Institutional Publications
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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 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 Use of wild relatives in breeding programs to develop climate resilient wheat(Elsevier B.V., 2025) Chaurasia, Shiksha; Bhatia, SabhyataThe changing climate is having a significant impact on wheat production. This impact is not limited to increasing heat and drought stress but also includes other stresses, extreme weather events, and adverse conditions. To meet the growing food demands of a rising population, wheat breeding requires incorporating new, diversified resources that can produce high-quality wheat in various stressful environments. Wild relatives that are genetically similar are countless resources for improving yield-related traits and increasing tolerance to environmental stress. By using wild relatives to introduce genes into widely grown crops and contribute to environmental tolerance, we can develop crops resilient to climate change. In this chapter, we confer the impression of climate change on wheat production, as well as its wild relatives. We also highlight the challenges of hybridization, such as genetic distance, crossover frequencies, and selecting desirable traits while minimizing linkage drag. Finally, we deliver an index of valuable traits that could exist in these species and potentially be exploited through interspecific hybridization approaches. Here is an outline of how introgression works and what factors distress the breeding approach. We will also discuss optimization methods to increase the chances of recovering desired climate-resilient introgressive lines in wheat improvement programs.Item Key determinants of seed size for enhancing genetic gain in legumes(John Wiley & Sons, 2026) Padhy, Asish Kumar; Singh, Ananya; Chaurasia, Shiksha; Parida, Swarup Kumar; Tripathi, Kuldeep; Bhatia, SabhyataLegumes play a pivotal role in human nutrition due to their high nutritional value, especially protein content. Therefore, enhancing the productivity of grain legumes is desirable for ensuring food and nutritional security. Seed size and seed weight are key factors influencing productivity. This article consolidates the substantial amount of research conducted to uncover the molecular signatures associated with seed size into a structured format, providing a one-stop platform of available resources for enhancing genetic gains in legumes. The advent of NGS technologies enabled the decryption of genomes and transcriptomes of important grain legumes. Moreover, molecular signatures such as SSRs, SNPs, transcription factors, methylation patterns and so forth scanned from phenotypically and genotypically well-characterized natural and mapping populations helped identify the QTLs, MTAs and candidate genes associated with seed size. Many of these QTLs and candidate genes have been utilized in marker-assisted breeding for achieving larger seeds and enhanced yield in legumes. Besides, the characterization of legume orthologs of candidate genes from other crops using different omics approaches helped in understanding the regulatory pathways involved in seed size determination in legumes. This review provides a direction for the effective utilization of available resources to enhance legume productivity.Item Delineating microRNA169-Nuclear Factor Y-Subunit a module for its potential implications in crop improvement(John Wiley & Sons, 2026) Chakraborty, Anirban; Sharma, Shambhavi; Pandey, Girdhar K.; Bhatia, Sabhyata; Prasad, ManojClimate change considerably impacts plant growth and productivity by inducing stress responses. This, along with the problems of feeding the ever-increasing global population, could be mitigated by generating climate-resilient crop varieties with enhanced productivity. However, an exhaustive account of the key regulatory processes that underlie developmental and stress-responsive pathways is a prerequisite for generating improved crop varieties. Towards this, our study, for the first time, provides an exhaustive compilation of the potential regulatory pathways impacted by the miR169-NFYA network in plants. The NFYA transcription factors belong to a class of nuclear factor-encoding genes directly influencing the transcription of many genes involved in developmental and stress responses. Meanwhile, miR169 provides a layer to NFYA-mediated gene regulation by post-transcriptionally suppressing the expression of these transcription factors. Evidence from several studies shed light on key molecular signatures related to hormone synthesis and signaling, calcium signaling, epigenetic regulation, nutrient starvation and miRNA biogenesis that could serve as downstream components of the miR169-NFYA cascade in plants. This ability of miR169-NFYA nexus to impact a wide range of biological processes makes it a suitable toolbox for developing tailor-made crop varieties through appropriate genetic manipulation strategies.Item Innovations in industrial and functional food applications of lentil in the era of biofortification(Springer Nature Publishing AG, 2025) Padhy, Asish Kumar; Chaurasia, Shiksha; Manivannan, Abinaya; Tripathi, Kuldeep; Sapna, Sapna; Bhatia, SabhyataLentil can serve as a prebiotic and therapeutic healthy food due to the presence of essential micronutrients, functional proteins, minerals, and carbohydrates, as well as phytochemicals that have shown to be promising in the prevention of several chronic diseases. Nutraceutical properties derived from the phytochemicals present in lentil has expanded its scope of usage to a broader perspective. In this regard, a lot of innovations have been carried out to use lentil in the form of crisps, chips, bakery products, yogurt, pasta, including in the brewing industries. Eforts