Publications of NIPGR Scientists
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Item Rice phosphate transporter reduces the low phosphate response through jasmonate signaling(Oxford University Press, 2026) Mani, Balaji; Maurya, Kanika; Verma, Lokesh; Gupta, Priya; Kohli, Pawandeep Singh; Gupta, Gagan; Jaskolowski, Aime; Poirier, Yves; Giri, JitenderPhosphorus (P) is an essential macronutrient for plant growth, and its deficiency severely limits crop productivity. The PHOSPHATE1 (PHO1) protein family, defined by an N-terminal SPX domain, four transmembrane (4TM) domains, and a C-terminal EXS domain, mediates phosphate (Pi) loading into the xylem for root-to-shoot transport. In rice, OsPHO1;2 is critical for Pi export, and loss-of-function mutants exhibit severe growth retardation and Pi deficiency symptoms despite sufficient external Pi. To dissect the functional contributions of PHO1 domains beyond Pi transport, we generated CRISPR/Cas9 rice lines expressing either the EXS domain containing part of the SPX domain (S-EXS) or the 4TM+EXS domains (T-EXS) of OsPHO1;2. Phenotypic analyses under Pi-sufficient and Pi-deficient conditions revealed that S-EXS lines displayed improved early growth compared to ospho1;2 mutants, despite similar shoot Pi levels. These plants exhibited reduced jasmonic acid accumulation and attenuated phosphate starvation responses, resembling wild-type hormone profiles. In contrast, T-EXS lines mirrored the growth defects of ospho1;2 mutants. Transcriptome profiling confirmed that defense and phosphate starvation pathways were less activated in S-EXS lines relative to mutants. However, both S-EXS and T-EXS lines retained seed development defects and reduced seed phosphorus content, consistent with ospho1;2 phenotypes. Heterozygous plants carrying one functional OsPHO1;2 allele exhibited normal growth and seed development, confirming the recessive nature of the mutation. Collectively, these findings demonstrate that the S-EXS domain of OsPHO1;2 promotes plant growth independently of Pi transport by modulating jasmonate signaling and suppressing phosphate starvation responses. This highlights a signaling role for PHO1 domains, offering new insights into Pi homeostasis and potential strategies for breeding Pi-efficient crops.Item Unearthing root response mechanisms to soil compaction in legumes(John Wiley & Sons, 2026) Ganotra, Jahanvi; Pandey, Mandavi; Pandey, Bipin K.; Giri, JitenderRoots are essential for the survival and functioning of plants, serving as anchors in the soil and drawing in vital nutrients and water. Roots also engage in diverse microbial interactions, including pathogenic interactions that cause plant disease and non-pathogenic interactions, such as symbiotic and commensal relationships. Mechanical resistance in compacted soil is one of the biggest challenges for root exploration. Soil compaction hampers plant growth by restricting root elongation, reducing root proliferation, and limiting access to water, nutrients, and oxygen. These restrictions interfere with root-microbe interactions and also impair aboveground growth, leading to decreased shoot biomass, stunted development, and lower overall productivity. Legume roots form symbiotic relationships with soil-dwelling Rhizobium, resulting in root nodules that convert atmospheric nitrogen (N) into ammonia, thereby promoting plant growth. However, the impact of soil compaction on legume roots remains poorly studied. In this review, we examine key adaptive strategies used by legume roots to counteract soil compaction, focusing on the underlying molecular pathways. A complex signalling network regulates molecular processes that control root development and nodulation in legumes. We also explore the genetic and environmental factors that influence morphological, anatomical, and biochemical traits under mechanical stress, providing insights for improving stress resilience in legumes.Item Network-based multiomics and transgenic validation reveal that OsPHR3 modulates phosphate-carbon metabolic trade-offs during rice seed development(Elsevier B.V., 2026) Pazhamala, Lekha; Pandey, Mandavi; Deveshwar, Priyanka; Ghatak, Arindam; Weckwerth, Wolfram; Chaturvedi, Palak; Giri, JitenderPhosphate (Pi) allocation during the grain-filling stage is a major determinant of crop yield, supporting macromolecule synthesis, energy metabolism, and nutrient storage. However, its storage as phytic acid (PA) reduces nutritional quality by chelating essential