Browsing by Author "Giri, Jitender"

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Chickpea (Cicer arietinum) PHO1 family members function redundantly in Pi transport and root nodulation
(Elsevier B.V., 2024) Mani, Balaji; Maurya, Kanika; Kohli, Pawandeep Singh; Giri, Jitender
Phosphorus (P), a macronutrient, plays key roles in plant growth, development, and yield. Phosphate (Pi) transporters (PHTs) and PHOSPHATE1 (PHO1) are central to Pi acquisition and distribution. Potentially, PHO1 is also involved in signal transduction under low P. The current study was designed to identify and functionally characterize the PHO1 gene family in chickpea (CaPHO1s). Five CaPHO1 genes were identified through a comprehensive genome-wide search. Phylogenetically, CaPHO1s formed two clades, and protein sequence analyses confirmed the presence of conserved domains. CaPHO1s are expressed in different plant organs including root nodules and are induced by Pi-limiting conditions. Functional complementation of atpho1 mutant with three CaPHO1 members, CaPHO1, CaPHO1;like, and CaPHO1;H1, independently demonstrated their role in root to shoot Pi transport, and their redundant functions. To further validate this, we raised independent RNA-interference (RNAi) lines of CaPHO1, CaPHO1;like, and CaPHO1;H1 along with triple mutant line in chickpea. While single gene RNAi lines behaved just like WT, triple knock-down RNAi lines (capho1/like/h1) showed reduced shoot growth and shoot Pi content. Lastly, we showed that CaPHO1s are involved in root nodule development and Pi content. Our findings suggest that CaPHO1 members function redundantly in root to shoot Pi export and root nodule development in chickpea.
A citrate efflux transporter important for manganese distribution and phosphorus uptake in rice
(John Wiley & Sons, 2023) Panchal, Poonam; Bhatia, Chitra; Chen, Yi; Sharma, Meenakshi; Bhadouria, Jyoti; Verma, Lokesh; Maurya, Kanika; Miller, Anthony J.; Giri, Jitender
The plant citrate transporters, functional in mineral nutrient uptake and homeostasis, usually belong to the multidrug and toxic compound extrusion transporter family. We identified and functionally characterized a rice (Oryza sativa) citrate transporter, OsCT1, which differs from known plant citrate transporters and is structurally close to rice silicon transporters. Domain analysis depicted that OsCT1 carries a bacterial citrate-metal transporter domain, CitMHS. OsCT1 showed citrate efflux activity when expressed in Xenopus laevis oocytes and is localized to the cell plasma membrane. It is highly expressed in the shoot and reproductive tissues of rice, and its promoter activity was visible in cells surrounding the vasculature. The OsCT1 knockout (KO) lines showed a reduced citrate content in the shoots and the root exudates, whereas overexpression (OE) line showed higher citrate exudation from their roots. Further, the KO and OE lines showed variations in the manganese (Mn) distribution leading to changes in their agronomical traits. Under deficient conditions (Mn-sufficient conditions followed by 8 days of 0 μm MnCl2 · 4H2 O treatment), the supply of manganese towards the newer leaf was found to be obstructed in the KO line. There were no significant differences in phosphorus (P) distribution; however, P uptake was reduced in the KO and increased in OE lines at the vegetative stage. Further, experiments in Xenopus oocytes revealed that OsCT1 could efflux citrate with Mn. In this way, we provide insights into a mechanism of citrate-metal transport in plants and its role in mineral homeostasis, which remains conserved with their bacterial counterparts.
Comparative morphophysiological analyses and molecular profiling reveal Pi-efficient strategies of a traditional rice genotype
(Frontiers Media S.A., 2016) Mehra, Poonam; Pandey, Bipin K.; Giri, Jitender
Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant), and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance mechanisms of the traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater root growth than PB1 under low Pi, resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of the traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.
