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    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, Sabhyata
    In 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.
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    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, Sabhyata
    Delineating 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.
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    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, Sabhyata
    Legumes 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.
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    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, Manoj
    Climate 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.
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    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, Sabhyata
    Lentil 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.
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    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, Sabhyata
    Metal 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.
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    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, Sabhyata
    Development 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.
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    Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo
    (Life Science Alliance LLC, 2024) Junaid, Alim; Singh, Baljinder; Bhatia, Sabhyata
    Eukaryotic 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.
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    Delineation of novel genomic loci and putative candidate genes associated with seed iron and zinc content in lentil (Lens culinaris Medik.)
    (Elsevier B.V., 2023) Singh, Baljinder; Singh, Sangeeta; Mahato, Ajay Kumar; Dikshit, Harsh Kumar; Tripathi, Kuldeep; Bhatia, Sabhyata
    The use of molecular breeding approaches for development of lentil genotypes biofortified with essential micro-nutrients such as iron and zinc, could serve as a promising solution to address the problem of global malnutrition. Thus, genome-wide association study (GWAS) strategy was adopted in this study to identify the genomic regions associated with seed iron and zinc content in lentil. A panel of 95 diverse lentil genotypes, grown across three different geographical locations and evaluated for seed iron and zinc content, exhibited a wide range of variation. Genotyping-by-sequencing (GBS) analysis of the panel identified 33,745 significant single nucleotide polymorphisms (SNPs) that were distributed across all the 7 lentil chromosomes. Association mapping revealed 23 SNPs associated with seed iron content that were distributed across all the chromosomes except chromosome 3. Similarly, 14 SNPs associated with seed zinc content were also identified that were distributed across chromosomes 1, 2, 4, 5 and 6. Further, 80 genes were identified in the proximity of iron associated markers and 36 genes were identified in the proximity of zinc associated markers. Functional annotation of these genes revealed their putative involvement in iron and zinc metabolism. For seed iron content, two highly significant SNPs were found to be located within two putative candidate genes namely iron-sulfur cluster assembly (ISCA) and flavin binding monooxygenase (FMO) respectively. For zinc content, a highly significant SNP was detected in a gene encoding UPF0678 fatty acid-binding protein. Expression analysis of these genes and their putative interacting partners suggests their involvement in iron and zinc metabolism in lentil. Overall, in this study we have identified markers, putative candidate genes and predicted putative interacting protein partners significantly associated with iron and zinc metabolism that could be utilized in future breeding studies of lentil for nutrient biofortification.
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    Comparative transcriptomic and metabolite profiling reveals genotype-specific responses to Fe starvation in chickpea
    (John Wiley & Sons, 2023) Singh, Gourav; Ambreen, Heena; Jain, Priyanka; Chakraborty, Anirban; Singh, Baljinder; Manivannan, Abinaya; Bhatia, Sabhyata
    Iron deficiency is a major nutritional stress that severely impacts crop productivity worldwide. However, molecular intricacies and subsequent physiological and metabolic changes in response to Fe starvation, especially in leguminous crops like chickpea, remain elusive. In the present study, we investigated physiological, transcriptional, and metabolic reprogramming in two chickpea genotypes (H6013 and L4958) with contrasting seed iron concentrations upon Fe deficiency. Our findings revealed that iron starvation affected growth and physiological parameters of both chickpea genotypes. Comparative transcriptome analysis led to the identification of differentially expressed genes (DEGs) between the genotypes related to strategy I uptake, metal ions transporters, reactive oxygen species (ROS) associated genes, transcription factors, and protein kinases that could mitigate Fe deficiency. Our gene correlation network discovered several putative candidate genes like CIPK25, CKX3, WRKY50, NAC29, MYB4 and PAP18, which could facilitate the investigation of the molecular rationale underlying Fe tolerance in chickpea. Furthermore, the metabolite analysis also illustrated the differential accumulation of organic acids, amino acids and other metabolites associated with Fe mobilization in chickpea genotypes. Overall, our study demonstrated the comparative transcriptional dynamics upon Fe starvation. The outcomes of the current endeavour will enable the development of Fe deficiency tolerant chickpea cultivars.