Publications of NIPGR Scientists
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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 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 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 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 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 Next-generation translational genomics for developing future crops(Springer Nature Publishing AG, 2025) Basu, Udita; Parida, Swarup K.Advancements in translational genomics have revolutionized crop breeding, driving us from traditional breeding methods towards next-generation strategies that integrate genomic, transcriptomic, and phenotypic data to expedite crop improvement. There has been a shift from single genomes to pan-genomes, which better capture intraspecific diversity, and from bulk transcriptome analyses to single-cell transcriptomics, enabling cell-specific insights into gene regulation and functional genomics. Both high throughput genopyting and phenotyping approaches are now possible due to rapid technological advancement in the field of translational genomics. Large-scale phenotyping data from multi-environment field trials is now possible due to AI-enabled digital and drone-based scanning. In the era of artificial intelligence and machine learning we have developed flexible models to handle complex genetic architecture of trait regulation using various tools and approaches. These genetic and genomic resources are the foundation for generating novel, adaptable, and high-yielding varieties, accelerating trait discovery and mapping. This review explores the comprehensive landscape of modern translational genomics, highlighting key shifts and innovations that enhance our capacity to address agricultural challenges. Integrative pipelines that unify these next-generation approaches could facilitate faster, more precise, and sustainable crop improvement, ultimately meeting the growing demands for future-ready crops.Item Assessing cold stress resilience in wild chickpea accessions using physiological, biochemical, and reproductive traits(Springer Nature, 2025) Kaur, Sarbjeet; Padhiar, Deeksha; Singh, Mohar; Parida, Swarup K.; Jha, Uday C.; Sharma, Kamal Dev; Prasad, P. V. Vara; Siddique, Kadambot H. M.; Nayyar, HarshDomesticated chickpea (Cicer arietinum L.) exhibits high sensitivity to temperatures below 20/10 °C during its reproductive phase resulting in substantial loss of flowers, pods and crop yields. With the aim to add new sources of cold tolerance and elucidate mechanism of cold-tolerance in wild species of chickpea, the present study evaluated 36 wild accessions of three Cicer species (Cicer judaicum, Cicer pinnatifidum, Cicer reticulatum) at the reproductive stage for yield, and reproductive, physiological and biochemical traits under cold stress (15/7 °C) for two consecutive years. Cluster analysis based on yield-related traits such as pod number, seed weight, and total seed count categorized these accessions as cold-tolerant and cold-sensitive. Six C. judaicum accessions (ILWC 256, ICC 13852, ILWC 263, ILWC 20, ILWC 223, and ILWC 30) were tolerant to cold whereas the remaining ones were cold-sensitive. Under cold stress, cold-tolerant accessions exhibited lower impairment of physiological processes as compared to the cold-sensitive accessions e.g. lower tissue damage and electrolyte leakage, and higher chlorophyll content, carotenoid content, chlorophyll fluorescence, and leaf water content, thereby resulting in higher photosynthetic efficiency and carbohydrate accumulation in cold-tolerant accessions. At the biochemical level, the tolerant accessions demonstrated significantly higher amounts of cryoprotectants and enhanced activities of enzymatic and non-enzymatic antioxidants resulting in substantially lower levels of reactive oxygen species. Cold-tolerant accessions also accumulated more proline and trehalose compared to their sensitive counterparts. Slight disruptions in physiological processes, low oxidative stress and accumulation of cryoprotectants under cold stress were associated with higher pollen viability, pollen germination, pollen load, ovule receptivity, pod set, number of pods and seed yield in cold-tolerant accessions while opposite was true for cold-sensitive accessions. The wild chickpea accessions exhibiting high seed yield under cold stress are promising candidates for breeding programs aimed at cold tolerance.Item Analysis of genomic-transcriptomic dynamics delineates key molecular signatures modulating seed size and weight in lentil(John Wiley & Sons, 2026) Padhy, Asish Kumar; Singh, Sangeeta; Tripathi, Kuldeep; Parida, Swarup K.; Bhatia, SabhyataDelineating key genetic determinants associated with seed size/weight is crucial for increasing productivity. In this study, the advantages of an integrated approach combining QTL mapping, GWAS and transcriptomics to identify robust candidates governing seed size and weight were demonstrated in lentil, an important grain legume. QTL mapping identified three stable QTLs harbouring 5113 genes. GWAS identified 42 MTAs (5 consistent) containing 192 underlying genes. Comparative transcriptome analysis identified 1202 differentially expressed transcripts. Integrated analysis of the results obtained from QTL mapping and GWAS revealed nine SNPs located in the three robust QTLs harbouring 32 candidate genes. Upon integration with transcriptome data, only one (LcWDL1) was identified as the most promising candidate. LcWDL1 (a member of TPX2 family involved in microtubule organisation and cell expansion) and its predicted interacting partners that is, LcGLIPs are known to function as regulators of seed size. Candidate gene-based association analysis identified a SNP on second exon of LcWDL1 to be significantly associated with seed size and weight of lentil. The genomic loci/candidate gene identified in the study will serve to expedite the molecular breeding and gene editing programs for enhancing seed size and seed weight in lentils.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 Shaping the future: Unravelling regulators modulating plant architecture for next-generation crops(Elsevier B.V., 2025) Kumbhakar, Rajib; Mondal, Mayulika; Thakro, Virevol; Tripathi, Shailesh; Parida, Swarup K.Plant architecture traits in crops are modulated through intricate interactions of various genetic pathways, which helps them to adapt to diverse environmental conditions. Key developmental pathways involved in forming plant architecture include the LAZY-TAC (Tiller Angle Control) module regulating branch and tiller angle, the CLAVATA-WUSCHEL pathway controlling shoot apical meristem fate and the GID1-DELLA pathway governing plant height and tillering in major food crops. These pathways function in concert to shape the overall architecture of plants, which is essential for optimizing light capture, resource allocation, reproductive success and eventual crop yield enhancement. Presently, plant architecture of modern crops has been shaped especially by artificial selection of natural alleles that target yield traits. Recent advances in CRISPR-Cas-based genome editing and genomics-assisted breeding strategies have enabled precise genetic manipulation of natural alleles in the functionally relevant genes regulating plant architecture traits in crops. This will assist researchers to select and introgress superior natural alleles in popular cultivars strategically for restructuring their desirable plant-types suitable for mechanical harvesting as well as enhancing the crop yield potential.