Publications of NIPGR Scientists

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Author: search.filters.author.Jha, Uday ChandStart date: 2020

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    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.
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    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, Harsh
    Chickpeas 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.
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    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, Harsh
    Chickpea, 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.
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    Differential resilience of chickpea's reproductive organs to cold stress across developmental stages: insights into antioxidant strategies for enhanced fertility
    (Frontiers Media S.A., 2025) Padhiar, Deeksha; Kaur, Sarbjeet; Jha, Uday Chand; Prasad, P. V. Vara; Sharma, Kamal Dev; Kumar, Sanjeev; Parida, Swarup Kumar; Siddique, Kadambot H M; Nayyar, Harsh
    Chickpea is highly sensitive to cold stress during its reproductive stages, leading to significant reductions in potential pod formation due to decreased reproductive success. This study aimed to investigate the specific responses of anthers and ovules to cold stress, explore the role of oxidative stress and antioxidant mechanisms, and understand the relationship between oxidative stress and reproductive function to enhance our understanding of chickpea responses to cold stress. Chickpea seeds of contrasting genotypes—cold-tolerant (ICC 17258, ICC 16349) and cold-sensitive (ICC 15567, GPF 2)—were sown outdoors in early November under optimal conditions (25.5/15.4°C mean day/night temperatures). At 50 days after sowing, plants were subjected to 13/7°C cold stress (12 h light/dark in walk-in growth chambers. Cold stress significantly increased membrane damage and reduced cellular viability in anthers and ovules, particularly in cold-sensitive (CS) genotypes. Oxidative damage was more pronounced in anthers, particularly at anthesis (stage 2), as indicated by elevated malondialdehyde and hydrogen peroxide levels. Cold-tolerant (CT) genotypes exhibited increased antioxidant activity under stress, especially at pre-anthesis (stage 1), followed by declines at later stage, although responses varied by genotype. Anthers exhibited higher overall antioxidants activity than ovules, while ovules demonstrated notably high catalase activity. Among the antioxidants studied, ascorbate peroxidase and glutathione reductase were most prominent in the CT genotype, along with higher levels of ascorbate (AsA) and glutathione (GSH), highlighting the critical role of the AsA–GSH cycle in conferring cold tolerance to chickpea. Exogenous supplementation with 1 mM ascorbate (AsA) and glutathione (GSH) significantly stimulated pollen germination in cold-stressed plants under in vitro conditions, with a greater effect observed in CS genotypes. Furthermore, antioxidant activity strongly correlated with key reproductive traits such as pollen germination and ovule viability. This study revealed that the anthers and ovules exhibited distinct responses to cold stress, with significant genotypic differences across key reproductive stages. These insights provide a deeper understanding of cold tolerance mechanisms in chickpea and provide vital clues for breeding strategies to enhance resilience and reproductive success under cold stress.
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    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, Harsh
    Growing 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.
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    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.
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    Delineation of genes for a major QTL governing heat stress tolerance in chickpea
    (Springer Nature Publishing AG, 2024) Mohanty, Jitendra K.; Thakro, Virevol; Yadav, Antima; Nayyar, Harsh; Dixit, Girish P.; Agarwal, Pinky; Parida, Swarup K.; Jha, Uday Chand
    Chickpea (Cicer arietinum) is a cool season grain legume experiencing severe yield loss during heat stress due to the intensifying climate changes and its associated gradual increase of mean temperature. Hence, understanding the genetic architecture regulating heat stress tolerance has emerged as an important trait to be addressed for enhancing yield and productivity of chickpea under heat stress. The present study is intended to identify the major genomic region(s) governing heat stress tolerance in chickpea. For this, an integrated genomics-assisted breeding strategy involving NGS-based high-resolution QTL-seq assay, QTL region-specifc association analysis and molecular haplotyping was deployed in a population of 206 mapping individuals and a diversity panel of 217 germplasm accessions of chickpea. This combinatorial strategy delineated a major 156.8 kb QTL genomic region, which was subsequently narrowed-down to a functional candidate gene CaHSFA5 and its natural alleles associated strongly with heat stress tolerance in chickpea. Superior natural alleles and haplotypes delineated from the CaHSFA5 gene have functional signifcance in regulating heat stress tolerance in chickpea. Histochemical staining, interaction studies along with diferential expression profling of CaHSFA5 and ROS scavenging genes suggest a cross talk between CaHSFA5 with ROS homeostasis pertaining to heat stress tolerance in chickpea. Heterologous gene expression followed by heat stress screening further validated the functional signifcance of CaHSFA5 for heat stress tolerance. The salient outcomes obtained here can have potential to accelerate multiple translational genomic analysis including marker-assisted breeding and gene editing in order to develop high-yielding heat stress tolerant chickpea varieties.
