genes based on microarray data, as well as by semi-quantitative RT-PCR showed differential expression when subjected to different stresses suggesting the involvement of OsATG6 genes in abiotic stresses (heat, cold and drought) and hormone (abscisic acid) responses. Analysis of co-expressed genes showed that most of them annotated to DNA repair pathways and proteolysis, etc. Collectively, these results suggest the involvement of OsATG6 genes in different stresses, and provide a basis for further functional studies to investigate the biological mechanism of action of these genes under abiotic stresses.