Abstract
Background
Despite plant's ability to adapt and withstand challenging environments, drought poses a severe threat to their growth and development. Although pigeon pea is already quite resistant to drought, the prolonged dehydration induced by the aberrant climate poses a serious threat to their survival and productivity.
Objective
Comparative physiological and transcriptome analyses of drought-tolerant (CO5) and drought-sensitive (CO1) pigeon pea genotypes subjected to drought stress were carried out in order to understand the molecular basis of drought tolerance in pigeon pea.
Methods
The transcriptomic analysis allowed us to examine how drought affects the gene expression of C. cajan. Using bioinformatics tools, the unigenes were de novo assembled, annotated, and functionally evaluated. Additionally, a homology-based sequence search against the droughtDB database was performed to identify the orthologs of the DEGs.
Results
1102 potential drought-responsive genes were found to be differentially expressed genes (DEGs) between drought-tolerant and drought-sensitive genotypes. These included Abscisic acid insensitive 5 (ABI5), Nuclear transcription factor Y subunit A-7 (NF-YA7), WD40 repeat-containing protein 55 (WDR55), Anthocyanidin reductase (ANR) and Zinc-finger homeodomain protein 6 (ZF-HD6) and were highly expressed in the tolerant genotype. Further, GO analysis revealed that the most enriched classes belonged to biosynthetic and metabolic processes in the biological process category, binding and catalytic activity in the molecular function category and nucleus and protein-containing complex in the cellular component category. Results of KEGG pathway analysis revealed that the DEGs were significantly abundant in signalling pathways such as plant hormone signal transduction and MAPK signalling pathways. Consequently, in our investigation, we have identified and validated by qPCR a group of genes involved in signal reception and propagation, stress-specific TFs, and basal regulatory genes associated with drought response.
Conclusion
In conclusion, our comprehensive transcriptome dataset enabled the discovery of candidate genes connected to pathways involved in pigeon pea drought response. Our research uncovered a number of unidentified genes and transcription factors that could be used to understand and improve susceptibility to drought.
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Data availability
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, PRJNA846977.
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Acknowledgements
We are grateful to the directors of the ICAR-NIPB and ICAR-IARI, New Delhi, India for providing the facilities needed to conduct the research. The authors also acknowledge the financial support received from ICAR-CRP on Genomics, NBFGR, Lucknow. We also acknowledge the support and guidance received from the Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India.
Funding
This research was supported by Joint CSIR-UGC Fellowship awarded by Department of Higher Education, Ministry of Education, India. The work is also supported by funds received from, ICAR-NIPB, New Delhi, India. Council of Scientific and Industrial Research, India. 09/752(0093)2019-EMR-I.
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SP designed and performed the experiments, data analysis and writing of the original manuscript draft. HS and KT performed the bioinformatics analysis and data interpretation. TK performed the library preparation. KG, SG, and NKS conceptualized the work, provided the resources, supervised the experiments and reviewed the manuscript. SwS assisted in experimentation, data analysis and reviewing of the manuscript. SaS and KT were involved in manuscript reviewing and finalization. All authors contributed to the article and agreed to submit a version of the manuscript.
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Pahal, S., Srivastava, H., Saxena, S. et al. Comparative transcriptome analysis of two contrasting genotypes provides new insights into the drought response mechanism in pigeon pea (Cajanus cajan L. Millsp.). Genes Genom 46, 65–94 (2024). https://doi.org/10.1007/s13258-023-01460-z
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DOI: https://doi.org/10.1007/s13258-023-01460-z