minerals. Despite its importance, a comprehensive understanding of the molecular mechanisms integrating Pi transport, carbohydrate metabolism, and PA biosynthesis during seed development remains incomplete. To address this gap, we investigated stage-specific phosphate regulatory networks in rice by integrating transcriptomic, proteomic, and metabolomic approaches. Temporal expression profiling and gene coexpression network analyses of phosphate regulators and transporter genes revealed their distinct roles during early and mid-grain filling stages. PHOSPHATE STARVATION RESPONSE 3 (OsPHR3) emerged as a central regulatory hub, coordinating the balance of Pi, sugar, starch and phytate, along with other metabolites. Network-based multiomics integration further identified 126 genes involved in nutrient storage and stress tolerance, with myo-inositol-1-phosphate synthase (OsMIPS1) and starch synthase 3 (OsSSIII) as key genes. CRISPR/Cas9-generated osphr3 knockout lines confirmed the critical role of OsPHR3 in regulating these target genes. Mutants exhibited significantly reduced seed starch, PA, and total phosphorus contents, while scanning electron microscopy revealed aberrant starch granule morphology. Loss-of-function of OsPHR3 lowered PA levels by 19.46–22.50 %, with moderate trade-offs in yield-related traits. Although, OsPHR3 is known to contribute to nitrogen and phosphorus homeostasis, our findings establish it as a key regulator orchestrating a stage-specific phosphate-carbon allocation during seed development. These insights provide key targets for refining nutrient partitioning to achieve increased yields, reduced phytic acid, and enhanced phosphorus use efficiency for agricultural sustainability.Item 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, JitenderJasmonates (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.Item 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, JitenderLipids 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.Item Method for the dissection of genomic loci associated with chickpea root penetration traits in compact soil(Springer Nature Publishing AG, 2026) Ganotra, Jahanvi; Pandey, Mandavi; Donde, Ravindra; Giri, JitenderMechanical impedance in agricultural land is a significant constraint in modern agriculture. It dramatically affects seed germination, plant growth, development, and grain yield. Soil compaction hinders root growth and the ability to access deeper nutrients and water resources, impacting climate resilience, crop productivity, and global food security. Crops display variations in root system architecture (RSA) traits when grown in compacted soils. We can better understand the mechanisms behind soil compaction by examining root-related traits and their associated genes. Our recently published study investigated RSA traits across different soil compaction levels and identified significant genomic associations in chickpeas. We developed reliable methods for creating soils with varying bulk densities (i.e., compaction levels), growing chickpea seedlings, and harvesting the roots. We also conducted high-throughput phenotyping and screening of root-related traits using winRHIZO software. By integrating these phenotypic data with available genotypic data through Genome-Wide Association Studies (GWAS), we could identify genetic loci influencing root penetration in response to increasing soil compaction. These methods will help us identify key architectural traits of roots that can be targeted in crop breeding efforts to enhance resilience and productivity in compacted soils. By improving the root system and understanding the genes involved, we aim to develop plants more responsive to root penetration.Item Physiological and genetic basis of superior phosphate uptake and utilization efficiency in the rice landrace Wazuhophek(Oxford University Press, 2025) Kohli, Pawandeep Singh; Donde, Ravindra; Sirohi, Ujjwal; Singh, Bhagat; Anantha, M S; Bhadana, Vijai Pal; Sundaram, Raman Meenakshi; Mangrauthia, Satendra K; Giri, JitenderLow phosphorus (P) availability due to edaphic conditions or the scarcity of P fertilizers restricts agricultural productivity. Various rice-growing regions experience poor P availability. Landraces from these regions, such as Wazuhophek in Northeast India, may provide a source of critical genetic variation needed for developing highly efficient, tolerant rice varieties. This study identifies the physiological and genetic basis of higher efficiency and tolerance in