Publications of NIPGR Scientists
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Item Genotypic variability and trait associations for cold stress tolerance in cultivated chickpea (Cicer arietinum L.) during the reproductive stage(PLOS, 2026) Padhiar, Deeksha; Kaur, Sarbjeet; Parida, Swarup K.; Jha, Uday C; Shama, Kamal Dev; Prasad, Pagadala Venkat Vara; Siddique, Kadambot H M; Nayyar, HarshChickpea (Cicer arietinum L.), a major winter legume in northern South Asia and Australia, frequently encounters low temperatures (0–15 °C) during reproduction, causing substantial yield losses. The present study involved screening two independent sets of 100 genotypes over consecutive winters to identify sources of reproductive-stage cold tolerance and to elucidate the underlying mechanisms. Following outdoor establishment, plants were exposed to controlled cold stress (15/7 °C day/night) during flowering and pod development (15 d) in walk-in growth chambers. Ten representative cold-tolerant (CT) and ten cold-sensitive (CS) genotypes were selected each year based on integrated performance across yield, physiological, biochemical, and reproductive traits for a detailed mechanistic analysis. Cold-sensitive genotypes exhibited severe dysfunction, characterized by high electrolyte leakage (50−59% above CT) and malondialdehyde (39−51% above CT), indicating membrane damage. Reduced chlorophyll content (21−23%), photosystem II efficiency (23−29%), and stomatal conductance (40−43%) impaired photosynthesis. Inadequate cryoprotectants (reduced by 25−58%) and antioxidants (reduced by 38−55%) caused oxidative damage. Reproductive collapse followed, with pollen viability and germination declining by 24−46%, stigma receptivity and ovule viability decreasing by 41−68%, and seed yields falling by 85−95%. Cold-tolerant genotypes-maintained homeostasis through integrated protection in terms of superior membrane stability, enhanced compatible solutes, and elevated antioxidant activities, which sustained photosynthesis and reproductive success, achieving better yields under cold stress. Principal component analysis revealed cold tolerance as an integrated system (PC1:72.6–81.3% variance), clearly separating the CT from the CS genotypes. Membrane stability, photosynthetic efficiency, and pollen viability emerged as diagnostic traits (r = 0.85–0.91 with yield, p < 0.001; heritability 70−99%). Tolerance operated independently of maturity (R² = 0.10–0.18), enabling donor identification across maturity classes. Twenty cold-tolerant genotypes were identified, spanning the early, medium, and late maturity groups, respectively. These findings establish a mechanistic understanding of reproductive-stage cold tolerance, provide vital selection markers, and identify genetic resources for breeding cold-resilient chickpea cultivars.Item Cross-kingdom global proteomics reveals specific modulation of disease signaling in multi-host fungal pathogen infection in chickpea and worm(American Chemical Society, 2026) Narula, Kanika; Ghosh, Shobha; Khan, Iqra Nafees; Sengupta, Atreyee; Chakraborty, Niranjan; Chakraborty, SubhraAn interconnected loop of messages and counter-messages determine the outcome of host-pathogen interactions. Multihost pathogenicity across plants and animals, particularly nematode, is a major source of new infectious diseases. Fusarium oxysporum, a multihost pathogen, causes vascular wilt in chickpea and fusariosis in worm and humans. To comprehend Fusarium-responsive multihost pathogenicity, we temporally profiled cross-kingdom species, chickpea and worm using SWATH-mass spectrometry. Morphological analyses revealed that increased wilting and intestinal disintegration elicits a disease response in chickpea and worm. Peptide-spectrum library consisted of 5629 and 3138 proteins from Fusarium infected chickpea and worm, respectively. SWATH analysis identified 1573 and 2249 disease-responsive chickpea (CaDRPs) and worm proteins (CeDRPs) linked to diverse organs, organelles, and functionality. Pairwise comparisons; over-representation analysis between time, treatment, and organism; wilt, and fusariosis diseasome revealed common and unique modules. CaDRPs involved in preformed defense, biomolecule synthesis, phytohormone regulation, ser/thr kinase, and ATP signaling have perturbed interactions and functions, majorly in chloroplast. CeDRPs linked to the cuticular support, muscle organization, neuronal information, intestinal metabolism, G-protein, and notch signaling showed a deregulated function, especially in the cytoplasm. Common biological processes, included primary metabolism, ribosome biogenesis, calcium signaling, and proteostasis. Our data provide first evidence of translational plasticity in the Fusarium diseasome providing novel insights into multihost pathogenesis.Item A genome-wide association analysis identifies a key candidate gene controlling