Publications of NIPGR Scientists
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Item The Mediator complex subunit, OsMED26_2, modulates plant growth, seed set and seed traits related to starch quality in rice(Elsevier B.V., 2026) Prusty, Ankita; Malik, Naveen; Ranjan, Rajeev; Agarwal, Pinky; Parida, Swarup K.; Kapoor, Sanjay; Tyagi, Akhilesh K.The Mediator (MED) complex is a multi-subunit structure crucial for RNA polymerase II-dependent transcription in eukaryotes. In this study, we investigated the function of a seed-preferential subunit of the rice Mediator complex, namely, OsMED26_2, for the first time. Knockdown of OsMED26_2 in rice reduced plant height and altered panicle morphology with shorter panicles, lesser branching, and fewer seeds per panicle. OsMED26_2 knockdown also led to shorter grains with shorter length and chalky endosperm. A significantly higher percentage of grains with chalkiness (PGWC) and degree of chalky endosperm (DCE) was observed in OsMED26_2 knockdown lines. OsMED26_2-knockdown seeds contained lower starch levels and altered proportions of amylose and amylopectin. Scanning electron microscopy further showed that these changes caused irregular, round, and loosely packed starch granules in the endosperm, contributing to the chalky phenotype. Decreased amylose content and increased grain chalkiness were corroborated by the downregulation of the Waxy (Wx) gene, which is involved in amylose synthesis, and altered expression of AMY3A, CHALK5, FLO4, GPA3, and SUSY3 genes, which regulate grain chalkiness. Our findings demonstrate that OsMED26_2 is critical in regulating panicle architecture, impacting yield, and modulating starch level and composition to control grain chalkiness and thereby suggesting its functional significance especially in manipulating yield attributing grain cooking quality traits of rice.Item 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, AmarjeetThe 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.Item Pangenome-wide identification, evolutionary analysis, and characterization of WOX gene family among Brassica Triangle of U's genomes(Elsevier B.V., 2025) Soundararajan, Prabhakaran; Vivek, AT; Suresh, Gokul Babu; Shukla, Bhavya; Singh, Kanchan B.M.; Kumar, Shailesh; Manivannan, AbinayaWUSCHEL-related homeobox (WOX) is an evolutionarily important gene family involved in key developmental processes such as embryo patterning, stem cell regulation, apical meristem maintenance, etc. Brassica contains several widely diversified and economically important vegetables grown worldwide. In this study, a pangenome-wide identification and characterization of the WOX gene family among all the species of Brassica Triangle of U's have been performed. WOX gene family was identified from the genomes of 31 Brassica species/morphotypes. About 26–28, 28, and 26–31 copies of WOX genes are present in diploid progenitors such as B. rapa (AA), B. nigra(BB), and B. oleracea (CC), respectively. In allotetraploid species, the number of WOX genes exceeds more than 50 copies. However, their number varies between morphotypes at the pangenome level. Motif and gene structure analysis showed distinct and conserved patterns between homoeologous genes. Non-synonymous (Ka)/Synonymous (Ks) ratio indicated that more number of modern/WUS clade orthologs underwent positive selection followed by those of the intermediate clade. Interacting networks between the WOX and miRNA showed that the CC genome has more complex network pattern compared to the AA genome. Although the WOX-miRNA interactions observed in both AABB and AACC genomes were distinct, they exhibited similarity in overlapping connections. Transcriptome data, analyzed from unfertilized ovule to seven developmental stages of embryos and their seed coat, sourced from public databases across six genomes, illustrated that WOX genes are expressed in a spatio-temporal manner throughout these developmental stages. Furthermore, qPCR analysis of WOX genes at two stages, such as 2–3 days old (leaf and root primordia) and 3 weeks old seedlings (leaf and root) in B. juncea and B. oleracea provides details of stage- and tissues-specific expression patterns between AB and C genomes. Overall, the present study sheds light on evolution and characterization of the WOX gene family in Brassica at the pangenome level for further functional validation.Item Revisiting development and physiology of wild rice relatives for crop improvement and climate resilience(Springer Nature Publishing AG, 2025) Mathan, Jyotirmaya; Dwivedi, Aditi; Ranjan, AashishIncreasing rice yield and productivity under changing climatic conditions is imperative for sustainable food security, given rice is a major staple crop around the world. Natural variation in crop plants, including wild relatives, offers remarkable genetic variability to explore the desirable developmental and physiologic traits for crop improvement. Wild relatives of rice, with distinct developmental and physiologic features compared to cultivated varieties, are the potential genetic and genomic resource for rice yield increases under changing climate. A thorough genetic basis of rice developmental and architectural changes during domestication is now established with the identification and characterization of domestication genes. Photosynthetically efficient wild rice accessions, with desirable developmental, physiologic, and metabolic traits, have been identified in recent years that could be instrumental for rice improvement. While several abiotic and biotic stress-tolerant wild relatives of rice along with the associated genetic loci have been identified over the years, a comprehensive insight into the desirable developmental and physiologic attributes of the wild rice is limited. Moreover, the usage of wild rice is not streamlined in rice-improvement programs due to genetic and genomic constraints. In this review, we summarize the desirable developmental and physiologic features of wild rice species that can be exploited for combining yield increases with climate resilience in rice-improvement programs.Item Genome-wide identification and molecular characterization of core ABA signaling components under abiotic stresses and during development in chickpea(Springer Nature Publishing AG, 2025) Kamali, Saravanappriyan; Sonkar, Kamankshi; Ankit, Ankit; Deepika, Deepika; Sharma, Ankita; Singh, AmarjeetAbscisic acid (ABA) signaling is vital for plant's response to abiotic stresses and development. Core components of ABA signaling include ABA receptors PYR/PYL/RCAR, group-A PP2Cs (PP2C-As) and SnRK2 serine/threonine kinases. These have been well studied in