A meta-analysis of microarray data revealed hub genes and transcription factors involved in drought stress response in rice (Oryza sativa L.)
Sedigheh Soltanpour A , AliReza Tarinejad
A * , Karim Hasanpur B and Mohammad Majidi B
+ Author Affiliations
- Author Affiliations
A Department of Agricultural Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran.
B Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
Functional Plant Biology 49(10) 898-916 https://doi.org/10.1071/FP22028
Submitted: 16 February 2022 Accepted: 21 June 2022 Published: 8 July 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Although there are various studies attempted to clarify the genetic mechanism of plant response to drought stress that reduces crop yield, a meta-analysis can integrate the results of them to provide a better picture of the issue. Therefore, in this study, several microarray datasets of rice were meta-analysed under drought stress and normal condition using the R packages. Accordingly, differentially expressed genes (meta-DEGs) were identified. The results showed 643 and 677 upregulated and downregulated genes, respectively. The significant common Gene Ontology (GO) terms between the up- and downregulated genes were responses to abiotic stimulus, water deprivation, oxygen-containing compound and abscisic acid. The transcription factors (TF) survey showed that bHLH under drought stress activates up genes 42% more than down genes while bzip Homeodomain activates down genes 54% more than up genes. The hub downregulated genes obtained from this study were mainly related to photosynthesis and the hub upregulated genes were mainly related to stress tolerance which include heat shock proteins (HSPs), late embryogenesis abundant (LEAs), calmodulin-like protein (CML), phosphatase 2C (PP2Cs) and IAA genes. Moreover, this meta-analysis data were compared with other experimental data and the results confirmed the up and down expression of them. Our findings can provide novel insights into the molecular mechanism of rice (Oryza sativa L.) response to drought stress.
Keywords: abiotic stress, CO2 fixation, functional genomic, gene discovery, gene ontology, Oryza sativa L., process, up-regulation.
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