Institutional Publications
Permanent URI for this collectionhttps://ndkr-library.nipgr.ac.in/handle/123456789/11
Browse
7 results
Search Results
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 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 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 Understanding abiotic stress responses in lentil under changing climate regimes(Springer Nature Publishing AG, 2023) Singh, Baljinder; Padhy, Asish Kumar; Ambreen, Heena; Yadav, Manisha; Bhardwaj, Shubham; Singh, Gourav; Pandey, Vimal; Chakraborty, Anirban; Bhatia, SabhyataLentil (Lens culinaris Medik.) is a cool-season grain legume crop that is mainly cultivated across the semi-arid regions of Australia, South Asia, Africa, and North America. The crop is highly valued for its nutritional attributes such as dietary proteins (22–35%), carbohydrates, minerals, and fiber that play a significant role in alleviating malnutrition and micronutrient deficiencies across populations in developing countries. The last five decades have seen an upward trend in global production of lentils from 0.85 to 5.73 Mt. suggesting its increasing demand and utilization. However, various abiotic stresses such as drought, heat, cold, salinity, and nutrient deficiency impose severe threats to the global lentil yield and productivity. The current book chapter is an attempt to comprehend the morpho-physiological and biochemical changes occurring during these stresses and the developmental plasticity shown by the plant to counteract them. Furthermore, the current status of research focusing on the development of novel molecular and functional markers/tags, identification of candidate genes/QTLs responsible for abiotic stress tolerance, the intervention of high throughput genotyping and phenotyping platforms, development of populations and linkage maps, and omics studies have been discussed. Some tolerant germplasm and varieties developed through conventional and next-generation breeding approaches are also enlisted making the book chapter a concise platform for reports of abiotic stress tolerance in lentils.Item 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, SabhyataIron 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.Item Integrated genomic approaches delineate the novel role of ROP1 ENHANCER1 in regulating seed protein content of chickpea(Oxford University Press, 2023) Chakraborty, Anirban; Junaid, Alim; Parida, Swarup K.; Bhatia, SabhyataUtilizing a combinatorial approach of QTL-Seq and candidate gene-based association mapping, the QTLs and genes responsible for seed protein content (SPC), a major quality trait in chickpea were identified. Whole Genome Re-sequencing based QTL-Seq analysis of bulked RILs from a mapping population contrasting for SPC led to identification of two QTLs (0.94 Mb on Linkage Group (LG)5 and 1.16 Mb on LG6) encompassing three SNPs displaying the highest ΔSNP-index. These highly significant SNPs and their associated genes were validated in 211 chickpea mini-core accessions varying in SPC that revealed a tightly associated marker affecting CaREN1 (ROP1 ENHANCER1) with phenotypic variation explained of 23%. This SNP was subsequently converted into a cost effective allele specific PCR based marker that could be utilized for rapid screening of SPC during marker assisted breeding. Further, in planta functional validation via knockdown of CaREN1 led to significant reduction in SPC of chickpea. This decrease in seed protein is likely due to disruption in the formation of CaREN1 protein complexes comprising of chaperones, phosphopeptide-binding proteins and GTPases that mediate folding, transport and accumulation of seed storage proteins as indicated through AP-MS. Taken together, the information generated would expedite tailoring of chickpea cultivars with augmented SPC.Item Identification and molecular characterization of miRNAs and their target genes associated with seed development through small RNA sequencing in chickpea(Springer Nature Publishing AG, 2021) Pradhan, Seema; Verma, Subodh; Chakraborty, Anirban; Bhatia, SabhyataMultiple studies have attempted to dissect the molecular mechanism underlying seed development in chickpea (Cicer arietinum L.). These studies highlight the need to focus on the role of miRNAs in regulating storage protein accumulation in seeds. Therefore, a total of 8,856,691 short-read sequences were generated from a small RNA library of developing chickpea seeds and were analyzed using miRDeep-P to identify 74 known and 26 novel miRNA sequences. Known miRNAs were classified into 22 miRNA families with miRNA156 family being most abundant. Of the 26 putative novel miRNAs identified, only 22 could be experimentally validated using stem loop end point PCR. Differential expression analyses led to the identification of known as well as novel miRNAs that could regulate various stages of chickpea seed development. In silico target prediction revealed several important target genes and transcription factors like SPL, mediator of RNA Polymerase II transcription subunit 12, aspartic proteinase and NACs, which were further validated by real-time PCR analysis. A comparative expression analysis in chickpea genotypes with contrasting seed protein content revealed one known (Car-miR156h) and two novel miRNA (CarnovmiR7 and Car-novmiR23) candidates to be highly expressed in the LPC (low protein content) chickpea genotypes, targets of which are known to regulate seed storage protein accumulation. Therefore, this study provides a useful resource in the form of miRNA and their targets which can be further utilized to understand and manipulate various regulatory mechanisms involved in seed development with the overall aim of improving yield and nutrition attributes in chickpea.