Evolutionary Analysis Of Heat Shock Transcription Factors In Rice(Oryza Sativa L.)

Rice is one of the most important crops in the world, more than half of the population in the world use rice as the main source of food. However, the rice plants are growing under various biotic and abiotic stresses. Heat shock proteins (HSPs) plays an important role in plants in response to environmental stresses. Heat shock transcription factors (HSFs) is the upstream regulation gene of HSPs, which can not only regulate the expression of HSPs, but also take part in other physiological and biochemical pathways in plants. With the development of the next generation sequencing (NGS) technology, the genome DNA sequence of a variety of wild rice and cultivated rice have been completed, which would provide new opportunities for the researcher to identify HSFs and carry out HSFs phylogenetic analysis in the whole genomic scale.In this paper, six wild rice varieties and one cultivated rice genotype, Nipponbare, were employed as materials. Six wild rice varieties were Oryza barthii, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctate and Oryza rufipogon. HMMER was used to search the HSFs in the 6 wild rice and 1 cultivated rice genomes. The phylogenetic, replicationand synteny of HSFs were analyzed. The results are summarized in the following.1. In Oryza.barthii, Oryza. glumaepatula, Oryza. meridionalis, Oryza. nivara Oryza.punctata Oryza.rufipogon genome, we identified 22,23,24,24,25 and 25 HSF genes, respectively. Three, two, one and one HSF genes were absent in Oryza barthii, Oryza glumaepatula, Oryza meridionalis and Oryza nivara genomes compared to Nipponbare. Two HSF genes in Oryza nivara genome are translocation compare with Nipponbare genome. MEGA6 software were used to construct the phylogenetic tree for HSF genes between wild rice and cultivated rice. The HSF genes in the wild rice genome were clustered to A, B, C categories.2. The duplicated type of HSF genes in wild rice and cultivated rice were analyzed by MCScanX software. The result shows that gene repeat and whole genome duplication contribute to the expansion of HSF genes between Nipponbare and wild rice genotypes.3. Ka and Ks of HSF gene members between wild rice and cultivated rice genotypes by ParaAt and Ka_Ks Calculator tools. The results showed that the evolution of HSF genes in rice genome was mainly due to purifying selection. However, positive selection was also showed effect on some HSF gene members, including OGLUM02G19090 in Oryza glumaepatula, OMERI02G10900 in Oryza meridionalis, ONIVA02G10840 in Oryza nivara and ORUFI09G13720 in Oryza rufipogon. These HSF genes might have different function between wild rice and cultivated rice genotypes.4. SNPs in HSFs gene in the 6 wild rice genotypes were analyzed with Nipponbare genome DNA sequence as reference. After that, whether non synonymous SNPs (nSNPs) affect the function of target protein or not was predicted by 5 predictors, which was further confirmed by the protein structural variation of HSF genes. Then, these HSF genes were selected, including OBART06G18790 in Oryza.barthii, OGLUM08G23900 in Oryza.glumaepatula, OMERI01G17700 and OMERI05G20360 in Oryza.meridionalis, ONIVA08G25630 in Oryza.nivara, OPUNC01G29770 in Oryza.puctata and ORUFI02G09810 in Oryza.rufipogon.In summary, the results in this paper would give insight into the evolution and function of HSF gene members in rice.The result is useful for further study the different function and differdent agricultural characterized between wild rice and cultivated rice.