1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Integrative gene network analysis of rice transcriptome to identification of key microRNAs involved in salinity stress
Paper ID : 1288-ICB10
Authors:
Zohreh Ebrahimi *1, Yaser Biniaz2, Fatemeh Amiri3, Ali Moghadam3, S. Mohsen Taghavi4
1Department of Plant Protection, Shiraz University, Shiraz, Iran
2Plant Virology Research Center, Shiraz University, Shiraz, Iran
3Institute of Biotechnology, Shiraz University, Shiraz, Iran
4Department of Plant Protection, School of Agriculture, Shiraz University
Abstract:
Salt stress is a harsh abiotic stress that decreases the crop yield dramatically. Rice (Oryza sativa), a major cereal, the main food source for many countries, is sensitive to this stress. Understanding the molecular mechanisms of rice under salt stress is a pivotal factor for developing stress-tolerant genotypes [2]. Therefore, an integrative transcriptome data analysis was performed. For this purpose, some RNA-seq data were retrieved from European Bioinformatics Institute (EBI) database. CLC Genomics Workbench v.12 software used for data analysis. After quality control, reads were mapped to rice reference genome. The adjusted P-values (FDR < 0.01) [1] were considered the significant and, thus, differentially expressed genes (DEGs) were used for further analysis. Gene ontology analysis of DEGs showed that the genes were enriched for response to cellular process, metabolic process, organic substance metabolic process in biological process category. Furthermore, the DEGs in molecular function category were enriched for catalytic activity, organic cyclic compound binding and oxidoreductase activity. In cellular component category, most genes were referred to cellular anatomical entity and intracellular anatomical structure. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that pathways that involve most of DEGs are metabolic pathways, biosynthesis of secondary metabolites, and biosynthesis of amino acids respectively. The microRNA analysis showed that miR156, miR160, and miR396 were the candidates that involved the most families. Genetic engineering has been proved to be an efficient approach to the development of salinity-tolerant genotypes, and this approach will become more powerful as more regulatory elements like key microRNAs associated with salinity tolerance are identified.
Keywords:
Key words: RNA-seq, microRNA, Gene ontology, Rice, Salinity
Status : Paper Accepted (Poster Presentation)