CRISPR-Cas9 based plant genome editing: Significance, opportunities and recent advances
(Elsevier B.V., 2018) Soda, Neelam; Verma, Lokesh; Giri, Jitender
Precise genome editing is a quantum leap in the field of plant sciences. Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated Cas9 protein have emerged as a powerful tool for precise genome editing. CRISPR-Cas9 system introduces small heritable mutations (indels) in the genome of an organism. This system also enables precise gene characterization in plants with complex genomes. Besides, it offers new opportunities of trait stacking, where addition of desirable traits or removal of undesirable traits can be achieved simultaneously in a single event. With CRISPR-Cas9 RNPs technology, raising transgene free genetically modified plants is within realm of possibility which would be helpful in addressing regulatory concerns of transgenic plants. Several new advancements have been made in this technology which has extended its applications in almost every aspect of plant science. For example, recently developed catalytically inactive dCas9 fused with transcriptional effector domains allows targeted activation or silencing of the gene of interest. Apart from this, dCas9 fused with fluorescent labels is a budding tool in chromatin imaging studies. In this review, we summarize these recent advancements in CRISPR/Cas system and methods for analyzing the induced mutations, and its implementations in crop improvement.
Differential expression of salt-responsive genes to salinity stress in salt-tolerant and salt-sensitive rice (Oryza sativa L.) at seedling stage
(Springer Nature, 2018) Singh, Vijayata; Singh, Ajit Pal; Bhadoria, Jyoti; Giri, Jitender; Singh, Jogendra; T. V., Vineeth; Sharma, P. C.
The understanding of physio-biochemical and molecular attributes along with morphological traits contributing to the salinity tolerance is important for developing salt-tolerant rice (Oryza sativa L.) varieties. To explore these facts, rice genotypes CSR10 and MI48 with contrasting salt tolerance were characterized under salt stress (control, 75 and 150 mM NaCl) conditions. CSR10 expressed higher rate of physio-biochemical parameters, maintained lower Na/K ratio in shoots, and restricted Na translocation from roots to shoots than MI48. The higher expression of genes related to the osmotic module (DREB2A and LEA3) and ionic module (HKT2;1 and SOS1) in roots of CSR10 suppresses the stress, enhances electrolyte leakage, promotes the higher compatible solute accumulation, and maintains cellular ionic homeostasis leading to better salt stress tolerance than MI48. This study further adds on the importance of these genes in salt tolerance by comparing their behaviour in contrasting rice genotypes and utilizing specific marker to identify salinity-tolerant accessions/donors among germplasm; overexpression of these genes which accelerate the selection procedure precisely has been shown.
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, Jitender
Soil 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.
Dual localization of JA receptor, CaCOI2, explains JA perception dynamics in chickpea
(John Wiley & Sons, 2025) Singh, Ajit Pal; Bhatia, Chitra; Singh, Ekampreet; Singh, Amit Kumar; Fatima, Urooj; Senthil-Kumar, Muthappa; Giri, Jitender
Jasmonates (JAs) are a group of oxylipin-derived phytohormones involved in various biotic and abiotic stress responses and regulate plant development. JAs are perceived by receptor proteins called coronatine insensitive (COI). These JA receptors encode F-box proteins that form the SCFCOI ubiquitin ligase complex (comprising Skp, Cullin, and F-box) and activate JA signaling by promoting the degradation of the transcriptional repressor JAZ (JA associated ZIM domain containing) proteins via the 26S proteasomal pathway. However, JA signaling is not well understood in chickpea, a vital legume. In this study, we identified two potential chickpea JA receptors, named CaCOI1 and CaCOI2, and characterized CaCOI2 as a functional JA receptor. Subcellular localization experiments revealed that CaCOI2 is localized outside the nucleus but moves into the nucleus upon JA perception to activate signaling. Using domain-swapping experiments between CaCOI1 and CaCOI2, we demonstrated that the leucine-rich repeat region of the receptors, which interacts with bioactive JA such as JA-Isoleucine, also plays a crucial role in controlling the subcellular localization of CaCOI proteins. Our findings identify a functional JA receptor in chickpea and reveal new aspects of JA signaling and perception, which may also be relevant to other plants.
