Publications of NIPGR Scientists

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    Genomic, structural, and molecular analysis of calmodulin-binding transcriptional activators (CAMTAs) suggests their role in plant development and abiotic stress tolerance in chickpea
    (Elsevier B.V., 2025) Sonkar, Kamankshi; Kamali, Saravanappriyan; Kumar, Atul; Deepika, Deepika; Ankit, Ankit; Singh, Amarjeet
    The calmodulin-binding transcriptional activator (CAMTA) transcription factors regulate the expression of target genes in Ca2 + dependent cellular functions. CAMTAs are known to regulate biotic and abiotic stress tolerance, and development in plants. CAMTA family has been characterized in Arabidopsis, it is yet to be explored in the legume plant chickpea. Here, we have identified and characterized the chickpea CAMTA family. Total seven CAMTA genes (CaCAMTA1–7) were identified in chickpea. Gene and domain structure analyses suggested that CAMTAs are structurally conserved. The phylogenetic analysis demarcated CaCAMTAs into three groups namely; group I, II and III, and indicated that CaCAMTAs have co-evolved in dicot leguminous plants whereas, they have divergent evolution in monocots. Protein homology modeling revealed their three-dimensional structure, and composition & conformations of α-helix, β-sheets and p-loops. Subcellular localization showed that CaCAMTA4 was localized both, in the nucleus and the cytosol whereas, CaCAMTA5 was localized in the nucleus. CaCAMTA promoters contain various cis-regulatory elements related to abiotic stresses and plant development. Expression profiling using RNA-seq data revealed differential expression of CaCAMTAs during various stages of plant development. RT-qPCR expression analysis showed that most CaCAMTA genes are drought, salt, and ABA responsive, suggesting their role in abiotic stress tolerance in chickpea. Moreover, CaCAMTA regulon was identified based on the presence of CAMTA binding motif (CGCG box) in the promoters of target genes, and in-silico interaction analysis of TF and putative targets. Overall, CaCAMTAs are crucial for abiotic stress tolerance and plant development in chickpea. Key CaCAMTA genes will be functionally characterized, and will be exploited for developing stress tolerant chickpea varieties.
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    BURP domain-containing genes in legumes: genome-wide identification, structure, and expression analysis under stresses and development
    (Springer Nature Publishing AG, 2022) Chitkara, Pragya; Poddar, Nikita; Singh, Amarjeet; Kumar, Shailesh
    BURP domain-containing proteins are a plant-specific protein family which play an important role in plant metabolism and development. These proteins have also been involved in various abiotic and biotic stress responses. In this study, genome-wide identification and characterization of BURP domain protein encoding gene family is performed in four important legumes, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Vigna radiata. BURP genes were distributed randomly across chromosomes in all four legume plants. The phylogenetic analysis classified all BURP proteins into five major subfamilies, namely, USP-like, RD22-like, BNM2-like, PG1β-like, and BURPV. Our findings revealed that BURP gene family descended from common ancestors with segmental gene duplication events playing a critical role in their evolution and expansion in legumes. The intron–exon and conserved protein motifs analysis revealed that BURP genes are structurally conserved in legumes. The promoter analysis revealed the presence of hormone, and stress-responsive cis-regulatory elements in BURP promoters, implying that BURP functions in both hormone and abiotic stress signaling. Global expression analysis revealed that several BURP genes in all four legumes express differentially during plant development, and under biotic and abiotic stresses. This indicates crucial role of BURP proteins in regulating the development of legumes and adaptation to different abiotic/biotic stresses. This study will provide the starter for cloning and detail functional investigation of BURP proteins in legume crops.
