Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach
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RESEARCH ARTICLE
Open Access
Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach Raheleh Mirdar Mansuri1,2, Zahra-Sadat Shobbar1* , Nadali Babaeian Jelodar2, Mohammadreza Ghaffari1, Seyed Mahdi Mohammadi1 and Parisa Daryani1
Abstract Background: Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review. Results: A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein. Conclusions: The obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress. Keywords: Meta- analysis, RNA-seq, Microarray, QTLs, Salinity stress, Oryza sativa
Background Currently, rice ranks as the most important food crop in the world before wheat and maize supplying a major source of calorie for more than 3.5 billion people all over the world [1, 2]. However, rice is classified as a very sensitive crop to salinity in both seedling and reproductive stages, while excess salt in soil is one of the most * Correspondence: [email protected] 1 Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), PO Box 31535-1897, Karaj, Iran Full list of author information is available at the end of the article
widespread abiotic stresses in Asia and some river deltas in Europe [3, 4]. Salinity challenge at the seedling stage causes the g
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