Editing cis-elements of OsPHO1;2 improved phosphate transport and yield in rice
(John Wiley & Sons, 2025) Maurya, Kanika; Mani, Balaji; Singh, Bhagat; Sirohi, Ujjwal; Jaskolowski, Aime; Sharma, Sandeep; Tatiparthi, Harsha Vardhan; Mangrauthia, Satendra Kumar; Pandey, Renu; Poirier, Yves; Giri, Jitender
Increasing grain yield is the primary goal of crop improvement, which is globally affected by the low availability of soil phosphate (Pi). Overexpressing Pi transporters to enhance Pi uptake often results in Pi toxicity and growth retardation. Despite advances in genetic engineering, targeting the cis-regulatory motifs of Pi transporters remains underexplored for understanding plant mechanisms and improving Pi status. Here, we demonstrate that the excision of the transcription inhibitor motif from the promoter of the Pi transporter OsPHO1;2 enhances its expression and increases root-to-shoot Pi transport, leading to improved grain yield. Through in silico and DNA-protein interaction studies, we show the role of the OsWRKY6 transcription factor in negatively regulating OsPHO1;2 expression by binding to the cis-regulatory element (W-box) present in its promoter. The oswrky6 knockout lines exhibit higher OsPHO1;2 expression and improved shoot Pi levels. Furthermore, we engineered the OsPHO1;2 promoter to precisely remove the W-box and enhance OsPHO1;2 expression. Phenotypic and physiological evaluations at the vegetative stage indicate that OsPHO1;2 promoter-edited (OsPHO1;2:PE) lines have increased shoot length, plant biomass and greater root-to-shoot Pi export under both low and normal P conditions. Notably, the 33P uptake assay reveals that OsPHO1;2:PE lines display enhanced root Pi uptake, supported by higher expression of root-associated Pi transporters (OsPHTs). An extensive agronomic assessment shows that OsPHO1;2:PE lines achieve increased seed and panicle numbers, thereby raising yield without affecting seed quality. Our findings provide valuable insights into the potential of promoter editing to improve Pi use and enhance crop yield.
Emerging molecular strategies for improving rice drought tolerance
(Bentham Science, 2021) Giri, Jitender; Parida, Swarup K.; Raghuvanshi, Saurabh; Tyagi, Akhilesh K.
Rice occupies a pre-eminent position as a food crop in the world. Its production, however, entails up to 3000 liters of water per kilogram of grain produced. Such high demand makes rice prone to drought easily. Sustainable rice cultivation with limited water resources requires the deployment of a suitable strategy for better water use efficiency and improved drought tolerance. Several drought-related genes have been evaluated in rice for their mode of action in conferring drought tolerance. Manipulation of components of abscisic acid signal transduction, stomatal density, deposition of cuticular wax, and protein modification pathways are emerging as priority targets. Gene reprogramming by microRNAs is also being explored to achieve drought tolerance. Genetically dissected Quantitative Trait Loci (QTLs) and their constituent genes are being deployed to develop drought-tolerant rice varieties. Progressive research and challenges include a better understanding of crucial components of drought response and search for new targets and the deployment of improved varieties in the field.
Emerging trends in epigenetic regulation of nutrient deficiency response in plants
(Springer, 2016) Sirohi, Gunjan; Pandey, Bipin K.; Deveshwar, Priyanka; Giri, Jitender
Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.
Genome-wide association study for phosphate deficiency responsive root hair elongation in chickpea
(Springer Nature Publishing AG, 2020) Kohli, Pawandeep Singh; Verma, Pankaj Kumar; Verma, Rita; Parida, Swarup K.; Thakur, Jitendra K.; Giri, Jitender
Root hairs (RHs) are single-celled elongated epidermal cells and play a vital role in nutrient absorption, particularly for immobile minerals like phosphorus (P). As an adaptive response to P deficiency, an increase in RH length enhances root-soil contact and absorptive area for P absorption. Genetic variations have been reported for RH length and its response to P deficiency in plants. However, only a few association studies have been conducted to identify genes and genetic loci associated with RH length. Here, we screened desi chickpea accessions for RH length and its plasticity under P deficiency. Further, the genome-wide association study (GWAS) was conducted to identify the genetic loci associated with RH length in P deficient and sufficient conditions. Although high variability was observed in terms of RH length in diverse genotypes, majority of the accessions showed typical response of increase in RH length in low P. Genome-wide association mapping identified many SNPs with significant associations with RH length in P-sufficient and P-deficient conditions. A few candidate genes for RH length in P deficient (SIZ1-like and HAD superfamily protein) and sufficient (RSL2-like and SMAP1-like) conditions were identified which have known roles in RH development and P deficiency response or both. Highly associated loci and candidate genes identified in this study would be useful for genomic-assisted breeding to develop P-efficient chickpea.