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    Molecular analysis indicates the involvement of Jasmonic acid biosynthesis pathway in low-potassium (K+) stress response and development in chickpea (Cicer arietinum)
    (Elsevier B.V., 2022) Deepika, Deepika; Ankit; Jonwal, Sarvesh; Mali, Komal Vitthalrao; Sinha, Alok Krishna; Singh, Amarjeet
    K+ is a major macronutrient and its deficiency hampers plant growth and yield. Plants combat low-K+ stress by modifying their root system architecture (RSA). Here, morphophysiological analysis revealed that chickpea plants exhibit sensitivity to low-K+ stress as shown by impaired primary root growth. Phytohormone JA regulates various facets of plant root growth, however, information of JA biosynthesis genes in chickpea is missing. We performed genome-wide identification and molecular characterization of JA biosynthesis pathway genes in chickpea. Total 33 genes belonging to different families i.e., LOXs-18, AOSs-3, AOCs-2, OPRs-6 and JARs-4 were identified in the chickpea genome. In-planta analysis revealed the localization of CaLOX7, − 10, CaAOS1, − 2 and CaAOC1 at subcellular compartments, such as membrane, chloroplast and cytoplasm. Protein expression and in-vitro enzymatic activity analysis showed that CaAOS1 an CaOPR2 are the functional enzymes in chickpea. Promoters of most genes harboured abiotic stress, hormone and development related cis-regulatory elements, suggesting their role in nutrient deficiency, abiotic stress and plant development. qRT-PCR expression profiling showed that about 15 JA biosynthesis genes from different families express differentially whereas, JA catabolism genes were repressed in chickpea root and shoot under low-K+ stress. In addition, JA biosynthesis genes showed differential expression in vegetative and reproductive development, senescence stages, desiccation, salinity and cold stress. These findings indicate the involvement of JA biosynthesis pathway in low-K+ stress response and development in chickpea. Low-K+ stress and development related genes identified in this study could be utilized in genetic engineering of chickpea plants for improved traits.
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    Genome-wide investigation of GRAM-domain containing genes in rice reveals their role in plant-rhizobacteria interactions and abiotic stress responses
    (Elsevier B.V., 2020) Tiwari, Shalini; Shweta; Prasad, Manoj; Lata, Charu
    A comprehensive genome-wide survey of GRAM-domain containing genes in rice identified total 64 genes which were grouped into six classes and were physically mapped onto different rice chromosomes. GRAM domain-containing genes showed total 8 segmental and 3 tandem duplications. Comparative physical mapping between rice OsGRAM and its orthologs in related C4-crops depicted evolutionary insights into this gene family. Expression analyses of OsGRAM genes in rice roots subjected to salt stress with or without Bacillus amyloliquefaciens (SN13) inoculation revealed significant differential expression patterns suggesting their crucial role in beneficial plant-rhizobacteria interactions under stress. Further, expression analyses of selected 15 candidate genes with ≥3.0-fold induction in salt + SN13 treated samples indicated their precise and overlapping expression patterns under various abiotic stresses and phytohormones at early (1 h) and late (24 h) durations which might be ultimately responsible for functional divergence and beneficial plant-microbe interactions. Furthermore, OsGRAM27 and OsGRAM47 could be considered as potential candidate genes for further functional characterization and application in crop improvement since these genes showed positive modulation in stress under the influence of SN13. This study provides new dimensions into the evolution and divergence of OsGRAM and their role in plant-rhizobacteria interactions that could be utilized for improving stress tolerance in crops.
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    Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice
    (Springer, 2012) Sharma, Rita; Agarwal, Pinky; Ray, Swatismita; Deveshwar, Priyanka; Sharma, Pooja; Sharma, Niharika; Nijhawan, Aashima; Jain, Mukesh; Singh, Ashok Kumar; Singh, Vijay Pal; Khurana, Jitendra Paul; Tyagi, Akhilesh K.; Kapoor, Sanjay
    Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.
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    Identification, phylogeny and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato
    (Springer, 2010) Sharma, Manoj K.; Kumar, Rahul; Solanke, Amolkumar U.; Sharma, Rita; Tyagi, Akhilesh K.; Sharma, Arun K.
    Ethylene responsive transcription factors have been shown to be intimately connected to plant development, defense responses and stress signaling pathways and in order to use them for plant improvement, we need to have better understanding of these proteins. In this study, 85 ERF genes have been identified from tomato using raw EST data in various public repositories. Phylogenetic analysis with tomato ERF domains revealed their distribution in all the groups, previously identified in model systems. MEME motif analysis resulted in identification of conserved domains, characteristic to member of each clade, in addition to ERF domain. Expression analysis during vegetative and reproductive stages of development using QPCR and tomato GeneChip arrays, revealed their tissue-specific/preferential accumulation. In total, 57 genes were found to be differentially expressed during temporal stages of tomato fruit development. The expression analysis of 23 ERF family genes representing each clade in response to seven abiotic stress treatments revealed their differential expression in response to more than one abiotic stress treatments. Results suggest that ERF genes play diverse roles in plant's life and comprehensive data generated will be helpful in conducting functional genomics studies to understand their precise role during plant development and stress response.