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.

De Novo Assembly and Analysis of Tartary Buckwheat (Fagopyrum tataricum Garetn.) Transcriptome Discloses Key Regulators Involved in Salt-Stress Response

“…Through comparison of gene expression patterns between control and salt treatment, we obtained 455 DEGs. This is relatively a smaller number compared with the DEGs numbers obtained in Arabidopsis [ 60 , 61 ], wheat [ 15 ], and rice [ 62 ]. We speculated that this gap could result from the fact that our RNA-seq data mainly reflected the early-stage gene expression profiles under salt stress (24 h after salt treatment).…”

Salinity Response in Chloroplasts: Insights from Gene Characterization

“…However, the photosynthetic machinery and chloroplast metabolic pathways for salt tolerance are too complicated to be interpreted by the genes characterized so far. Although a large number of candidate genes/proteins have been identified in chloroplasts from plants under salt treatments using large-scale genomic, transcriptomic, and proteomic approaches [9,10,11,12,92], further investigations of their biological functions in salinity tolerance are needed. More importantly, a deeper analysis of the post-translational modifications and protein-protein interactions of these salt-responsive proteins will facilitate a thorough understanding of the complicated salt-responsive networks in chloroplasts.…”

“…Previous gene characterization studies have revealed a number of genes/proteins involved in various signaling and metabolic processes in chloroplasts [7,8]. However, the characterization of salinity-responsive genes encoding chloroplast-localized proteins is limited, although many genes/proteins have been proposed to be involved in salt tolerance using transcriptomic and proteomic approaches [9,10,11,12]. …”

Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings

“…For example, cold tolerance at the rice germination stage has been described by RNA-seq methods in Indica genotypes (Dametto et al 2015). Comparative transcriptomics has been used to measure cold stress responsiveness in two rice varieties (Zhang et al 2012) and to detect cold, iron, and salt stress in rice plants (do Amaral et al 2016). Transcriptome analysis has been used to analyze salt stress responsiveness at the seedling stage in Dongxiang wild rice (Zhou et al 2016) and to detect phosphorus stress responsiveness in seedlings of Dongxiang wild rice (Deng et al 2017, Deng et al 2018a, 2018b.…”