Publications of NIPGR Scientists
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Item Genome-wide identification and expression analysis of chickpea U-box E3 ligases identifies CaPUB4 and CaPUB16 as candidate responsive genes for abiotic stress tolerance(Springer Nature Publishing AG, 2026) Fernandes, Nithya; Unnati, G. Meher; Bhattacharjee, Surjit; Pandey, Ashutosh; Mishra, NeelamU-box E3 ubiquitin ligases play a crucial role in post-translational protein modification, stress signaling, and cellular adaptation in plants. In this study, 38 non-redundant CaPUB genes were identified from the chickpea (Cicer arietinum) genome and characterized for their phylogenetic relationships, domain architecture, gene structures, and expression profiles. Synteny and gene ontology analyses revealed evolutionary conservation with Lotus japonicus and Arabidopsis thaliana, and functional involvement in processes such as ubiquitination, signaling, and stress responses. RNA sequencing and qPCR analyses demonstrated distinct tissue-specific expression patterns. Specifically, CaPUB14 and CaPUB2 were predominantly expressed in particular organs, whereas CaPUB4 and CaPUB16 were upregulated under drought and salt stress in the stress-tolerant ICC4958 cultivar. Functional interaction network analysis revealed that CaPUB4 and CaPUB16 proteins interact with an identical set of partner proteins, supporting the hypothesis that these ligases may function collaboratively in stress adaptation. Collectively, these findings provide insights into the diversity, expression patterns, and potential regulatory roles of the CaPUB gene family, highlighting promising candidate genes for future functional characterization and their possible utility in improving crop stress resilience.Item Dissecting the genetic basis of seed-iron content in Chickpea using a combinatorial approach of QTL-Seq and molecular haplotyping(Springer Nature Publishing AG, 2026) Singh, Gourav; Chakraborty, Anirban; Singh, Sangeeta; Bhardwaj, Shubham; Parida, Swarup K.; Bhatia, SabhyataIn order to map the QTL(s) and genes regulating the complex seed-iron content (SFC) trait in chickpea, the quantitative trait locus (QTL)-seq approach was used. Whole genome re-sequencing of DNA bulks derived from a mapping population (ICC8261 × 1CC4958) contrasting for SFC led to the identification of three QTLs, [CaqFe4.1 (0.10 Mb), CaqFe4.2 (0.54 Mb) and CaqFe7.1 (0.83 Mb)] in chickpea. In-silico expression analysis of genes underlying the QTLs revealed their varied levels during stages of seed development. Moreover, estimation of Gʹ values of the SNPs identified in the QTL region revealed a SNP that generated synonymous variant of the MAIN-like-2 gene. Haplotype analysis of MAIN-like-2 in a diverse panel of chickpea germplasm varying for SFC further exemplified its haplotypes that displayed strong association to this trait. Homology-based protein interaction analysis coupled with quantitative-real time PCR based-expression analysis revealed several co-expressing co-chaperone and heat shock proteins including P23-1, HSP 90.5 and HSP90.6, having well established roles in seed development as protein components of MAIN-like-2 proteins in chickpea. The functional loci as well as the molecular signatures defined in this study have potential to expedite marker assisted breeding of iron-rich chickpea varieties.Item Novel method for rapid screening of chickpea for combined dry root rot disease and osmotic stress(Springer Nature Publishing AG, 2026) Ranjan, Shubhashish; Chavan, Chaitali Narendra; Senthil-Kumar, MuthappaChickpea (Cicer arietinum L.), confronts substantial challenges from the emerging pathogenic fungus Macrophomina phaseolina (Tassi) Goid, causing dry root rot (DRR) disease. Chickpea plants severely affected by combined DRR and drought stress. Currently sick plot and sick pot method are utilized for germplasm screening to identify tolerant genotypes. These methods are time-consuming; therefore, we propose a novel methodology for the rapid screening of chickpea under combined DRR and osmotic stress conditions. This chapter introduces an adept high-throughput phenotyping methodology, conducted within controlled laboratory conditions, aiming to investigate the interaction between osmotic stress and DRR disease in chickpea crops. The methodology employs an innovative pouch technique for screening combined stress, providing a streamlined temporal investigation process and precise control over stress parameters. The incorporation of polyethylene glycol (PEG) enables the simultaneous imposition of osmotic stress alongside pathogen infection, making