Publications of NIPGR Scientists
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Item Differential regulation of nitric oxide mediated by phytoglobin1 plays a role in resistance during Botrytis cinerea infection in Arabidopsis thaliana(Springer Nature Publishing AG, 2026) Jaiswal, Rekha; Saini, Deepak; Swain, Jagannath; Gupta, Kapuganti JagadisBotrytis cinerea is a prominent necrotrophic pathogen responsible for gray mold disease, affecting a wide range of plant species, including economically vital crops such as tomatoes, grapes, strawberries, etc. Nitric oxide (NO) is considered as a crucial player in plant responses to biotic stress. NO homeostasis is regulated by phytoglobin (Pgb1), a potential scavenger of NO. However, the role of the Pgb1-NO cycle in regulating defense response against B. cinerea remains largely unknown. In the current study, we investigated the defense response of Arabidopsis thaliana against B. cinerea infection using antisense (Pgb1 AS) and overexpression (Pgb1 OE) lines, which produce differential levels of NO. The Pgb1 AS line accumulated higher NO levels and conferred resistance against B. cinerea infection, with reduced ROS levels, reduced cell death, and increased stomatal closure. Conversely, Pgb1 OE showed reduced NO levels accompanied by increased susceptibility. The elevated NO level in Pgb1 AS was associated with increased nitrate reductase (NR) activity and upregulation of NIA1 and NIA2 gene expression. Interestingly, ethylene-mediated defense pathway genes such as ERF1, ACS2, and ACS6 were upregulated while pathogen-related genes such as PR1, PR2, PR5, and NPR1 were downregulated in Pgb1 AS line. The elevated expression of ethylene genes corresponded with the higher ethylene levels in Pgb1 AS. Overall, our results confirmed the crucial role of phytoglobin-modulated NO in defense against B. cinerea infection by activating the ethylene-mediated defense pathway.Item The confluence of TOR signaling and plant growth regulators in development and stress responses(Oxford University Press, 2026) Saksena, Harshita B; Kumar, Mukesh; Samtani, Harsha; Sharma, Aishwarye; Rawat, Sanjay Singh; Awasthi, Prakhar; Botta, Halidev Krishna; Sandhya, Shital; Pande, Anjali; Naaz, Sheeba; Kushwah, Sunita; Shukla, Brihaspati N; Laxmi, AshveryaThe Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that serves as a crucial signaling hub, seamlessly integrating a wide range of internal and external signals to meticulously regulate cellular and organismal physiology. TOR is crucial in regulating the different phases of lifecycle in plants including embryogenesis, seed germination, meristem activation, root and leaf development, flowering and senescence. Beyond its central role in growth and development, emerging research has revealed its significant involvement in the response to environmental stresses. Even though plant growth regulators such as auxin, cytokinin (CK), brassinosteroid (BR), gibberellin (GA), abscisic acid (ABA), ethylene (ET), salicylic acid (SA), jasmonic acid (JA) and nitric oxide (NO) function as pivotal signaling molecules in modulating plant development and stress responses, how they coordinate with the energy status still remains obscure. Here we summarize the current findings on the dynamic interconnection between TOR and these discrete phytoregulators and their potential role in executing diverse biological processes in plants.Item Dissecting chickpea genomic loci associated with the root penetration responsive traits in compacted soil(Springer Nature Publishing AG, 2024) Donde, Ravindra; Kohli, Pawandeep Singh; Pandey, Mandavi; Sirohi, Ujjwal; Singh, Bhagat; Giri, JitenderSoil compaction is a major concern for modern agriculture, as it constrains plant root growth, leading to reduced resource acquisition. Phenotypic variation for root system architecture (RSA) traits in compacted soils is present for various crops; however, studies on genetic associations with these traits are lacking. Therefore, we investigated RSA traits in diferent soil compaction levels and identifed signifcant genomic associations in chickpea. We conducted a Genome-Wide Association Study (GWAS) of 210 chickpea accessions for 13 RSA traits under three bulk densities (BD) (1.1BD, 1.6BD, and 1.8BD). Soil compaction decreases root exploration by reducing 12 RSA traits, except average diameter (AD). Further, AD is negatively correlated with lateral root traits, and this correlation increases in 1.8BD, suggesting the negative efect of AD on lateral root traits. Interestingly, we identifed probable candidate genes such as GLP3 and LRX for lateral root traits and CRF1-like for total length (TL) in 1.6BD soil. In heavy soil compaction, DGK2 is associated with lateral root traits. Reduction in laterals during soil compaction is mainly due to delayed seedling establishment, thus making lateral root number a critical trait. Interestingly, we also found a higher contribution of the GxE component of the number of root tips (Tips) to the total variation than the other lateral traits. We also identifed a pectin esterase, PPE8B, associated with Tips in high soil compaction and a signifcantly associated SNP with the relative change in Tips depicting a trade-of between Tips and AD. Identifed genes and loci would help develop soil-compaction-resistant chickpea varieties.Item Fruit ripening specific expression of β-D-N-acetylhexosaminidase (β-Hex) gene in tomato is transcriptionally regulated by Ethylene Response Factor SlERF.E4(Elsevier B.V., 2022) Irfan, Mohammad; Kumar, Pankaj; Kumar, Vinay; Datta, AsisN-glycans and N-glycan processing enzymes are key players in regulating the ripening of tomato (Solanum lycopersicum) fruits, a model for fleshy fruit ripening. β-D-N-acetylhexosaminidase (β-Hex) is a N-glycan processing enzyme involved in fruit ripening. The suppression of β-Hex results in enhanced fruit shelf life and firmness in both climacteric and non-climacteric fruits. Previously, we have shown that ripening specific expression of β-Hex is regulated by RIPENING INHIBITOR (RIN), ABSCISIC ACID STRESS RIPENING 1 (SlASR1) and ethylene. However, the precise mechanism of ethylene-mediated regulation of β-Hex remains elusive. To gain insights into this, we have performed 5’ deletion mapping of tomato β-Hex promoter and a shorter promoter fragment (pD-200, 200 bp upstream to translational start site) is identified, which was found critical for spatio-temporal transcriptional regulation of β-Hex. Further, site specific mutagenesis in RIN and ASR1 binding sites in pD-200 provides key insights into ripening specific promoter activity. Furthermore, induction of GUS activity by ethylene, yeast one hybrid assay and EMSA identify Ethylene Response Factor SlERF.E4 as a positive regulator of β-Hex. Taken together, our study suggest that SlERF.E4 together with RIN and SlASR1 transcriptionally regulates β-Hex and all these three proteins are essential for fruit ripening specific expression of β-Hex in tomato.Item Novel microRNAs regulating ripening-associated processes in banana fruit(Springer Nature Publishing AG, 2020) Lakhwani, Deepika; Sanchita; Pandey, Ashutosh; Sharma, Deepika; Asif, Mehar H.; Trivedi, Prabodh K.MicroRNAs (miRNAs) modulate gene expression and regulate various physiological and developmental processes in plants. During fruit ripening phase, several physiological and biochemical variations take place resulting changes in colour and texture, softening and production of aroma volatiles. A number of pathways leading to cell wall hydrolysis, ethylene signaling, biosynthesis of fatty acids, esters and a number of secondary plant products play important role during fruit ripening. However, detailed analysis of various processes regulated by miRNAs has not been studied in detailed in a number of fruits. In this study, we sequenced small RNA libraries from ripe and un-ripe fruit of Banana (Musa acuminata), an important and staple food crop, to identify miRNAs regulating fruit ripening. Our analysis identifed a number of novel miRNAs which are diferentially expressed during fruit ripening. These novel miRNAs were analyzed for their precursors, chromosome localization and targets. Some of these miRNAs were identifed to target genes involved in miRNA biogenesis, fruit softening and aroma biosynthesis. This study advances our knowledges in the area of fruit ripening process regulated by miRNAs.Item Petal abscission in roses is associated with the activation of a truncated version of the animal PDCD4 homologue, RbPCD1(Elsevier B.V., 2019) Singh, Priya; Singh, Amar Pal; Tripathi, Siddharth Kaushal; Kumar, Vinod; Sane, Aniruddha P.Abscission is a developmental process that leads to shedding of organs not needed