Genome-wide DNA polymorphisms in low phosphate tolerant and sensitive rice genotypes
(Nature Publishing Group, 2015) Mehra, Poonam; Pandey, Bipin K.; Giri, Jitender
Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes.
Glycinebetaine and abiotic stress tolerance in plants
(Landes Bioscience, 2011) Giri, Jitender
The accumulation of osmolytes like glycinebetaine (GB) in cell is known to protect organisms against abiotic stresses via osmoregulation or osmoprotection. Transgenic plants engineered to produce GB accumulate very low concentration of GB, which might not be sufficient for osmoregulation. Therefore, other roles of GB like cellular macromolecule protection and ROS detoxification have been suggested as mechanisms responsible for abiotic stress tolerance in transgenic plants. In addition, GB influences expression of several endogenous genes in transgenic plants. The new insights gained about the mechanism of stress tolerance in GB accumulating transgenic plants are discussed.
Glycinebetine-induced water-stress tolerance in Cod A-expressing transgenic India rice is associated with up-regulation of several stress responsive genes
(Wiley-Blackwell, 2009) Kathuria, Hitesh; Giri, Jitender; Nataraja, Karaba N.; Murata, Norio; Udayakumar, Makarla; Tyagi, Akhilesh K.
Rice (Oryza sativa L.), a non-accumulator of glycinebetaine (GB), is highly susceptible to abiotic stress. Transgenic rice with chloroplast-targeted choline oxidase encoded by the codA gene from Arthrobacter globiformis has been evaluated for inheritance of transgene up to R5 generation and water-stress tolerance. During seedling, vegetative and reproductive stages, transgenic plants could maintain higher activity of photosystem II and they show better physiological performance, for example, enhanced detoxification of reactive oxygen species compared to wild-type plants under water-stress. Survival rate and agronomic performance of transgenic plants is also better than wild-type following prolonged water-stress. Choline oxidase converts choline into GB and H2O2 in a single step. It is possible that H2O2/GB might activate stress response pathways and prepare transgenic plants to mitigate stress. To check this possibility, microarray-based transcriptome analysis of transgenic rice has been done. It unravelled altered expression of many genes involved in stress responses, signal transduction, gene regulation, hormone signalling and cellular metabolism. Overall, 165 genes show more than two-fold up-regulation at P-value < 0.01 in transgenic rice. Out of these, at least 50 genes are known to be involved in plant stress response. Exogenous application of H2O2 or GB to wild-type plants also induces such genes. Our data show that metabolic engineering for GB is a promising strategy for introducing stress tolerance in crop plants and which could be imparted, in part, by H2O2- and/or GB-induced stress response genes.
IBR5 regulates leaf serrations development via modulation of the expression of PIN1
(MDPI AG, 2019) Kong, Xiuzhen; Huang, Guoqiang; Xiong, Yali; Zhao, Chunyan; Wang, Jun; Song, Xiaoyun; Giri, Jitender; Zuo, Kaijing
Biodiversity in plant shape is mainly attributable to the diversity of leaf shape, which is largely determined by the transient morphogenetic activity of the leaf margin that creates leaf serrations. However, the precise mechanism underlying the establishment of this morphogenetic capacity remains poorly understood. We report here that INDOLE-3-BUTYRIC ACID RESPONSE 5 (IBR5), a dual-specificity phosphatase, is a key component of leaf-serration regulatory machinery. Loss-of-function mutants of IBR5 exhibited pronounced serrations due to increased cell area. IBR5 was localized in the nucleus of leaf epidermis and petiole cells. Introducing a C129S mutation within the highly conserved VxVHCx2GxSRSx5AYLM motif of IBR5 rendered it unable to rescue the leaf-serration defects of the ibr5-3 mutant. In addition, auxin reporters revealed that the distribution of auxin maxima was expanded ectopically in ibr5-3. Furthermore, we found that the distribution of PIN1 on the plasma membrane of the epidermal and cells around the leaf vein was compromised in ibr5-3. We concluded that IBR5 is essential for the establishment of PIN-FORMED 1 (PIN1)-directed auxin maxima at the tips of leaf serration, which is vital for the elaborated regulation during its formation.
