title: Comparative transcriptomics of rice plants under cold, iron, and salt stresses.
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.
authors.affiliation: Departament of Botany, Federal University of Pelotas, Pelotas, RS, Brazil. theoamaral@hotmail.com.
authors.forename: Marcelo Nogueira
authors.initials: MN
authors.lastname: do Amaral
authors.affiliation: Plant Breeding Center, Federal University of Pelotas, Pelotas, RS, Brazil.
authors.forename: Luis Willian Pacheco
authors.initials: LW
authors.lastname: Arge
authors.affiliation: Departament of Botany, Federal University of Pelotas, Pelotas, RS, Brazil.
authors.forename: Letícia Carvalho
authors.initials: LC
authors.lastname: Benitez
authors.affiliation: Plant Breeding Center, Federal University of Pelotas, Pelotas, RS, Brazil.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Danielowski
authors.affiliation: Plant Breeding Center, Federal University of Pelotas, Pelotas, RS, Brazil.
authors.forename: Solange Ferreira da Silveira
authors.initials: SF
authors.lastname: Silveira
authors.affiliation: Plant Breeding Center, Federal University of Pelotas, Pelotas, RS, Brazil.
authors.forename: Daniel da Rosa
authors.initials: Dda R
authors.lastname: Farias
authors.affiliation: Plant Breeding Center, Federal University of Pelotas, Pelotas, RS, Brazil.
authors.forename: Antonio Costa
authors.initials: AC
authors.lastname: de Oliveira
authors.affiliation: Plant Breeding Center, Federal University of Pelotas, Pelotas, RS, Brazil.
authors.forename: Luciano Carlos
authors.initials: LC
authors.lastname: da Maia
authors.affiliation: Departament of Botany, Federal University of Pelotas, Pelotas, RS, Brazil.
authors.forename: Eugenia Jacira Bolacel
authors.initials: EJ
authors.lastname: Braga
mesh_terms: D003080:Cold Temperature; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D007501:Iron / Q000633:toxicity; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010940:Plant Proteins / Q000096:biosynthesis* / Q000235:genetics; D012965:Sodium Chloride / Q000633:toxicity; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D012965:Sodium Chloride; D007501:Iron
keywords: Cold stress; Differentially expressed genes; Iron stress; Oryza sativa L; RNA-seq; Saline stress