title: Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea.
abstract: Drought and salinity are the major factors that limit chickpea production worldwide. We performed whole transcriptome analyses of chickpea genotypes to investigate the molecular basis of drought and salinity stress response/adaptation. Phenotypic analyses confirmed the contrasting responses of the chickpea genotypes to drought or salinity stress. RNA-seq of the roots of drought and salinity related genotypes was carried out under control and stress conditions at vegetative and/or reproductive stages. Comparative analysis of the transcriptomes revealed divergent gene expression in the chickpea genotypes at different developmental stages. We identified a total of 4954 and 5545 genes exclusively regulated in drought-tolerant and salinity-tolerant genotypes, respectively. A significant fraction (~47%) of the transcription factor encoding genes showed differential expression under stress. The key enzymes involved in metabolic pathways, such as carbohydrate metabolism, photosynthesis, lipid metabolism, generation of precursor metabolites/energy, protein modification, redox homeostasis and cell wall component biogenesis, were affected by drought and/or salinity stresses. Interestingly, transcript isoforms showed expression specificity across the chickpea genotypes and/or developmental stages as illustrated by the AP2-EREBP family members. Our findings provide insights into the transcriptome dynamics and components of regulatory network associated with drought and salinity stress responses in chickpea.
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Rohini
authors.initials: R
authors.lastname: Garg
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Rama
authors.initials: R
authors.lastname: Shankar
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Bijal
authors.initials: B
authors.lastname: Thakkar
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India.
authors.forename: Himabindu
authors.initials: H
authors.lastname: Kudapa
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India.
authors.forename: Lakshmanan
authors.initials: L
authors.lastname: Krishnamurthy
authors.affiliation: School of Applied Sciences, RMIT University, Victoria, Australia.
authors.forename: Nitin
authors.initials: N
authors.lastname: Mantri
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Sabhyata
authors.initials: S
authors.lastname: Bhatia
authors.affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.|School of Computational &Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Mukesh
authors.initials: M
authors.lastname: Jain
mesh_terms: D000220:Adaptation, Biological; D029863:Cicer / Q000502:physiology*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D010641:Phenotype; D015203:Reproducibility of Results; D054712:Salinity; D013312:Stress, Physiological / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D014157:Transcription Factors