are being carried out to develop meat analogs out of lentil four. However, niche area specifc consumer preferences have limited its explorations in other innovative areas. This will also necessitate developing genetic resources and varieties aligning to the needs of producers and consumers with acceptable sensory properties. Hence, demand driven development of breeding materials for biofortifcation and crop improvement programs needs considerable amount of investment in research and development of the crop. This review is a campedium of innovations in development of industrial, functional food products from lentil along with their nutritional properties and sensory acceptability serve a foundation for the researchers to invent more to popularize lentil among the consumers to ensure nutritional security.Item Global identification of metal ion transporters in chickpea and delineating the role of CaYSL4 in orchestrating iron content(Elsevier B.V., 2025) Singh, Gourav; Manivannan, Abinaya; Pandey, Vimal; Bhatia, SabhyataMetal ion transporters (MITs) are vital to maintain proper metal homeostasis during growth and development of plants thereby necessitating their identification and characterization. Considering the economic importance of chickpea in human nutrition, the molecular behaviour and biological functions of the metal ion transporters (MIT) encoding gene families remains highly relevant in recent times. Global identification of MITs revealed a total of 12 CAXs, 6 CTRs, 11 MGTs, 15 MTPs, 9 NRAMPs, 16 OPTs, and 14 ZIPs responsible for metal ion transport. Assessment of phylogenetic relationships, chromosomal distribution, gene structure and motif analysis of MITs suggested their diverse functions. The yellow stripe-like (YSL) family of transporters is an important family whose members have been suggested to have a role in metal ion translocation and assimilation. Expression analysis of key YSLs including CaYSL1, CaYSL4, CaYSL6 and CaYSL16 indicated their significant involvement in conferring tolerance to Fe starvation. Notable was the expression of CaYSL4 that showed specific expression in flower, leaf, shoot, seed at 30 DAA and 40DAA after 7 and 10 day of Fe-deficiency treatment. It was found to be localized in the plasma membrane. RNAi-mediated silencing of CaYSL4 demonstrated its critical role in orchestrating Fe, Zn, Cu and Mn translocation in chickpea seeds. Collectively, the comprehensive analysis of MITs coupled with the functional role of CaYSL4 provides critical insight into the complex regulation of Fe ion transport and distribution that will enable breeding of nutritionally enhanced chickpea varieties.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 Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo(Life Science Alliance LLC, 2024) Junaid, Alim; Singh, Baljinder; Bhatia, SabhyataEukaryotic genomes show an intricate three-dimensional (3D) organization within the nucleus that regulates multiple biological processes including gene expression. Contrary to animals, understanding of 3D genome organization in plants remains at a nascent stage. Here, we investigate the evolution of 3D chromatin architecture in legumes. By using cutting-edge PacBio, Illumina, and Hi-C contact reads, we report a gap-free, chromosome-scale reference genome assembly of Vigna mungo, an important minor legume cultivated in Southeast Asia. We spatially resolved V. mungo chromosomes into euchromatic, transcriptionally active A compartment and heterochromatic, transcriptionally-dormant B compartment. We report the presence of TAD-like-regions throughout the diagonal of the HiC matrix that resembled transcriptional quiescent centers based on their genomic and epigenomic features. We observed high syntenic breakpoints but also high coverage of syntenic sequences and conserved blocks in boundary regions than in the TAD-like region domains. Our findings present unprecedented evolutionary insights into spatial 3D genome organization and epigenetic patterns and their interaction within the V. mungo genome. This will aid future genomics and epigenomics research and breeding programs of V. mungo.Item Emerging roles of melatonin in mitigating salinity stress of legumes(Elsevier B.V., 2023) Chaurasia, Shiksha; Sapna, Sapna; Padhy, Asish Kumar; Bhatia, SabhyataMelatonin (N-acetyl-5‑methoxy tryptamine) is a multi-functional molecule that is distributed in all living organisms and it performs essential roles in environmental stress tolerance. Salt stress enhances the rapid accumulation of melatonin in plants. Melatonin provides resistance to salt stress by manipulating various regulatory mechanisms at the biochemical and molecular levels throughout different plant developmental stages. Conventionally, legumes are consumed along with cereal-based staples to ensure wholesome nutritional intake. After confirming their nutritional and health-promoting effects, recently their demand is constantly increasing. This has guided the researchers to focus on developing legumes to cope with the changing climate scenario. In legumes, melatonin concentration varies from crop to crop under salt stress. This review emphasizes melatonin biosynthesis in plants with a special focus on legumes and their responses to endogenous and exogenous melatonin application. This manuscript also throws light on the physiological, biochemical, and molecular basis of melatonin-mediated salinity stress tolerance in legumes. The future directions for enhancing the salt stress tolerance in legumes are also discussed. As, Melatonin promotes germination potential, seedling biomass, photosynthesis rate, pod number, and yield of legumes under the influence of salinity stress, this review can provide insights for using melatonin to develop salt stress tolerant legumes for sustainable food production.