Abstract
To reveal the genetic potentiality of a rice line for stress tolerance, the conventional way is physiological and biochemical profiling under induced stress followed by validation through RT PCR based gene expression analysis. Though this technology is very useful and dependable, in the era of Plant Genomics and Post-Genomic bioinformatics, global transcriptome analysis is the current trend for identifying the potential genotype for their promising stress tolerance attributes. In the present study, RNA-seq analysis was performed on a potential upland-improved rice line (var. CR Dhan 40) to get a molecular insight into drought tolerance through a cataloguing of differentially expressed genes. Young seedlings (11 days old) of the selected line were exposed to water stress (12.5% relative to control) for 10 days and the leaves were subjected to transcriptome analysis. Total RNA extraction followed by preparation of cDNA libraries generated ~ 549 million high-quality reads which were mapped and aligned with the Oryza sativa indica reference rice genome. A total of 635 differentially expressed genes (DEGs) were enumerated, of which 445 were upregulated and 190 were downregulated. GO enrichment analysis of the DEGs resulted in different functional categories of genes and pathways, of which six groups were highlighted that give us a clear idea about the water stress tolerance mechanism in rice. This work yielded genomic information that will enrich the available information on drought tolerance in rice, which is a typical quantitative trait regulated by a cluster of genetic elements across the whole rice genome.
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Abbreviations
- RT-PCR:
-
Real-time polymerase chain reaction
- GO:
-
Gene ontology
- DEGs:
-
Differentially expressed genes
- ROS:
-
Reactive oxygen species
- TFs:
-
Transcription factors
- RH:
-
Relative humidity
- SNP:
-
Single nucleotide polymorphism
- INDELs:
-
Insertion or deletions of nucleotide(s)
- ABA:
-
Abscisic acid
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Acknowledgements
The authors gratefully recognize financial support for the present investigation, received from the Department of Science and Technology, Govt. of India, under the Indo-Hungarian Joint Project (INT/HUN/P-08/2016). The authors also acknowledge the Departmental research facilities created under the UGC-SAP and DST-FIST programs.
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This work was financially supported by the Department of Science and Technology, Govt. of India, under the Indo-Hungarian Joint Project (INT/HUN/P-08/2016).
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RKK and GK envisaged the study. RKK, ND, GK and GG designed the work. AC performed the experiments. All authors participated in the preparation of the manuscript and approved the final manuscript.
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Chatterjee, A., Galiba, G., Kocsy, G. et al. Molecular insight into drought tolerance of CR Dhan 40: an upland rice line from Eastern India. J. Crop Sci. Biotechnol. 27, 225–234 (2024). https://doi.org/10.1007/s12892-023-00222-3
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DOI: https://doi.org/10.1007/s12892-023-00222-3