Publications of NIPGR Scientists
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Item Genome-wide association analysis using multi model approach identified novel associations for plant architectural traits in chickpea germplasm collection(Springer Nature Publishing AG, 2026) Raiya, Rahul; Yadav, Hemant Kumar; Kumar, Kuldeep; Prakash, Nitish Ranjan; Parida, Swarup K.; Bharadwaj, Chellapilla; Hegde, Venkatraman; Tripathi, ShaileshCrop plant architecture dictates plant performance under different ecological conditions and is responsible for its establishment, development, and morphology. It plays an important role in plant breeding for yield optimization, regulating photosynthetic rate and efficiency, utilization of resources, occurrence of pests and diseases, effective mechanical harvesting, space optimization, and improving the quality of plant produce. The subtle changes in the plant’s architecture could help the plant adapt to different ecological niches and are very important, keeping in view the challenges posed due to climate change. A set of 280 diverse genotypes, which included the core collection of chickpea was evaluated during the rabi season of 2021 and 2022. A total of 10 plant architecture related traits, including plant height, first pod height, canopy width, inter-nodal length, and days to flowering were studied and significant variability was observed as per the analysis of variance (ANOVA) and phenotypic descriptors. Diversity based on π and θ estimates suggests the presence of substantial diversity, while Tajima’s D reflects balancing selection due to the abundance of shared alleles. Significant marker trait associations (MTAs) for traits like plant height (PH), first pod height (FDPH) and days to flowering were observed using trait based or BLUP estimates. In total, 97 and 51 MTAs were identified using trait based and BLUP based on multi model GWAS analysis, respectively. Among these 17 were consistent MTAs being present either across the year or were identified using more than one GWAS model. Likewise, 9 consistent MTAs were identified using the BLUP estimates. Interestingly, two genomic regions present on chromosome 5 and 7 were found to harbor multiple MTAs for PH and FPDH. The linkage disequilibrium (LD) block analysis reflects the prevalence of multiple LD blocks in these regions. The allelic effects of the MTAs reflect their additive nature in determining the phenotype. Overall, the MTAs identified in the current study are highly useful for the chickpea breeder in modulating the plant architecture, mainly PH and FPDH.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 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 Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes(Springer Nature Publishing AG, 2022) Singh, Ritu; Kumar, Kamal; Bharadwaj, Chellapilla; Verma, Praveen K.The modern crop improvement programs rely heavily on two major steps—trait-associated QTL/gene/marker’s identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.Item A chickpea genetic variation map based on the sequencing of 3,366 genomes(Springer Nature Publishing AG, 2021) Varshney, Rajeev K; Roorkiwal, Manish; Sun, Shuai; Bajaj, Prasad; Chitikineni, Annapurna; Thudi, Mahendar; Singh, Narendra P; Du, Xiao; Upadhyaya, Hari D; Khan, Aamir W; Wang, Yue; Garg, Vanika; Fan, Guangyi; Cowling, Wallace A; Crossa, José; Gentzbittel, Laurent; Voss-Fels, Kai Peter; Valluri, Vinod Kumar; Sinha, Pallavi; Singh, Vikas K; Ben, Cécile; Rathore, Abhishek; Punna, Ramu; Singh, Muneendra K; Tar'an, Bunyamin; Bharadwaj, Chellapilla; Yasin, Mohammad; Pithia, Motisagar S; Singh, Servejeet; Soren, Khela Ram; Kudapa, Himabindu; Jarquín, Diego; Cubry, Philippe; Hickey, Lee T; Dixit, Girish Prasad; Thuillet, Anne-Céline; Hamwieh, Aladdin; Kumar, Shiv; Deokar, Amit A; Chaturvedi, Sushil K; Francis, Aleena; Howard, Réka; Chattopadhyay, Debasis; Edwards, David; Lyons, Eric; Vigouroux, Yves; Hayes, Ben J; Wettberg, Eric von; Datta, Swapan K; Yang, Huanming; Nguyen, Henry T; Wang, Jian; Siddique, Kadambot H M; Mohapatra, Trilochan; Bennetzen, Jeffrey L; Xu, Xun; Liu, XinZero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.Item Nitric oxide accelerates germination via the regulation of respiration in chickpea(Oxford University Press, 2019) Pandey, Sonika; Kumari, Aprajita; Shree, Manu; Kumar, Vinod; Singh, Pooja; Bharadwaj, Chellapilla; Loake, Gary J.; Parida, Swarup K.; Masakapalli, Shyam Kumar; Gupta, Kapuganti JagadisSeed germination is crucial for the plant life cycle. We investigated the role of nitric oxide (NO) in two chickpea varieties that differ in germination capacity: Kabuli, which has a low rate of germination and germinates slowly, and Desi, which shows improved germination properties. Desi produced more NO than Kabuli and had lower respiratory rates. As a result of the high respiration rates, Kabuli had higher levels of reactive oxygen species (ROS). Treatment with the NO donor S-nitroso-N-acetyl-D,L-penicillamine (SNAP) reduced respiration in Kabuli and decreased ROS levels, resulting in accelerated germination rates. These findings suggest that NO plays a key role in the germination of Kabuli. SNAP increased the levels of transcripts encoding enzymes involved in carbohydrate metabolism and the cell cycle. Moreover, the levels of amino acids and organic acids were increased in Kabuli as a result of SNAP treatment. 