plant growth habit in chickpea(Springer Nature Publishing AG, 2026) Kumbhakar, Rajib; Mondal, Mayulika; Thakro, Virevol; Yadava, Yashwant K.; Jha, Uday Chand; Tripathi, Shailesh; Parida, Swarup K.Identification of molecular markers governing plant growth habit (PGH) traits that enable mechanical harvestability is pivotal for boosting production efficiency of crops under changing climates and increasing global food demand. With a combinatorial integrated genomics-assisted breeding strategy comprising of association mapping, haplotype-based association, molecular haplotyping and gene expression analysis in a 286 association panel of chickpea (Cicer arietinum), we dissected the genetic basis of PGH traits. This study employed 382,171 genome-wide SNPs (single-nucleotide polymorphisms) obtained from whole-genome sequencing (WGS) of 286 desi and kabuli chickpea accessions and delineated a major genomic locus associated with PGH traits variation, particularly between erect (E)/semi-erect (SE) versus spreading (S)/semi-spreading (SS) types. Within this genomic loci, CaPAR1 (Cicer arietinum PAR1) and its derived natural alleles/haplotypes was identified as the candidate gene. These findings can facilitate generation of high-yielding, erect/semi-erect, mechanically harvestable cultivars through translational genomics and molecular breeding for genetic enhancement of chickpea.Item Nitric oxide-mediated modulation of reproductive resilience under cold stress in chickpea(Frontiers Media S.A., 2025) Kaur, Sarbjeet; Padhiar, Deeksha; Jha, Uday Chand; Kumar, Sanjeev; Sharma, Kamal Dev; Parida, Swarup Kumar; Siddique, Kadambot H. M.; Prasad, P. V. Vara; Nayyar, HarshChickpeas are particularly sensitive to cold stress during the reproductive phase, which can significantly impair pod set and yield. This study examined the role of sodium nitroprusside (SNP), a nitric oxide (NO) donor, in mitigating cold-induced reproductive damage in cold-tolerant (CT) and cold-sensitive (CS) chickpea genotypes. After 100 days of outdoor growth, plants were subjected to cold stress (15/8°C day/night; 12 h photoperiod) for 21 days in walk-in growth chambers during the reproductive stage of development. Control plants were maintained at 25/15°C day/night temperature. SNP treatment (1 mM) was applied exogenously each time, first two days prior to stress onset and then at seven-day intervals (three applications total). Cold stress significantly lowered endogenous NO levels in leaves, anthers, and ovules, particularly in CS genotypes, thereby leading to reduced pollen viability and germination. SNP treatment restored NO and improved reproductive performance, with stronger responses in the CS than the CT genotype. For instance, pollen germination increased by 57.9% in CS versus 17.6% in CT, and pollen viability increased by 28.0% and 13.1%, respectively. Enhanced anther function resulted in a 157.2% increase in pod set and 62.0% higher seed yield in CS. SNP also improved physiological traits, including a 43.9% increase in cellular viability, 18.6% in stomatal conductance, and 41.9% in chlorophyll content in CS genotypes. Cryoprotectants (proline, trehalose, and sucrose) accumulated in anthers, reinforcing cold resilience, while oxidative stress was simultaneously alleviated through reduced malondialdehyde, hydrogen peroxide, and electrolyte leakage, together with the upregulation of both enzymatic (superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APx), and glutathione reductase (GR)) and non-enzymatic (ascorbic acid (ASC) and reduced glutathione (GSH)) components. Notably, CS genotypes showed more pronounced improvements from SNP application than CT genotypes, particularly in terms of reproductive success and yield-related traits. These findings highlight the potential of NO donors, such as SNP, to enhance cold tolerance in chickpeas, with promising implications for safeguarding productivity under low-temperature stress, especially in sensitive cultivars.Item Trans-QTL alliance of HKT1 and PHL7 modulate salinity stress tolerance and enhance crop yield endurance(John Wiley & Sons, 2026) Mohanty, Jitendra K.; Yadav, Antima; Narnoliya, Laxmi; Thakro, Virevol; Rathore, Deepanshi; Tripathi, Shailesh; Sinharoy, Senjuti; Agarwal, Pinky; Parida, Swarup K.Salinity stress can cause significant yield losses in crops because of its major impact on reproductive success. The complexity of salinity stress responses, particularly their tissue- and cell-specific regulation, continues to challenge the translation of molecular insights into tangible crop yield improvements. In the present study, the authors deployed a genomic strategy combining a genome-wide association study, regional association analysis, QTL mapping, fine mapping, and map-based cloning to delineate a pair of novel CaPHL7 and CaHKT1 alleles that regulate yield under salinity stress. The selected