by the plant. Apart from wallhydrolysis, the cells of the abscission zone (AZ) are also believed to undergo programmed cell death (PCD). Weshow that ethylene-induced petal abscission inRosa bourbonianais accompanied with the activation ofRbPCD1(PROGRAMMED CELL DEATH LIKE 1) encoding a protein of 78 amino acids. Its expression increases duringnatural and ethylene-induced petal abscission. Its transcription in most tissues is up-regulated by ethylene.RbPCD1 shows similarity to the N-terminal domain of animal PDCD4 (PROGRAMMED CELL DEATH PROTEIN 4)proteins that are activated during apoptosis and function as transcriptional and translational repressors. RbPCD1resides in the nucleus and cytoplasm and acts as a transcriptional repressor. Constitutive expression ofRbPCD1intransgenic Arabidopsis is seedling lethal. Heat-induced expression ofRbPCD1under the soybean heat-shockpromoter affects leaf function, inflorescence development, silique formation, seed yield and reduces survival.Nuclear localization of RbPCD1 is necessary for manifestation of its effects. RbPCD1 may be necessary to mediatesome of the ethylene-induced changes during abscission and senescence in specific tissues.Item Genome-wide identification and interactome analysis of members of two-component system in Banana(BioMed Central Ltd, 2019) Dhar, Yogeshwar V.; Lakhwani, Deepika; Pandey, Ashutosh; Singh, Shikha; Trivedi, Prabodh K.; Asif, Mehar H.BACKGROUND: Ethylene signal transduction in plants is conducted by the two-component system (TCS) which consists of histidine kinase (HK), histidine phosphotransferase (HPT) and response regulators (RRs). This system plays an important role in signal transduction during various cellular processes, including fruit ripening and response to multiple environmental cues. Though members of TCS have been identified in a few plants, no detailed analysis has been carried out in banana. RESULTS: Through genome-wide analysis, we identified a total of 80 (25 HK, 10 HPT and 45 RR) and 72 (25 HK, 5 HPT and 42 RR) TCS genes in Musa acuminata and Musa balbisiana respectively. The analysis of identified genes revealed that most of the genes are highly conserved however; there are subtle divergences among various members. Comparative expression analysis revealed an involvement of a set of TCS members during banana fruit ripening. Co-expression network analysis identified a working TCS module with direct interactions of HK-HPT and RR members. The molecular dynamics analysis of TCS module showed a significant change in structural trajectories of TCS proteins in the presence of ethylene. Analysis suggests possible interactions between the HK-HPTs and RRs as well as other members leading to banana fruit ripening. CONCLUSIONS: In this study, we identified and compared the members of TCS gene family in two banana species and showed their diversity, within groups on the basis of whole-genome duplication events. Our analysis showed that during banana fruit ripening TCS module plays a crucial role. We also demonstrated a possible interaction mechanism of TCS proteins in the presence and absence of ethylene by molecular dynamics simulations. These findings will help in understanding the functional mechanism of TCS proteins in plants in different conditions.Item Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato(Springer Science, 2012) Kumar, Rahul; Sharma, Manoj K.; Kapoor, Sanjay; Tyagi, Akhilesh K.; Sharma, Arun K.A thorough understanding of molecular mechanisms underlying ripening is the prerequisite for genetic manipulation of fruits for better shelf-life and nutritional quality. Mutation in LeMADS-RIN, a MADS-box gene, leads to non-ripening phenotype of rin fruits in tomato. Characterization of ripening-inhibitor (rin) mutant has elucidated important role of ethylene in the regulation of climacteric fruit ripening. A complete understanding of this mutation will unravel novel genetic regulatory mechanisms involved in fruit ripening. In this study, fruit transcriptomes of two genotypes, including a cultivated Indian cultivar Solanum lycopersicum cv. Pusa Ruby and a homozygous line harboring the rin mutation (LA1795) were compared to get better insight into RIN-regulated ethylene-dependent and ethylene-independent events during ripening. Cluster analysis of ripening-related genes indicated a major shift in their expression