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Comparative transcriptomics of rice plants under cold, iron, and salt stresses

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Abstract

Abiotic stresses such as salinity, iron toxicity, and low temperatures are the main limiting factors of rice (Oryza sativa L.) yield. The elucidation of the genes involved in responses to these stresses is extremely important to understand the mechanisms that confer tolerance, as well as for the development of cultivars adapted to these conditions. In this study, the RNA-seq technique was used to compare the transcriptional profile of rice leaves (cv. BRS Querência) in stage V3, exposed to cold, iron, and salt stresses for 24 h. A range of 41 to 51 million reads was aligned, in which a total range of 88.47 to 89.21 % was mapped in the reference genome. For cold stress, 7905 differentially expressed genes (DEGs) were observed, 2092 for salt and 681 for iron stress; 370 of these were common to the three DEG stresses. Functional annotation by software MapMan demonstrated that cold stress usually promoted the greatest changes in the overall metabolism, and an enrichment analysis of overrepresented gene ontology (GO) terms showed that most of them are contained in plastids, ribosome, and chloroplasts. Saline stress induced a more complex interaction network of upregulated overrepresented GO terms with a relatively low number of genes compared with cold stress. Our study demonstrated a high number of differentially expressed genes under cold stress and a greater relationship between salt and iron stress levels. The physiological process most affected at the molecular level by the three stresses seems to be photosynthesis.

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Acknowledgments

This study was supported by the Brazilian research funding agencies: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Fundação de Amparo à Pesquisa do Rio Grande do Sul (FAPERGS).

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    Authors and Affiliations

    1. Departament of Botany, Federal University of Pelotas, Pelotas, RS, Brazil

      Marcelo Nogueira do Amaral, Letícia Carvalho Benitez & Eugenia Jacira Bolacel Braga

    2. Plant Breeding Center, Federal University of Pelotas, Pelotas, RS, Brazil

      Luis Willian Pacheco Arge, Rodrigo Danielowski, Solange Ferreira da Silveira Silveira, Daniel da Rosa Farias, Antonio Costa de Oliveira & Luciano Carlos da Maia

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    1. Marcelo Nogueira do Amaral
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    Marcelo Nogueira do Amaral and Luis Willian Pacheco Arge contributed equally to this work.

    Electronic supplementary materials

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    Supplementary Material 1

    Phenotypic characterization of rice plants of cv. “BRS Querência” under a cold stress, b iron stress, and c salt stress (PDF 126 kb)

    Supplementary Material 2

    PCA cluster analysis of the different RNA-seq libraries based on Log2FC (PDF 10 kb)

    Supplementary Material 3

    List of primers used in RT-qPCR reactions (XLSX 10 kb)

    Supplementary Material 4

    Transcriptional profiles of rice plants (cv. BRS Querência) under cold, iron, and salt stress and their relations (PDF 259 kb)

    Supplementary Material 5

    List of differentially expressed genes identified by RNA-seq (FDR <0.01) in rice plants subjected to stress by cold, iron, and salt (XLS 2254 kb)

    Supplementary Material 6

    REViGO graphical representation of upregulated overrepresented GO terms under each stress. Graphical representation of interactions of GO terms with upregulated biological processes. a Cold stress, b Iron stress, c Salt stress (PDF 81 kb)

    Supplementary Material 7

    REViGO graphical representation of upregulated overrepresented GO terms under each stress. Graphical representation of interactions of GO terms with downregulated biological processes. a Cold stress, b Iron stress, c Salt stress. (PDF 36 kb)

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    do Amaral, M.N., Arge, L.W.P., Benitez, L.C. et al. Comparative transcriptomics of rice plants under cold, iron, and salt stresses. Funct Integr Genomics 16, 567–579 (2016). https://doi.org/10.1007/s10142-016-0507-y

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