the methodology versatile for studying combined stress scenarios. This approach fills a gap in concurrent stress imposition techniques, enhancing germplasm screening by identifying genotypes with varying susceptibility and resistance levels. Thus, we suggest use of high-throughput phenotyping in combination genome-wide association study (GWAS) can take combined stress resistance breeding in chickpea at next level to combat food security and climate change.Item A blotting paper technique for the screening of chickpea genotypes against dry root rot disease(Springer Nature Publishing AG, 2026) Durgadevi, Athimoolam; Pandey, Prachi; Senthil-Kumar, MuthappaDry root rot (DRR) disease is a major threat to chickpea production across the world. This disease is caused by a soil-borne necrotrophic fungal pathogen, Macrophomina phaseolina. The use of disease-resistant varieties paves the way to conquer the disease spread. Though chickpea germplasm with rich genetic diversity is available around the world, its response to DRR is still unexplored. In turn, this demands screening and identification of resistant genotypes for crop protection against the disease. Here we describe an improved blotting paper technique for the large-scale screening of chickpea genotypes for DRR resistance. The method is quick, cost-effective, less labour-intensive, and thus optimized for high-throughput screening and can be efficiently used to screen a large number of chickpea genotypes for resistance against DRR.Item Expression analysis of ROS-related genes during the germination of chickpea (Cicer Arietinum L.) seeds(Springer Nature Publishing AG, 2026) Babuta, Priyanka; Samant, Sanjib Bal; Saini, Deepak; Gupta, Kapuganti JagadisSeed germination is a critical physiological process that transforms a quiescent seed into a metabolically active seedling and is also a crucial factor in determining maximum crop production. This transition is influenced by various intrinsic and extrinsic factors. Interestingly, reactive oxygen species (ROS) plays an important role in breaking seed dormancy by oxidation of biomolecules, weakening of the testa and degradation of endosperm. Similarly, molecular internal oxygen is also considered vital for the transition of dormancy to seed germination. However, it is essential to establish a correlation between the internal oxygen and the generation of ROS during seed germination. This chapter details protocols for imaging internal oxygen concentrations using VisiSens and fluorescent detection of ROS using H2DCFDA in chickpea seeds, complemented by qPCR analysis of key ROS-related genes (RBOH, AOX 1, UCP 1, and NADH dehydrogenase). These findings from these methods help advance our understanding of the inverse relationship between molecular oxygen and ROS dynamics during seed germination.Item Identification of tRNA-derived fragments in legumes(Springer Nature Publishing AG, 2026) Arora, Simran; Aftab, Sahrish; Shree, Tanu; Kumar, ShaileshThe tRNA-derived noncoding RNAs (tncRNAs) belong to the novel class of noncoding RNAs, acting as important components of genome regulatory circuits. In planta, the mechanism of generation and function of tncRNAs is not fully elucidated. Production of important leguminous plants like chickpea, Medicago and soybean is majorly hampered due to different biotic and abiotic stresses. Identification and characterization of tncRNAs in legumes may open a new paradigm for molecular biologists to make novel tools for the improved varieties of legumes for sustainable agriculture. The first step in the study of tncRNAs is to identify and annotate them in small RNA sequencing datasets. Here, we have demonstrated the tncRNA Toolkit for the identification and annotation of tncRNAs in a small RNA sequencing dataset of the important legume crop chickpea.Item Induced post-invasive defenses in the nonhost plant Parthenium hysterophorus L. prevent root cortical colonization by Macrophomina phaseolina and impart resistance to dry root rot(Elsevier B.V., 2025) Mirchandani, Rishabh; Kandpal, Manu; Ranjan, Aashish; Sinharoy, Senjuti; Senthil-Kumar, MuthappaDry root rot (DRR) of chickpea is caused by the broad-range necrotrophic fungus Macrophomina phaseolina. Chickpea germplasm does not provide durable resistance to DRR, which is particularly devastating under drought. Even moderately resistant chickpea varieties become susceptible under combined stress. We hypothesized that nonhost resistance (NHR) is durable even under combined stress. Using the blotter paper assay and stereomicroscopic observations, we identified the asterid weed Parthenium hysterophorus as a