profiles in rin mutant fruit. A total of 112 genes, exhibiting expression patterns similar to that of LeMADS-RIN in wild-type fruits, showed down regulation of expression in the rin mutant. In silico analysis of putative promoters of these genes for the presence of CArG box along with ERE and ethylene inducibility of these genes revealed that genes lacking CArG box in their regulatory regions could be indirectly regulated by LeMADS-RIN. New regulators of ethylene-dependent aspect of ripening were also identified. In this study, we have made an attempt to distinguish between ethylene-dependent and ethylene-independent aspects of ripening, which will be useful for developing strategies to improve fruit-related agronomic traits in tomato and other crops.Item Cytokinin interplay with ethylene, auxin and glucose signaling controls Arabidopsis seedling root directional growth(Am. Soc. of Plant Biologists, 2011) Kushwah, Sunita; Jones, Alan M.; Laxmi, AshveryaOptimal root architecture is established by multiple intrinsic (e.g. hormones) and extrinsic (e.g. gravity and touch) signals and is established, in part, by directed root growth. We show that asymmetrical exposure of cytokinin (CK) at the root tip in Arabidopsis (Arabidopsis thaliana) promotes cell elongation that is potentiated by glucose in a hexokinase-influenced, G protein-independent manner. This mode of CK signaling requires the CK receptor, ARABIDOPSIS HISTIDINE KINASE4 and, at a minimum, its cognate type B ARABIDOPSIS RESPONSE REGULATORS ARR1, ARR10, and ARR11 for full responsiveness, while type A response regulators act redundantly to attenuate this CK response. Ethylene signaling through the ethylene receptor ETHYLENE RESISTANT1 and its downstream signaling element ETHYLENE INSENSITIVE2 are required for CK-induced root cell elongation. Negative and positive feedback loops are reinforced by CK regulation of the expression of the genes encoding these elements in both the CK and ethylene signaling pathways. Auxin transport facilitated by PIN-FORMED2 as well as auxin signaling through control of the steady-state level of transcriptional repressors INDOLE-3-ACETIC ACID7 (IAA7), IAA14, and IAA17 via TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX PROTEIN are involved in CK-induced root cell elongation. This action lies downstream of ethylene and CK induction. Intrinsic signaling in this response operates independently of the extrinsic signal touch, although actin filament organization, which is important in the touch response, may be important for this response, since latrunculin B can induce similar growth. This root growth response may have adaptive significance, since CK responsiveness is inversely related to root coiling and waving, two root behaviors known to be important for fitness.Item Identification, phylogeny and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato(Springer, 2010) Sharma, Manoj K.; Kumar, Rahul; Solanke, Amolkumar U.; Sharma, Rita; Tyagi, Akhilesh K.; Sharma, Arun K.Ethylene responsive transcription factors have been shown to be intimately connected to plant development, defense responses and stress signaling pathways and in order to use them for plant improvement, we need to have better understanding of these proteins. In this study, 85 ERF genes have been identified from tomato using raw EST data in various public repositories. Phylogenetic analysis with tomato ERF domains revealed their distribution in all the groups, previously identified in model systems. MEME motif analysis resulted in identification of conserved domains, characteristic to member of each clade, in addition to ERF domain. Expression analysis during vegetative and reproductive stages of development using QPCR and tomato GeneChip arrays, revealed their tissue-specific/preferential accumulation. In total, 57 genes were found to be differentially expressed during temporal stages of tomato fruit development. The expression analysis of 23 ERF family genes representing each clade in response to seven abiotic stress treatments revealed their differential expression in response to more than one abiotic stress treatments. Results suggest that ERF genes play diverse roles in plant's life and comprehensive data generated will be helpful in conducting functional genomics studies to understand their precise role during plant development and stress response.