Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.).

BACKGROUND: Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth. RESULTS: A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress. CONCLUSIONS: Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance.

Molecular cloning, identification of GSTs family in sunflower and their regulatory roles in biotic and abiotic stress.

Glutathione-S-transferase (GST) genes exist widely in plants and play major role in metabolic detoxification of exogenous chemical substances and oxidative stress. In this study, 14 sunflower GST genes (HaGSTs) were identified based on the sunflower transcriptome database that we had constructed. Full-length cDNA of 14 HaGTSs were isolated from total RNA by reverse transcription PCR (RT-PCR). Sunflower was received biotic stress (Sclerotinia sclerotiorum) and abiotic stress (NaCl, low-temperature, drought and wound). GST activity was measured by using the universal substrate. The results showed that most of the HaGSTs were up-regulated after NaCl and PEG6000-induced stresses, while a few HaGSTs were up-regulated after S. sclerotiorum, hypothermia and wound-induced stressed, and there was correlation between the changes of GST activity and the expression of HaGSTs, indicating that HaGSTs may play regulatory role in the biotic and abiotic stress responses. 14 HaGSTs from sunflower were identified, and the expression of HaGSTs were tissue-specific and played regulatory roles in both stress and abiotic stress.

Genome-wide analysis of maize PR-1 gene family and expression profiles induced by plant hormones and fungal phytopathogens.

OBJECTIVE: In order to find similarity of the protein X in maize with other species we performed a BLASTP search to identify the maize ZmPR-1 family genes. METHODS: We used a BLASTP search to identify the maize ZmPR-1 family genes that may show similarities between the protein X in maize and other species. RESULTS: A total of 17 ZmPR-1 genes were identified and these genes were unevenly distributed on 8 chromosomes of maize. All ZmPR-1 gene predicted proteins contained a conserved CAP domain, according to the results of multiple sequence alignment and gene structure analysis. Phylogenetic tree analysis of a total of 85 PR-1 protein sequences from maize, sorghum, rice and Arabidopsis showed that the PR-1 family proteins were divided into four categories, and the maize ZmPR-1 was closely related to sorghum PR-1. In the promoter of maize ZmPR-1 gene, hypothetical cis-elements related to fungal induction, defense stress response, plant hormones, low temperature and drought response were detected. Microarray data analysis showed that ZmPR-1 displayed a tissue-specific expression pattern at different developmental stages, and responded to the infections of five maize pathogens. In addition, we further verified that four ZmPR-1 genes (ZmPR-1-5, 12, 14 and 16) were not only significantly up-regulated after Setosphearia turcica infection, but also affected by exogenous cues such as SA, ABA, MeJA and H2O2. CONCLUSION: The ZmPR-1 family may be important in plant disease resistance. This study's data provide important clues for future research on the function of ZmPR-1 family genes.

Expression profile analysis of maize in response to Setosphaeria turcica.

Northern corn leaf blight (NCLB), caused by the hemibiotrophic fungal pathogen Setosphaeria turcica, is one of the major foliar diseases of maize. The use of resistant cultivars is the most effective, economical, and environmentally friendly means to control NCLB. At present, the molecular mechanisms of maize resistance to S. turcica is not clear. Elucidating the molecular resistance mechanisms of maize response to S. turcica would aid breeding for a maize variety with fungal tolerance. In this study, maize leaves before and after infection with S. turcica were sequenced by RNA-seq, and 5903 differentially expressed genes (DEGs) were screened. Among them, 950 and 2245 genes were up-regulated 12 h and 60 h (samples H12 and H60, respectively) after infection, 752 and 1956 genes were down-regulated in H12 and H60, respectively. The GO and KEGG enrichment analysis of the DEGs showed that the GO and Pathway with the most annotation sequences were closely related to plant resistance. The expression of eight randomly selected DEGs was analyzed using qRT-PCR, and expression was consistent with the RNA-seq data. The expression patterns of four categories of genes were analyzed namely, genes involved in plant and pathogen interactions, transcription factors related to plant stress-tolerance, genes related to plant hormones and plant antioxidant. Many resistant signaling pathways were initiated such as the MAPK signal transduction pathway and the expression of multiple antioxidant-related genes [Peroxidase (POD), Catalase (CAT), Glutathione-S-transferase (GST) and Superoxide Dismutase (SOD)] following S. turcica infection. Many disease resistance signal transduction pathways and defense response pathways were induced following maize infection by S. turcica, suggesting a multiple gene network system. To the best of our knowledge, this is the first time that RNA-seq technology has been used to perform transcription analysis of maize in response to S. turcica stress. Taken together, these data provide novel and valuable information that will help understand the resistance mechanism in maize against S. turcica and locate candidate genes related to maize resistance against S. turcica.