Browsing by Author "Pandey, Vimal"

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Dynamics of miRNA mediated regulation of legume symbiosis
(John Wiley & Sons, 2021) Tiwari, Manish; Pandey, Vimal; Singh, Baljinder; Bhatia, Sabhyata
Symbiotic nitrogen fixation in legume nodules is important in soils with low nitrogen availability. The initiation and sustainability of symbiosis requires cellular reprogramming that involves the miRNA‐mediated inhibition or activation of specific nodulation genes. The high‐throughput sequencing of small RNA libraries has identified miRNAs and their targets, which are the major players in the post‐transcriptional gene regulation (PTGS) of the different stages of legume‐rhizobia symbiosis ranging from bacterial colonization and organogenesis to symbiotic nitrogen fixation. Here we present an overview of information obtained from the miRNA libraries from nodulating tissues that have been sequenced to date. The functional analysis of miRNAs has revealed roles in phytohormone homeostasis and spatio‐temporal regulation, as well as the mobility of miRNAs and their functions in shoot to root signalling that affects diverse functions, including bacterial entry, meristem division and differentiation, nitrogen fixation and senescence. Furthermore, small RNA fragments of rhizobial origin repress complementary plant mRNAs. We also consider the roles of miRNAs in determinate or indeterminate nodules. Taken together, this overview confirms that miRNAs are master regulators of the legume‐rhizobia symbiosis.
Evolutionary and expression dynamics of LRR-RLKs and functional establishment of KLAVIER homolog in shoot mediated regulation of AON in chickpea symbiosis
(Elsevier B.V., 2021) Tiwari, Manish; Pandey, Vimal; Singh, Baljinder; Yadav, Manisha; Bhatia, Sabhyata
Chickpea shoot exogenously treated with cytokinin showed stunted phenotype of root, shoot and significantly reduced nodule numbers. Genome-wide identification of LRR-RLKs in chickpea and Medicago resulted in 200 and 371 genes respectively. Gene duplication analysis revealed that LRR-RLKs family expanded through segmental duplications in chickpea and tandem duplications in Medicago. Expression profiling of LRR-RLKs revealed their involvement in cytokinin signaling and plant organ development. Overexpression of KLAVIER ortholog of chickpea, Ca_LRR-RLK147, in roots revealed its localization in the membrane but showed no effect on root nodulation despite increased cle peptide levels. Two findings (i) drastic effect on nodule number by exogenous cytokinin treatment to only shoot and restoration to normal nodulation by treatment to both root and shoot tissue and (ii) no effect on nodule number by overexpression of Ca_LRR-RLK147 establishes the fact that despite presence of cle peptides in root, the function of Ca_LRR-RLK147 was shoot mediated during AON.
Evolutionary and functional analysis of Two-Component System in chickpea reveals CaRR13, a TypeB RR, as positive regulator of symbiosis
(John Wiley & Sons, 2021) Tiwari, Manish; Yadav, Manisha; Singh, Baljinder; Pandey, Vimal; Nawaz, Kashif; Bhatia, Sabhyata
The critical role of cytokinin in early nodulation in legumes is well known. In our study, exogenous cytokinin application to roots of the important crop legume, chickpea (Cicer arietinum L.) led to the formation of pseudo nodules even in the absence of rhizobia. Hence a genome-wide analysis of the cytokinin signaling, Two-Component System (TCS) genes was conducted in chickpea, Medicago and Cajanus cajan. The integrated phylogenetic, evolutionary and expression analysis of the TCS genes was carried out which revealed that Histidine Kinases (HKs) were highly conserved, whereas, there was diversification leading to neofunctionalization at the level of Response Regulators (RRs) especially the TypeB RRs. Further, the functional role of the CaHKs in nodulation was established by complementation of the sln1Δ mutant of yeast and cre1 mutants of (Medicago) which led to restoration of the nodule deficient phenotype. Additionally, the highest expressing TypeB RR of chickpea, CaRR13 was functionally characterized. Its localization in the nucleus and its Y1H assay-based interaction with the promoter of the early nodulation gene CaNSP2 indicated its role as a transcription factor regulating early nodulation. Overexpression, RNAi lines and complementation of cre1 mutants with CaRR13 revealed its critical involvement as an important signaling molecule regulating early events of nodule organogenesis in chickpea.
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.
High throughput identification of miRNAs reveal novel interacting targets regulating chickpea-rhizobia symbiosis
(Elsevier B.V., 2021) Tiwari, Manish; Singh, Baljinder; Yadav, Manisha; Pandey, Vimal; Bhatia, Sabhyata
Legumes developed symbiotic associations to meet its nitrogen requirement. The nitrogen fixation takes place in root nodules which involves bacterial colonization, organogenesis and nitrogen fixation. In order to unravel the miRNA mediated regulation of chickpea symbiosis, one microRNA and four parallel analysis of RNA ends (PARE) libraries were sequenced. Analysis of microRNA library identified a set of 91 miRNAs comprising of 84 conserved and 7 novel miRNAs. Additionally, PARE library analysis revealed 564 genes being targeted by 85 miRNAs. Phylogenetic analysis of the precursor sequences of the 91 miRNAs was carried out which revealed their ancestral relationships. Further, the mechanism of miRNAs biogenesis was predicted using the miRNAs information from other legumes. Reads from the nodule library were mapped to bacterial genomes to predict bacterial-encoded small RNAs. Real time expression analysis was used to validate the antagonistic expression pattern of important miRNA-mRNA target pairs. Four candidate miRNAs were selected for in planta study based on the antagonistic expression profiling as well as the novelty of their respective targets. miR171f, miR172c, miR394 and miR1509 targeted nodulation receptor kinase, Apetala2, histidine phosphotransferase, adenylate kinase respectively and were ectopically expressed in chickpea roots. The overexpression lines showed significant change in nodule numbers, the miR172c, miR394 and miR1509 resulted in an increase in nodule number whereas, miR171f overexpression led to a decrease in nodule number. Our analysis lays the foundation for functional characterization of novel miRNAs and their respective target pairs which control nodulation in chickpea and other leguminous crops.
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.
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, Sabhyata
Lentil (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.