contrasting accessions, developed near-isogenic lines (NILs), overexpressed chickpea lines and complemented Arabidopsis lines collectively underscore the functional significance of the identified alleles in relaying yield endurance under salinity stress conditions. Functional characterisation of the genes revealed the intricate transcriptional regulation of CaHKT1 by CaPHL7, which influences the degree of salinity stress tolerance. Furthermore, in our efforts to enhance yield endurance, we discovered a novel regulatory role for the phosphorus (P) starvation-responsive gene (PHL7) in legumes, facilitating salinity stress adaptation. This study provides the first functional validation of a trans-QTL regulatory model in chickpea, where CaPHL7, located on one chromosome, transcriptionally activates CaHKT1 on a separate chromosome. The regulatory mechanism plays a key role in excluding sodium from the transpiration stream, thereby protecting reproductive processes from salinity-induced damage and mitigating yield penalties. This inter-locus regulation explains yield stability and offers useful insights that may be considered in future efforts to enhance salt resilience in chickpea.Item A next-generation combinatorial genomic strategy scans genomic loci governing heat stress tolerance in chickpea(John Wiley & Sons, 2025) Mohanty, Jitendra K.; Yadav, Antima; Narnoliya, Laxmi; Thakro, Virevol; Nayyar, Harsh; Dixit, Girish P.; Jha, Uday Chand; Prasad, P. V. Vara; Agarwal, Pinky; Parida, Swarup K.In the wake of rising earth temperature, chickpea crop production is haunted by the productivity crisis. Chickpea, a cool season legume manifests tolerance in several agro-physiological level, which is complex quantitative in nature, and regulated by multiple genes and genetic networks. Understanding the molecular genetic basis of this tolerance and identifying key regulators can leverage chickpea breeding against heat stress. This study employed a genomics-assisted breeding strategy utilizing multi-locus GWAS to identify 10 key genomic regions linked to traits contributing to heat stress tolerance in chickpea. These loci subsequently delineated few key candidates and hub regulatory genes, such as RAD23b, CIPK25, AAE19, CK1 and WRKY40, through integrated genomics, transcriptomics and interactive analyses. The differential transcript accumulation of these identified candidates in contrasting chickpea accessions suggests their potential role in heat stress tolerance. Differential ROS accumulation along with their scavengers' transcript abundance aligning with the expression of identified candidates in the contrasting chickpea accessions persuade their regulatory significance. Additionally, their functional significance is ascertained by heterologous expression and subsequent heat stress screening. The high confidence genomic loci and the superior genes and natural alleles delineated here has great potential for swift genomic interventions to enhance heat resilience and yield stability in chickpea.Item MicroRNA164e suppresses NAC100 transcription factor-mediated synthesis of seed storage proteins in chickpea(John Wiley & Sons, 2024) Chakraborty, Anirban; Singh, Baljinder; Pandey, Vimal; Parida, Swarup K.; Bhatia, SabhyataDevelopment of protein-enriched chickpea varieties necessitates an understanding of specific genes and key regulatory circuits that govern the synthesis of seed storage proteins (SSPs). Here, we demonstrated the novel involvement of Ca-miR164e-CaNAC100 in regulating SSP synthesis in chickpea. Ca-miRNA164e was significantly decreased during seed maturation, especially in high-protein accessions. The miRNA was found to directly target the transactivation conferring C-terminal region of a nuclear-localized transcription factor, CaNAC100 as revealed using RNA ligase-mediated-rapid amplification of cDNA ends and target mimic assays. The functional role of CaNAC100 was demonstrated through seed-specific overexpression (NACOE) resulting in significantly augmented seed protein content (SPC) consequential to increased SSP transcription. Further, NACOE lines displayed conspicuously enhanced seed weight but reduced numbers and yield. Conversely, a downregulation of CaNAC100 and SSP transcripts was evident in seed-specific overexpression lines of Ca-miR164e that culminated in significantly lowered SPC. CaNAC100 was additionally demonstrated to transactivate the SSP-encoding genes by directly binding to their promoters as demonstrated using electrophoretic mobility shift and dual-luciferase reporter assays. Taken together, our study for the first time established a distinct role of CaNAC100 in positively influencing SSP synthesis and its critical regulation by CamiR164e, thereby serving as an understanding that can be utilized for developing SPC-rich chickpea varieties.Item Unraveling the genetics of heat tolerance in chickpea landraces (Cicer