potential nonhost of M. phaseolina among 82 potential nonhosts. Epidermal necrotic lesions were prevented in P. hysterophorus. In planta fungal load was 0.195 and 0.007 ng/ng total DNA in chickpea and P. hysterophorus, respectively. M. phaseolina could not colonize the P. hysterophorus root while up to 6 cortical cell layers were colonized in chickpea. Further, NHR was durable under combined stress. Dual RNA sequencing revealed that M. phaseolina actively attempted to infect the nonhost and activated specific genes in the xenobiotics degradation pathway. P. hysterophorus also showed an active defense response with1958 and 2294 differentially expressed genes at 2 and 4 DAI, respectively, with 363 upregulated at both time points. Differential expression of cell wall synthesis, phytohormone signaling, and other defense response pathways likely contributes to NHR. Few genes in the phenylpropanoid biosynthesis pathways in P. hysterophorus were also upregulated, possibly because these metabolites are linked to the distinct changes in the fungus during nonhost infection. We therefore conclude that P. hysterophorus exhibits post-invasive NHR to M. phaseolina and that general defense, phytohormone signaling and secondary metabolic pathways contribute to NHR.Item Deciphering the dynamics of enzymes associated with the synthesis of cryoprotectants during cold acclimation in contrasting chickpea genotypes(Springer Nature Publishing AG, 2025) Padhiar, Deeksha; Kaur, Sarbjeet; Rani, Anju; Jha, Uday Chand; Prasad, P. V. Vara; Sharma, Kamal Dev; Kumar, Sanjeev; Parida, Swarup K.; Siddique, Kadambot H. M.; Nayyar, HarshChickpea, a vital legume crop, is highly susceptible to cold stress, especially during its reproductive phase, resulting in significant flower and pod abortions and reduced seed yield. Our previous study demonstrated that cold acclimation is effective in enhancing cold tolerance but benefits only cold-tolerant (CT) genotypes, while cold-sensitive (CS) genotypes remain unaffected. In this extended study aimed at probing the detailed mechanisms of this differential response, we further examined the expression profiles of enzymes involved in the synthesis and breakdown of osmolytes (pyrroline-5-carboxylate synthase, proline dehydrogenase (PDH), betaine aldehyde dehydrogenase) and sugars (sucrose synthase, acid invertase, trehalose-6-phosphate synthase, trehalose-6-phosphate phosphatase, and trehalase activity), along with the expression of various antioxidants (superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase) in both CT and CS genotypes. Seeds of two contrasting chickpea genotypes, cold-tolerant ICC 17258 and cold-sensitive ICC 15567, were planted in pots during the first week of November in an outdoor field environment. After 40 days, the plants were transferred to walk-in growth chambers for cold acclimation at specific temperatures. Initially, the plants were exposed the plants to 25/18℃ (pre-acclimation stage; PAS) for 2 days, followed by a 21-day cold acclimation period with progressively decreasing temperatures over seven days for each cold acclimation stage (CAS): CAS1 (21/13℃), CAS2 (18/10℃), and CAS3 (15/8℃). Subsequently, the plants were subjected to cold stress at 13/7℃ for 15 days and then exposed to 30/23℃ (12 h day/night) until maturity. Our findings demonstrated that the expression of various enzymes involved in the synthesis of osmolytes and sugars in leaves, anthers, and ovules was significantly upregulated during the cold acclimation process in the CT chickpea genotypes but not in the CS genotypes. This enhanced metabolic activity, coupled with elevated levels of enzymatic antioxidants during the acclimation process, contributed to improved leaf water status, photosynthetic efficiency, and ultimately, superior reproductive performance (pollen germination, pollen viability, stigma receptivity, and ovule viability) under cold stress conditions compared to CS genotypes. The enhanced cold tolerance observed in the CT genotypes is likely attributable to their genetic predisposition and efficient stress defense mechanisms facilitated by the upregulated expression of cold-responsive enzymes.Item Global identification of metal ion transporters in chickpea and delineating the role of CaYSL4 in orchestrating iron content(Elsevier B.V., 2025) Singh, Gourav; Manivannan, Abinaya; Pandey, Vimal; Bhatia, SabhyataMetal ion transporters (MITs) are vital to maintain proper metal homeostasis during growth and development of plants thereby necessitating their identification and characterization. Considering the economic importance of chickpea in human