1 H-nuclear magnetic resonance analysis revealed that Kabuli has a higher capacity for glucose oxidation than Desi. An observed SNAP-induced increase in 13C incorporation into soluble alanine may result from enhanced oxidation of exogenous [13C]glucose via glycolysis and the pentose phosphate pathway. A homozygous hybrid that originated from a recombinant inbred line population of a cross between Desi and Kabuli germinated faster and had increased NO levels and a reduced accumulation of ROS compared with Kabuli. Taken together, these findings demonstrate the importance of NO in chickpea germination via the control of respiration and ROS accumulation.Item ABC transporter-mediated transport of glutathione conjugates enhances seed yield and quality in chickpea(American Society of Plant Biologists, 2019) Basu, Udita; Upadhyaya, Hari D.; Srivastava, Rishi; Daware, Anurag; Malik, Naveen; Sharma, Akash; Bajaj, Deepak; Narnoliya, Laxmi; Thakro, Virevol; Kujur, Alice; Tripathi, Shailesh; Bharadwaj, Chellapilla; Hegde, V. S.; Pandey, Ajay K.; Singh, Ashok K.; Tyagi, Akhilesh K.; Parida, Swarup K.The identification of functionally relevant molecular tags is vital for genomics-assisted crop improvement and enhancing the seed yield, quality and productivity in chickpea. The simultaneous improvement of yield/productivity as well as quality traits often requires pyramiding of multiple genes, which remains a major hurdle given various associated epistatic and pleotropic effects. Unfortunately, no single gene that can improve yield/productivity along with quality and other desirable agromorphological traits is known, hampering the genetic enhancement of chickpea. Using a combinatorial genomics-assisted breeding and functional genomics strategy, this study identified natural alleles and haplotypes of an ABCC3-type transporter gene that regulates seed weight, an important domestication trait, by transcriptional regulation and modulating the transport of glutathione conjugates in seeds of desi and kabuli chickpea. The superior allele/haplotype of this gene introgressed in desi and kabuli near-isogenic lines enhances the seed weight, yield, productivity and multiple desirable plant architecture and seed-quality traits without compromising the agronomic performance. These salient findings can expedite crop improvement endeavors and the development of nutritionally enriched high-yielding cultivars in chickpea.Item Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea(John Wiley & Sons, 2019) Basu, Udita; Bajaj, Deepak; Sharma, Akash; Malik, Naveen; Daware, Anurag; Narnoliya, Laxmi; Thakro, Virevol; Upadhyaya, Hari D.; Kumar, Rajendra; Tripathi, Shailesh; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, QTL mapping and expression profiling. This identified 16 potential SNP loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A-B binding protein-coding gene. The leaf tissue-specific pronounced up-regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype-specific association as well as in silico protein-protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A-B binding protein-coding gene and its interacting gene, Timing of CAB Expression 1, which appear to be most-promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker-assisted selection for developing PE-enriched cultivars with high seed yield in chickpea.Item Measurement of respiration and internal oxygen in germinating Cicer arietinum L. seeds using optic microsensor(Springer, 2017) Pandey, Sonika; Kumari, Aprajita; Bharadwaj, Chellapilla; Gupta, Kapuganti JagadisInternal oxygen concentrations vary in different tissues depending on tissue size, developmental stage, and their location. Respiratory rate of tissue also determines internal oxygen levels. For studying various signaling pathways it is essential to establish a correlation between respiration and internal oxygen. Seed germination is associated with increase in respiration which can dictate the internal oxygen and subsequent production of reactive oxygen species. Using optic oxygen microsensor we made an attempt to measure respiratory rate and internal oxygen. We found that microsensor is able to sense internal oxygen and it is also possible to measure oxygen levels in a close vial that contains seeds. Step-by-step protocol is described here along with illustration.Item Identifying transcription factor genes associated with yield traits in chickpea(Springer, 2017) Shimray, Philanim Wungmarong; Bajaj, Deepak; Srivastava, Rishi; Daware, Anurag; Upadhyaya, Hari D.; Kumar, Rajendra; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.Identification of potential transcription factor (TF) gene-derived natural SNP allelic variants regulating pod and seed yield component traits by large-scale mining and genotyping of SNPs in natural germplasm accessions coupled with high-resolution association mapping is vital for understanding the complex genetic architecture of quantitative yield traits in chickpea. In these perspectives, the current study employed a genome-wide GBS (genotyping-by-sequencing) and targeted gene amplicon resequencing-based simultaneous SNP discovery and genotyping assays, which discovered 1611 novel SNPs from 736 TF genes physically mapped on eight chromosomes and unanchored scaffolds of kabuli chickpea genome. These SNPs were structurally and functionally annotated in diverse synonymous and non-synonymous coding as well as non-coding regulatory and intronic sequence components of chickpea TF genes. A high-resolution genetic association analysis was performed by correlating the genotyping information of 1611 TF gene-based SNPs with multi-location/years field phenotyping data of six major pod and seed yield traits evaluated in a constituted association panel (326 desi and kabuli germplasm accessions) of chickpea. This essentially identified 27 TF gene-derived SNPs exhibiting significant association with six major yield traits, namely days to 50% flowering (DF), plant height (PH), branch number (BN), pod number (PN), seed number (SN) and seed weight (SW) in chickpea. These trait-associated SNPs individually and in combination explained 10–23% and 32% phenotypic variation respectively for the studied yield component traits. Interestingly, novel non-synonymous coding SNP allelic variants in five potential candidate TF genes encoding SBP (squamosal promoter binding protein), SNF2 (sucrose non-fermenting 2), GRAS [Gibberellic acid insensitive (GAI)-Repressor of GAI (RGA)-SCARECROW (SCR)], bZIP (basic leucine zipper) and LOB (lateral organ boundaries)-domain proteins associated strongly with DF, PH, BN, PN, SN and SW traits respectively were found most promising in chickpea. The functionally relevant molecular signatures (TFs and natural SNP alleles) delineated by us have potential to accelerate marker-assisted genetic enhancement by developing high pod and seed yielding cultivars of chickpea.