Arabidopsis, but their knowledge in the legume crop chickpea is missing. Here, we identified 8 PYLs, 11 PP2C-As and 13 SnRK2s genes in the chickpea genome. Gene duplication events have been found to drive their evolution and expansion in chickpea. Protein homology modeling revealed three-dimensional structure, and arrangements of α-helix, β-sheets and p-loops in respective families. In-planta subcellular localization analysis revealed that CaPYL3 and CaPYL5 proteins were localized at the plasma membrane, and CaPP2CA-1 and CaSnRK2.7 were localized in the cytoplasm and the nucleus. RNA sequencing data analysis indicated the regulatory role of CaPYLs, CaPP2C-As and CaSnRK2s in developmental stages particularly, stages of early embryogenesis to seed maturity. Through RT-qPCR analysis drought, salt and ABA responsive CaPYL, CaPP2C-A and CaSnRK2 genes, which might regulate abiotic stress response in chickpea were identified. Importantly, key genes like CaPYL4, CaPP2C-A4, CaPP2C-A11 and CaSnRK2.9 with overlapping expression in drought, ABA and seed development were identified, which might determine chickpea crop yield. In-silico interaction analysis revealed specific and overlapping interaction among ABA signaling proteins indicating their functional relevance. Overall, core ABA signaling components are crucial for abiotic stress tolerance and development in chickpea. These genes will be functionally validated in the future and will be utilized to generate abiotic stress resilience and high-yielding chickpea varieties.Item The developmental dynamics in cool season legumes with focus on chickpea(Springer Nature Publishing AG, 2023) Basu, Udita; Parida, Swarup K.Chickpea is one of the most widely consumed grain legume world-wide. Advances in next-generation sequencing and genomics tools have led to genetic dissection and identification of potential candidate genes regulating agronomic traits in chickpea. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored. Studies in crops such as rice, maize, tomato and pea have highlighted the contribution of key regulator of developmental events in yield related traits. A comprehensive knowledge on the development aspects of a crop can pave way for new vistas to explore. Pea and Medicago are the close relatives of genus Cicer and the basic developmental events in these legumes are similar. However, there are some distinct developmental features in chickpea which hold potential for future crop improvement endeavours. The global chickpea germplasm encompasses wide range of diversities in terms of morphology at both vegetative and reproductive stages. There is an immediate need for understanding the genetic and molecular basis of this diversity and utilizing them for the yield contributing trait improvement. The review discusses some of the key developmental events which have potential in yield enhancement and the lessons which can be learnt from model legumes in this regard.Item 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, ShaileshBURP 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.Item 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, AmarjeetK+ 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.Item Expression dynamics indicate the role of Jasmonic acid biosynthesis pathway in regulating macronutrient (N, P and K+) deficiency tolerance in rice (Oryza sativa L.)(Springer Nature Publishing AG, 2021) Deepika; Singh, AmarjeetKey message: Expression pattern indicates that JA biosynthesis pathway via regulating JA levels might control root system architecture to improve nutrient use efciency (NUE) and N, P, K+ defciency tolerance in rice. Abstract: Defciencies of macronutrients (N, P and K+) and consequent excessive use of fertilizers have dramatically reduced soil fertility. It calls for development of nutrient use efcient plants. Plants combat nutrient defciencies by altering their root system architecture (RSA) to enhance the acquisition of nutrients from the soil. Amongst various phytohormones, Jasmonic acid (JA) is known to regulate plant root growth and modulate RSA. Therefore, to understand the role of JA in macronutrient defciency in rice, expression pattern of JA biosynthesis genes was analyzed under N, P and K+ defciencies. Several members belonging to diferent families of JA biosynthesis genes (PLA1, LOX, AOS, AOC, OPR, ACX and JAR1) showed diferential expression exclusively in one nutrient defciency or in multiple nutrient defciencies. Expression analysis during developmental stages showed that several genes expressed signifcantly in vegetative tissues, particularly in root. In addition, JA biosynthesis genes were found to have signifcant expression under the treatment of diferent phytohormones, including Auxin, cytokinin, gibberellic acid (GA), abscisic acid (ABA), JA and abiotic stresses, such as drought, salinity and cold. Analysis of promoters of these genes revealed various cis-regulatory elements associated with hormone response, plant development and abiotic stresses. These fndings suggest that JA biosynthesis pathway by regulating the level of JA might control the RSA thus, it may help rice plant in combating macronutrient defciency.Item Kinase module of mediator complex: important signalling processor for development and survival of plants(Oxford University Press, 2021) Agrawal, Rekha; Jiří, Fajkus; Thakur, Jitendra K.Mediator, a multisubunit protein complex is a signal processor that conveys regulatory information from transcription factors (TFs) to RNA Polymerase II (RNA Pol II) and therefore, plays an important role in the regulation of gene expression. This mega Dalton complex comprises four modules namely Head, Middle, Tail, and Kinase. The first three modules form the core part of the complex whereas association of the Kinase module is facultative. Being able to tweak the function of Mediator, the Kinase module has established itself as a major transcriptional regulator of numerous developmental and biochemical processes. The Kinase module consists of MED12, MED13, CycC, and kinase CDK8. Upon association with Mediator, the Kinase module can alter its structure and function dramatically. In the last decade, it has been established that the Kinase module is very important for plant growth and development and the fight against biotic and abiotic challenges. However, there is no comprehensive review discussing these findings in detail and depth. In this review, we have surveyed the regulation of Kinase module subunits and highlighted the multitude of their functions in plants. Coordination between the subunits to process different signals for optimum plant growth and development is also discussed.