Identification of purple acid phosphatases in chickpea and potential roles of CaPAP7 in seed phytate accumulation
(Nature Publishing Group, 2017) Bhadouria, Jyoti; Singh, Ajit Pal; Mehra, Poonam; Verma, Lokesh; Srivastawa, Rishi; Parida, Swarup K.; Giri, Jitender
Purple acid phosphatases (PAPs) play important roles in phosphate (Pi) acquisition and utilization. These PAPs hydrolyze organic Phosphorus (P) containing compounds in rhizosphere as well as inside the plant cell. However, roles of PAPs in one of the most widely cultivated legumes, chickpea (Cicer arietnum L.), have not been unraveled so far. In the present study, we identified 25 putative PAPs in chickpea (CaPAPs) which possess functional PAP motifs and domains. Differential regulation of CaPAPs under different nutrient deficiencies revealed their roles under multiple nutrient stresses including Pi deficiency. Interestingly, most of the CaPAPs were prominently expressed in flowers and young pods indicating their roles in flower and seed development. Association mapping of SNPs underlying CaPAPs with seed traits revealed significant association of low Pi inducible CaPAP7 with seed weight and phytate content. Biochemical characterization of recombinant CaPAP7 established it to be a functional acid phosphatase with highest activity on most abundant organic-P substrate, phytate. Exogenous application of recombinant CaPAP7 enhanced biomass and Pi content of Arabidopsis seedlings supplemented with phytate as sole P source. Taken together, our results uncover the PAPs in chickpea and potential roles of CaPAP7 in seed phytate accumulation.
Improvement of phosphate acquisition and utilization by a secretory purple acid phosphatase (OsPAP21b) in rice
(John Wiley & Sons, 2017) Mehra, Poonam; Pandey, Bipin Kumar; Giri, Jitender
Phosphate (Pi) deficiency in soil system is a limiting factor for rice growth and yield. Majority of the soil Phosphorus (P) is organic in nature; not readily available for root uptake. Low Pi inducible purple acid phosphatases (PAPs) are hypothesized to enhance the availability of Pi in soil and cellular system. However, information on molecular and physiological roles of rice PAPs is very limited. Here, we demonstrate the role of a novel rice PAP, OsPAP21b in improving plant utilization of organic-P. OsPAP21b was found to be under the transcriptional control of OsPHR2 and strictly regulated by plant Pi-status at both transcript and protein levels. Biochemically, OsPAP21b showed hydrolysis of several organophosphates at acidic pH and possessed sufficient thermostability befitting for high temperature rice ecosystems with acidic soils. Interestingly, OsPAP21b was revealed to be a secretory PAP and encodes a distinguishable major APase (acid phosphatase) isoform under low Pi in roots. Further, OsPAP21b overexpressing transgenics showed increased biomass, APase activity and P content both in hydroponics supplemented with organic-P sources and soil containing organic manure as sole P source. Additionally, overexpression lines depicted increased root length, biomass and lateral roots under low Pi while RNAi lines showed reduced root length and biomass as compared to WT. In light of these evidences, present study strongly proposes OsPAP21b as a useful candidate for improving Pi acquisition and utilization in rice.
JAZ repressors: Potential involvement in nutrients deficiency response in rice and chickpea
(Frontiers Media S.A., 2015) Singh, Ajit P.; Pandey, Bipin K.; Deveshwar, Priyanka; Narnoliya, Laxmi; Parida, Swarup K.; Giri, Jitender
Jasmonates (JA) are well-known phytohormones which play important roles in plant development and defense against pathogens. Jasmonate ZIM domain (JAZ) proteins are plant-specific proteins and act as transcriptional repressors of JA-responsive genes. JA regulates both biotic and abiotic stress responses in plants; however, its role in nutrient deficiency responses is very elusive. Although, JA is well-known for root growth inhibition, little is known about behavior of JAZ genes in response to nutrient deficiencies, under which root architectural alteration is an important adaptation. Using protein sequence homology and a conserved-domains approach, here we identify 10 novel JAZ genes from the recently sequenced Chickpea genome, which is one of the most nutrient efficient crops. Both rice and chickpea JAZ genes express in tissue- and stimuli-specific manners. Many of which are preferentially expressed in root. Our analysis further showed differential expression of JAZ genes under macro (NPK) and micronutrients (Zn, Fe) deficiency in rice and chickpea roots. While both rice and chickpea JAZ genes showed a certain level of specificity toward type of nutrient deficiency, generally majority of them showed induction under K deficiency. Generally, JAZ genes showed an induction at early stages of stress and expression declined at later stages of macro-nutrient deficiency. Our results suggest that JAZ genes might play a role in early nutrient deficiency response both in monocot and dicot roots, and information generated here can be further used for understanding the possible roles of JA in root architectural alterations for nutrient deficiency adaptations.