arietinum L.) using genome-wide association studies(Frontiers Media S.A., 2024) Danakumara, Thippeswamy; Kumar, Neeraj; Patil, Basavanagouda Siddanagouda; Kumar, Tapan; Bharadwaj, Chellapilla; Jain, Pradeep Kumar; Nimmy, Manduparambil Subramanian; Joshi, Nilesh; Parida, Swarup Kumar; Bindra, Shayla; Kole, Chittaranjan; Varshney, Rajeev K.Chickpea, being an important grain legume crop, is often confronted with the adverse effects of high temperatures at the reproductive stage of crop growth, drastically affecting yield and overall productivity. The current study deals with an extensive evaluation of chickpea genotypes, focusing on the traits associated with yield and their response to heat stress. Notably, we observed significant variations for these traits under both normal and high-temperature conditions, forming a robust basis for genetic research and breeding initiatives. Furthermore, the study revealed that yield-related traits exhibited high heritability, suggesting their potential suitability for marker-assisted selection. We carried out single-nucleotide polymorphism (SNP) genotyping using the genotyping-by-sequencing (GBS) method for a genome-wide association study (GWAS). Overall, 27 marker-trait associations (MTAs) linked to yield-related traits, among which we identified five common MTAs displaying pleiotropic effects after applying a stringent Bonferroni-corrected p-value threshold of <0.05 [-log10(p) > 4.95] using the BLINK (Bayesian-information and linkage-disequilibrium iteratively nested keyway) model. Through an in-depth in silico analysis of these markers against the CDC Frontier v1 reference genome, we discovered that the majority of the SNPs were located at or in proximity to gene-coding regions. We further explored candidate genes situated near these MTAs, shedding light on the molecular mechanisms governing heat stress tolerance and yield enhancement in chickpeas such as indole-3-acetic acid-amido synthetase GH3.1 with GH3 auxin-responsive promoter and pentatricopeptide repeat-containing protein, etc. The harvest index (HI) trait was associated with marker Ca3:37444451 encoding aspartic proteinase ortholog sequence of Oryza sativa subsp. japonica and Medicago truncatula, which is known for contributing to heat stress tolerance. These identified MTAs and associated candidate genes may serve as valuable assets for breeding programs dedicated to tailoring chickpea varieties resilient to heat stress and climate change.Item Functional allele of a MATE gene selected during domestication modulates seed color in chickpea(John Wiley & Sons, 2024) Thakro, Virevol; Varshney, Nidhi; Malik, Naveen; Daware, Anurag; Srivastava, Rishi; Mohanty, Jitendra K; Basu, Udita; Narnoliya, Laxmi; Jha, Uday Chand; Tripathi, Shailesh; Tyagi, Akhilesh K.; Parida, Swarup K.Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.Item Natural alleles of Mediator subunit genes modulate plant height in chickpea(John Wiley & Sons, 2023) Malik, Naveen; Basu, Udita; Srivastava, Rishi; Daware, Anurag; Ranjan, Rajeev; Sharma, Akash; Thakro, Virevol; Mohanty, Jitendra K.; Jha, Uday Chand; Tripathi, Shailesh; Tyagi, Akhilesh K.; Parida, Swarup K.Plant height (PH) is an important plant architectural trait targeted during Green Revolution to enhance crop yields. Identification of genes and natural alleles governing plant height without compromising agronomic performance can fill the lacuna of knowledge connecting ideal plant architecture with maximum achievable yield in chickpea. Through coherent strategy involving genome-wide association study, QTL/fine mapping, map-based cloning, molecular haplotyping, and downstream functional genomics, the current study identified two Mediator subunit genes namely, CaMED23 and CaMED5b and their derived natural alleles/haplotypes underlying the major QTLs and trans-acting eQTLs regulating plant height in chickpea. Differential accumulation of haplotype-specific transcripts of these two Mediator genes in corresponding haplotype-introgressed near-isogenic lines (NILs) correlates negatively with the plant height trait. Quantitative as well as qualitative estimation based on histology, scanning electron microscopy, and histochemical assay unraveled the reduced lengths and cell sizes of internodes along with compromised lignin levels in dwarf/semi-dwarf chickpea NILs introgressed with superior CaMED23 and CaMED5b gene haplotypes. This observation, supported by global transcriptome profiling-based diminished expression of various phenylpropanoid pathway genes upstream of lignin biosynthesis in dwarf/semi-dwarf NILs, essentially links plant height with lignin accumulation. The identified molecular signatures in the Mediator subunit genes can be efficiently utilized to develop desirable dwarf/semi-dwarf-type chickpea cultivars without affecting their yield per plant via modulating lignin/phenylpropanoid biosynthesis.