Abstract
BackgroundRice plants show yellowing, stunting, withering, reduced tillering and utimately low productivity in susceptible varieties under low temperature stress. Comparative transcriptome analysis was performed to identify novel transcripts, gain new insights into different gene expression and pathways involved in cold tolerance in rice.ResultsComparative transcriptome analyses of 5 treatments based on chilling stress exposure revealed more down regulated genes in susceptible and higher up regulated genes in tolerant genotypes. A total of 13930 and 10599 differentially expressed genes (DEGs) were detected in cold susceptible variety (CSV) and cold tolerant variety (CTV), respectively. A continuous increase in DEGs at 6, 12, 24 and 48 h exposure of cold stress was detected in both the genotypes. Gene ontology (GO) analysis revealed 18 CSV and 28 CTV term significantly involved in molecular function, cellular component and biological process. GO classification showed a significant role of transcription regulation, oxygen, lipid binding, catalytic and hydrolase activity for tolerance response. Absence of photosynthesis related genes, storage products like starch and synthesis of other classes of molecules like fatty acids and terpenes during the stress were noticed in susceptible genotype. However, biological regulations, generation of precursor metabolites, signal transduction, photosynthesis, regulation of cellular process, energy and carbohydrate metabolism were seen in tolerant genotype during the stress. KEGG pathway annotation revealed more number of genes regulating different pathways resulting in more tolerant. During early response phase, 24 and 11 DEGs were enriched in CTV and CSV, respectively in energy metabolism pathways. Among the 1583 DEG transcription factors (TF) genes, 69 WRKY, 46 bZIP, 41 NAC, 40 ERF, 31/14 MYB/MYB-related, 22 bHLH, 17 Nin-like 7 HSF and 4C3H were involved during early response phase. Late response phase showed 30 bHLH, 65 NAC, 30 ERF, 26/20 MYB/MYB-related, 11 C3H, 12 HSF, 86 Nin-like, 41 AP2/ERF, 55 bZIP and 98 WRKY members TF genes. The recovery phase included 18 bHLH, 50 NAC, 31 ERF, 24/13 MYB/MYB-related, 4 C3H, 4 HSF, 14 Nin-like, 31 bZIP and 114 WRKY TF genes.ConclusionsTranscriptome analysis of contrasting genotypes for cold tolerance detected the genes, pathways and transcription factors involved in the stress tolerance.
Highlights
Rice plants show yellowing, stunting, withering, reduced tillering and utimately low productivity in susceptible varieties under low temperature stress
Phenotyping of contrasting genotypes for chilling stress tolerance Upon exposure to low temperature stress, the susceptible genotype, Shahabhagidhan turned pale green and rolled leaves exhibiting a score of 5 after 7 days of exposure at 15 °C; whereas the resistant genotype, Geetanjali remained normal in growth and leaf coloration
The cellular component characterization showed six Gene ontology (GO) terms enriched of which 3 GO terms were significantly involved in all three phase of cold susceptible variety (CSV) while in cold tolerant variety (CTV), these were enriched in 24 h recovery condition. This indicates the absence of photosynthesis related genes, storage products like starch and synthesis of other classes of molecules like fatty acids and terpenes used for energy production and as raw material for the synthesis of other molecules during cold stress condition in CSV
Summary
Rice plants show yellowing, stunting, withering, reduced tillering and utimately low productivity in susceptible varieties under low temperature stress. High temperature, drought, salinity and flooding affect adversely in rice production. Rice being chilling-sensitive plant shows yellowing, slow seedling growth, stunting, withering, reduced tillering and utimately low productivity in cold susceptible varieties under low temperature stress [1,2,3,4]. The stress covers around 4 million hectares of rice areas of the country targeting the seedling-stage causing delay in growth of the plant which coincide with high temperature stress during flowering stage [3, 7]. Developing high yielding varieties possessing cold stress tolerance may help in further augmenting rice production in these vulnerable regions. More insight into the molecular mechanisms of tolerance in response to chilling stress need to be revealed
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