A lipid synthase maintains metabolic flux for jasmonate synthesis to regulate root growth and phosphate homeostasis
(Oxford University Press, 2025) Pandey, Mandavi; Verma, Lokesh; Kohli, Pawandeep Singh; Singh, Bhagat; Kochi, Abhijith; Giri, Jitender
Plants require phosphate (Pi) for proper growth and development but often face scarcity of this vital nutrient in the soil. Pi-starvation triggers membrane lipid remodeling to utilize the membrane phospholipid-bound Pi in plants. In this process, phospholipids are replaced by non-Pi-containing galactolipids (MGDG, DGDG) and sulfolipids. The galactolipids ratio (MGDG:DGDG) is suggested to influence jasmonic acid (JA) biosynthesis. However, how the MGDG:DGDG ratio, JA levels, and root growth are coordinated under Pi deficiency in rice (Oryza sativa) remains unknown. Here, we characterized DGDG synthase 1 (OsDGD1) for its role in regulating root development by maintaining metabolic flux for JA biosynthesis. We showed that OsDGD1 is responsive under low Pi and is under the direct control of Phosphate Starvation Response 2 (OsPHR2), the master regulator of low Pi adaptations. Further, OsDGD1 knockout (KO) lines showed marked phenotypic differences compared to the wild type (WT), including a significant reduction in root length and biomass, leading to reduced Pi uptake. Further, lipidome analyses revealed reduced DGDG levels in the KO line, leading to reduced membrane remodeling, thus affecting P utilization efficiency. We also observed an increase in the MGDG: DGDG ratio in KO lines, which enhanced the endogenous JA levels and signaling. This imbalance of JA in KO plants led to changes in auxin levels, causing drastic root growth inhibition. These findings indicate the critical role of OsDGD1 in maintaining optimum levels of JA during Pi deficiency for conducive root growth. Besides acting as signaling molecules and structural components, our study widens the role of lipids as metabolic flux controllers for phytohormone biosynthesis.
Lipid-mediated responses to nutrient and other stresses: Roles in plant adaptation and signaling
(Oxford University Press, 2026) Pandey, Mandavi; Ganotra, Jahanvi; Singh, Astha; Parchuri, Prasad; Giri, Jitender
Lipids are essential components of biological membranes; however, their roles in plants go far beyond providing structural support. They are actively involved in signaling and metabolic regulation during abiotic and biotic stress. Plants use lipid-based strategies to adapt to nutrient shortages, toxic conditions, and changing environments. Signaling lipids such as phosphatidic acid (PA), phosphoinositides, sphingolipids, and oxylipins serve as molecular messengers that transmit stress signals to regulate ion transport, hormone interactions, and developmental flexibility. During nutrient deprivation, especially of phosphorus (P), nitrogen (N), and potassium (K), plants adjust membrane composition by replacing phospholipids with P-free glycolipids like galactolipids and sulfolipids, conserving critical nutrients while keeping membrane structure intact. Lipid intermediates, including PA, glycerol-3-phosphate, and negatively charged phospholipids, also act as secondary messengers in stress signaling networks. Lipid droplets and lipophagy help maintain carbon and redox balance, while enzymes like phospholipases and glycerophosphodiesterases recycle nutrients and alter lipid profiles. Under K deficiency and toxic metal exposure (e.g., aluminum (Al), cadmium (Cd)), lipid turnover influences membrane stability, reactive oxygen species (ROS) production, and transporter function. Lipid modifications also reduce toxic ion binding and cellular damage, and molecules derived from lipids, such as jasmonates, play roles in secondary metabolism and hormonal defense pathways. Although lipid-based stress responses are conserved throughout plant lineages, the regulatory mechanisms controlling lipid fluxes are not yet fully understood. New tools, like genetically coded lipid biosensors and lipidomics platforms, are uncovering the spatial and temporal dynamics of lipid signaling with unprecedented detail. Improving our understanding of lipid-mediated stress responses may enable the development of crops with better nutrient efficiency and resilience to climatic and edaphic stresses, contributing to sustainable agriculture.