Wazuhophek. Wazuhophek displays higher shoot P content across three different P regimes (0, 15, and 200 µM P) compared to the sensitive parent, Improved Samba Mahsuri (ISM). In 0 µM, Wazuhophek’s increased shoot P content can be attributed to greater root physiological P use efficiency and improved root-to-shoot P translocation. At 15 and 200 µM P, Wazuhophek exhibited a higher crown root number and surface area, with more efficient roots than ISM, facilitating better Pi acquisition and higher shoot P. Furthermore, the genetic basis was delineated by identifying quantitative trait loci (QTLs) for critical traits. Revealing Wazuhophek’s physiological mechanism of low P tolerance provides valuable insights for developing rice varieties suited for nutrient-poor soil. Additionally, the identified QTLs for key traits offer targets for breeding more efficient low P-tolerant rice.Item 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, JitenderIncreasing 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.Item Phosphate deficiency inducible OsGDPD5 affects root growth by regulating sugar-auxin crosstalk(John Wiley & Sons, 2025) Verma, Lokesh; Pandey, Mandavi; Bhatia, Chitra; Mehra, Poonam; Singh, Bhagat; Giri, JitenderGlycerophosphodiester phosphodiesterases (GDPDs) enzymes are known to be involved in phospholipids degradation pathways, where glycerophosphodiesters are hydrolyzed to glycerol-3-phosphate (G3P) and corresponding alcohol. In plants, GDPDs are involved in phosphate deficiency adaptive responses and have been shown to impact root length, but the precise mechanism remains unclear. This study focuses on the rice GDPD5 gene and its role in regulating primary root growth. Our research demonstrates that OsGDPD5 encodes a functional GDPD enzyme and could hydrolyze glycerophosphocholine and glycerophosphorylethanolamine. At transcriptional levels, OsGDPD5 is preferentially expressed in the root tip and regulated by transcription factor OsPHR2. We have used CRISPR/Cas9 to generate OsGDPD5 knock-out lines, allowing us to explore its role in root growth. Our findings show that osgdpd5 mutants had a shorter primary root, which could be restored to a normal level by the exogenous application of sugar or G3P. Further, knocking out OsGDPD5 alters endogenous levels of G3P and sugars, affecting auxin biosynthesis in the root and, ultimately, primary root growth. In this manner, OsGDPD5 has a crucial role in regulating physiological processes, specifically sugar and auxin signaling, which are known to be involved in root growth regulation in rice. Our research thus unraveled a link between rice phosphate deficiency-responsive lipid remodeling and root growth via sugar-hormone signaling.Item Tolerance of Oryza sativa to low phosphate is associated with adaptive changes in root architecture and metabolic exudates(Elsevier B.V., 2025) Srivastava, Akanksha; Gupta, Amber; Bishi, Sujit K.; Akhila, Pole; Latha, P.C.; Subrahmanyam, D.; Brajendra, P.; Anantha, M.S.; Ch, Suvarna Rani; Sakhare, Akshay S.; Bhadana, Vijai Pal; Giri, Jitender; Neeraja, C.N.; Sundaram, R.M.; Mangrauthia, Satendra K.The optimum usage of fertilizers is key for the sustainable agriculture. Among nutrients, phosphorus (P) is critical for plant growth and development. Due to complete reliance on natural resources (rock phosphate) for P, the availability of P fertilizers is emerging as a global challenge for crop cultivation. Moreover, the excess application of P fertilizers in rice, mostly grown under flooded conditions, leads to water pollution called eutrophication. In this study, we employed a mutagenesis approach for developing and characterizing rice EMS (ethyl meth anesulfonate) mutants with better adaptation to low soil P conditions. One such mutant of rice cultivar Nagina 22, named NH4824, was characterized comprehensively at seedling and reproductive growth stages under hy droponic and field conditions. The mutant exhibits low soil P tolerance due to combined adaptive changes in root system architecture, anatomy, organic acid exudates, plasma membrane (PM) H+-ATPase activity, induced expression of P transporter genes, and efficient mobilization and partitioning of P in different plant tissues. The activity of antioxidant enzymes and better photosynthesis suggested relatively less stress experienced by NH4824 than N22 under low soil P conditions. These insights are highly useful to develop P use efficient crop cultivars through breeding or genome editing approaches.