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    Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions
    (Elsevier B.V., 2023) Jha, Uday Chand; Nayyar, Harsh; Roychowdhury, Rajib; Prasad, P. V. Vara; Parida, Swarup K.; Siddique, Kadambot H. M.
    Unusual daily temperature fluctuations caused by climate change and climate variability adversely impact agricultural crop production. Since plants are immobile and constantly receive external environmental signals, such as extreme high (heat) and low (cold) temperatures, they have developed complex molecular regulatory mechanisms to cope with stressful situations to sustain their natural growth and development. Among these mechanisms, non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), small-interfering RNAs (siRNAs), and long-non-coding RNAs (lncRNAs), play a significant role in enhancing heat and cold stress tolerance. This review explores the pivotal findings related to miRNAs, siRNAs, and lncRNAs, elucidating how they functionally regulate plant adaptation to extreme temperatures. In addition, this review addresses the challenges associated with uncovering these non-coding RNAs and understanding their roles in orchestrating heat and cold tolerance in plants.
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    eQTL-seq: a rapid genome-wide integrative genetical genomics strategy to dissect complex regulatory architecture of gene expression underlying quantitative trait variation in crop plants
    (Springer Nature Publishing AG, 2024) Mohanty, Jitendra K.; Jha, Uday Chand; Dixit, G. P.; Bharadwaj, Chellapilla; Parida, Swarup K.
    We developed a combinatorial next generation sequencing (NGS)-based high-throughput expression QTL-seq (eQTL-seq) strategy for rapid elucidation of complex genetic architecture and regulatory pathways of gene expression underlying quantitative trait variation in crop plants. This high-resolution genome-wide integrative genetical genomics strategy assists us to delineate functionally relevant molecular tags (QTLs/eQTLs, genes, master regulators/transcription factors, and alleles) regulating vital agronomic traits in order to expedite genomics-assisted breeding and crop improvement. As a proof-of-concept, the optimized eQTL-seq-led genetical genomics approach was employed in 192 mapping individuals of an intra-specific recombinant inbred line (RIL) population (desi accession ICC 4958 x kabuli accession ICC 12968) with contrasting seed weight trait. This led to identification and mapping of high-resolution major QTLs/eQTLs associated with seed weight based on genome resequence-derived genomic SNP-index (Delta(gSNP-index)), global transcriptome sequence-based expression SNP-index (Delta(eSNP-index)), and relative gene expression (RGE)-index (Delta(RGE-index)). The eQTL-seq scaled down the major seed weight QTLs/eQTLs into the potential candidate gene(s) governing cis- and trans-regulated expression to decipher the gene regulatory modules controlling complex quantitative seed weight trait by deriving global allele-specific gene expression polymorphism in chickpea. Henceforth, the efficacy of NGS-driven integrative eQTL-seq strategy as compared to traditional QTL mapping, fine-mapping (map-based cloning), and QTL-seq approaches that are widely adopted for delineation of candidate genes underlying major QTLs was evident in chickpea. This will further accelerate quantitative dissection of regulatory architecture by decoding the molecular genetic basis of gene expression variation controlling diverse complex phenotypic trait diversity in chickpea and other crop plants as well.
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    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.