nutrition, the molecular behaviour and biological functions of the metal ion transporters (MIT) encoding gene families remains highly relevant in recent times. Global identification of MITs revealed a total of 12 CAXs, 6 CTRs, 11 MGTs, 15 MTPs, 9 NRAMPs, 16 OPTs, and 14 ZIPs responsible for metal ion transport. Assessment of phylogenetic relationships, chromosomal distribution, gene structure and motif analysis of MITs suggested their diverse functions. The yellow stripe-like (YSL) family of transporters is an important family whose members have been suggested to have a role in metal ion translocation and assimilation. Expression analysis of key YSLs including CaYSL1, CaYSL4, CaYSL6 and CaYSL16 indicated their significant involvement in conferring tolerance to Fe starvation. Notable was the expression of CaYSL4 that showed specific expression in flower, leaf, shoot, seed at 30 DAA and 40DAA after 7 and 10 day of Fe-deficiency treatment. It was found to be localized in the plasma membrane. RNAi-mediated silencing of CaYSL4 demonstrated its critical role in orchestrating Fe, Zn, Cu and Mn translocation in chickpea seeds. Collectively, the comprehensive analysis of MITs coupled with the functional role of CaYSL4 provides critical insight into the complex regulation of Fe ion transport and distribution that will enable breeding of nutritionally enhanced chickpea varieties.Item Exploring the synergistic effects of drought and heat stress on chickpea seed development: Insights into nutritional quality and seed yield(Elsevier B.V., 2024) Awasthi, Rashmi; Devi, Poonam; Jha, Uday Chand; Sharma, Kamal Dev; Roorkiwal, Manish; Kumar, Sanjeev; Pareek, Ashwani; Siddique, Kadambot H.M.; Prasad, PV Vara; Parida, Swarup K.; Nayyar, HarshGrowing chickpea (Cicer arietinum L.) faces significant challenges due to rising temperatures and drought stress, particularly during the reproductive and seed-filling phases. This study investigated the single and joint impacts of drought and heat stress on seed development, focusing on the responses of drought-tolerant (DT) and droughtsensitive (DS) chickpea genotypes. Initially raised in an outdoor environment (mean day and night temperature of 27 and 16±1 ◦C, respectively, light intensity of 1230–1440 µmol m− 2 s − 1 , relative humidity of 70/43 %) until seed filling (around 110–113 days after sowing) commenced. The plants were subsequently exposed to single or combined heat and drought stress under controlled conditions until maturity. Control pots were maintained at day and night temperature of 25 and 15 ◦C, respectively with 500 µmol m− 2 s − 1 light, 60–65 % RH, and regular irrigation, and drought-stressed pots were kept at 50 % field capacity under the same conditions of light and humidity. Heat stress in pots was gradually increased to 32(day)/20 ◦C (night) under regular irrigation, while combined stress pots experienced both drought (50 % field capacity) and heat stress conditions 32(day)/20 ◦C (night) under the same light and humidity conditions with irrigation. All stress treatments adversely affected cell membranes, photosynthesis, and water regulation, with more pronounced effects under combined stress. While heat stress increased stomatal conductance, drought and combined stress significantly reduced it. Seed filling rate and duration decreased under all stress conditions, especially combined stress. The stresses in combination severely reduced seed weight and pod numbers compared to individual stresses. Enzyme activities involved in starch and sucrose synthesis and hydrolysis substantially decreased under the combined stress. Seed composition elements (starch, storage proteins, sugars, fat, crude fiber, and ash) exhibited significant reductions across all stress treatments, particularly for the combined stress. Thus, under combined stresses, starch, proteins, and soulube sugars were markedly decreased to 13–20 %, 6.4–12.4 %, and 3–5 % in seeds, compared to 37–39 %, 21–24 %, and 6 % in control seeds. The DT genotype outperformed the DS genotype for all traits under individual and combined stress conditions. Principal component analysis revealed a complex interplay among various physiological responses (membrane damage, chlorophyll, chlorophyll fluorescence, relative leaf water content, and stomatal conductance), seed yield, and seed composition under the combined stress. This study highlighted that combined heat and drought stress severely impacted chickpea yield and nutritional traits, such as seed starch and protein content, compared to individual stresses underscoring the need to develop cultivars tolerant to this stress combination.