Identification of key genes effective in tolerance to drought stress in rice through meta-analysis of microarray data

Abstract

ObjectiveEnvironmental stresses such as drought, high temperature, salinity and high CO2 are a serious threat to sustainable agriculture. Drought stress is one of the most important abiotic stresses in rice, which causes a decrease in crop yield. Several researches have been carried out separately to clarify the molecular mechanism of plant response to drought stress. Therefore, meta-analysis can lead to a better understanding of drought stress tolerance mechanisms by integrating the results of several related studies.Materials and MethodsIn this regard, four series of good quality microarray data of rice under drought stress and normal condition were selected and then analyzed by R software limma packages. For meta-analysis were used of meta-RNAseq package and Fisher's method to combine p-values obtained from individual data analysis. Up and down regulated meta-analysis genes under drought stress were identified. Then, Gene ontology, hub genes and Co-expression network analysis were performed. The results were evaluated using real-time quantitative PCR test in Hashemi rice as sensitive variety and native rice as tolerant variety to water deficit stress in vitro with PEG treatment.ResultsThe results of present study, 578 up-regulated genes and 660 down-regulated genes were obtained. Gene ontology (GO) analysis showed drought response mechanisms and drawing the protein-protein interaction network revealed that the down regulated hub genes under drought stress is mainly related to photosynthesis process and up regulated hub genes under drought stress mainly related to stress tolerance including HSP, LEAs, PP2Cs genes. Finally, the data obtained from the present meta-analysis were confirmed by real-time quantitative PCR on peroxidase 47, OsDSSR1, homeobox-leucine zipper protein and an unknown gene. These findings significantly improve our understanding of drought stress pathway. Identification of hub genes in this study can be effective to obtain an overview of hub genes that play an important role in response to drought stress in riceConclusionIdentifying downstream of hub genes can help in the production of drought-tolerant rice through classical breeding methods by pyramiding genes or genome manipulation and increase tolerance to drought stress.The result will lead to sustainable agriculture.

Keywords

• meta-analysis
• microarray
• drought stress
• hub genes
• sustainable agriculture