Publications of NIPGR Scientists
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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 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.Item 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 ChandChickpea (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.Item 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.Item Harnessing the hidden allelic diversity of wild Cicer to accelerate genomics-assisted chickpea crop improvement(Springer Nature Publishing AG, 2022) Mohanty, Jitendra Kumar; Jha, Uday Chand; Dixit, G.P.; Parida, Swarup K.Chickpea, commonly called Bengal gram or Garbanzo bean, faces a productivity crisis around the globe due to numerous biotic and abiotic stresses. The eroded genetic base of the cultivated Cicer gene pool is becoming a significant bottleneck in developing stress-resilient chickpea cultivars. In this scenario, the crop wild relatives (CWR) of chickpea, with the useful genomic wealth of their wild adaptation, give a ray of hope to improve the genetic background of the cultivated Cicer gene pool. To extrapolate these unearthed genomic diversities of wild, we require a thorough understanding of the pre-historic domestication episodes that are changing their shape with the expansion of the available scientific evidence. Keeping aforesaid in view, the current review article provides a glimpsed overview on several efforts done so far to reveal the mysterious origin and evolution of the Cicer gene pool, along with the constraints in their utilization for chickpea crop improvement. It encapsulates various stress-resilient CWR of chickpea and their use in several pre-breeding programs to develop numerous breeding populations for crop genetic enhancement. Further, this review will recapitulate the significant contributions of structural, functional and comparative genomics, pan-genomics and diverse genomics-assisted breeding strategy in dissecting the untapped trait-specific allelic/gene diversity and domestication pattern behind the CWR of chickpea, along with their potential and promises. We expect the newly explored genetic variations may be used in the breeding programs for re-wilding the cultigens’ genomic background to open a new avenue for genetic gain and crop improvement capacity of chickpea.Item Transcriptome landscape of early inflorescence developmental stages identifies key flowering time regulators in chickpea(Springer Nature Publishing AG, 2022) Basu, Udita; Hegde, Venkatraman S.; Daware, Anurag; Jha, Uday Chand; Parida, Swarup K.The early stages of inflorescence development in plants are as crucial as the later floral developmental stages. Several traits, such as inflorescence architecture and flower developmental timings, are determined during those early stages. In chickpea, diverse forms of inflorescence architectures regarding meristem determinacy and the number of flowers per node are observed within the germplasm. Transcriptome analysis in four desi chickpea accessions with such unique inflorescence characteristics identifies the underlying shared regulatory events leading to inflorescence development. The vegetative to reproductive stage transition brings about major changes in the transcriptome landscape. The inflorescence development progression associated genes identified through co-expression network analysis includes both protein-coding genes and long non-coding RNAs (lncRNAs). Few lncRNAs identified in our study positively regulate flowering-related mRNA stability by acting competitively with miRNAs. Bulk segregrant analysis and association mapping narrowed down an InDel marker regulating flowering time in chickpea. Deletion of 11 bp in first exon of a negative flowering time regulator, Early Flowering 3a gene, leads to early flowering phenotype in chickpea. Understanding the key players involved in vegetative to reproductive stage transition and floral meristem development will be useful in manipulating flowering time and inflorescence architecture in chickpea and other legumes.Item The DNA replication, repair, and recombination pathway genes modulating yield and stress tolerance traits in chickpea(Springer Nature Publishing AG, 2022) Basu, Udita; Sharma, Akash; Bajaj, Deepak; Malik, Naveen; Jha, Uday Chand; Upadhyaya, Hari D.; Parida, Swarup K.DNA replication, repair, and recombination (DRRR) are the fundamental processes required for faithful transmission of genetic information within and between generations. The DRRR genes protect the cells from potential mutations and damage during the developmental phases and stress conditions. Thus, these genes indirectly regulate diverse important agronomic traits in a crop plant. A genome-wide survey of six DRRR pathway genes, namely, DNA replication, Base Excision Repair, Nucleotide Excision Repair, Homologous Recombination, Mismatch Excision Repair, and Non-Homologous End-Joining, identifed 157 DRRR genes in chickpea. Phylogenetic analysis of these genes within the legume clades and model plant Arabidopsis identifed 42 conserved DRRR genes exhibiting clade-specifc evolutionary patterns. Integrating the gene-based association mapping with diferential expression profling identifed the natural alleles of the potential DRRR genes, primarily regulating fowering and maturation time and involved in drought tolerance of chickpea. Identifying and understanding DRRR genes’ roles in regulating yield and stress tolerance traits in a vital grain legume like chickpea is requisite for its future crop improvement endeavors. Manipulation of promising functionally relevant DRRR genes will pave the way for simultaneous improvement in multiple benefcial agronomic traits in chickpea.Item Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.)(Springer, 2018) Jha, Uday Chand; Jha, Rintu; Bohra, Abhishek; Parida, Swarup K.; Kole, Paresh Chandra; Thakro, Virevol; Singh, Deepak; Singh, Narendra PratapUnderstanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.