Browsing by Author "Pandey, Bipin K."

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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.
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 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.
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 mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate
(Nature Publishing Group, 2018) Bhosale, Rahul; Giri, Jitender; Pandey, Bipin K.; Giehl, Ricardo F.H.; Hartmann, Anja; Traini, Richard; Truskina, Jekaterina; Leftley, Nicola; Hanlon, Meredith; Swarup, Kamal; Rashed, Afaf; Voß, Ute; Alonso, Jose; Stepanova, Anna; Yun, Jeonga; Ljung, Karin; Brown, Kathleen M.; Lynch, Jonathan P.; Dolan, Liam; Vernoux, Teva; Bishopp, Anthony; Wells, Darren; Wirén, Nicolaus von; Bennett, Malcolm J.; Swarup, Ranjan
Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
A novel glycerophosphodiester phosphodiesterase improves phosphate deficiency tolerance in rice
(John Wiley & Sons, 2019) Mehra, Poonam; Pandey, Bipin K.; Verma, Lokesh; Giri, Jitender
Soil phosphate (Pi) deficiency is major constraint for rice cultivation world‐wide. Cellular membranes account for one‐third of cellular P (Phosphorus) in the form of phospholipids. Therefore, remobilization of Pi from membrane phospholipids under Pi deficiency can be an important strategy to improve PUE (Phosphorus Use Efficiency). GDPDs (Glycerophosphodiester phosphodiesterases) hydrolyse intermediate product of phospholipid catabolism, glycerophosphodiesters to glycerol‐3‐phosphate (G3P); a precursor for P and non P‐lipid biosynthesis. Here, we show that OsGDPD2 is a Pi deficiency responsive gene which is transcriptionally regulated by OsPHR2. In silico analysis of active site residues and enzymatic assays confirmed phosphodiesterase activity of OsGDPD2. All overexpression lines showed higher GDPD activity, Pi content, root growth and biomass accumulation as compared to wild‐type. Conversely, silencing of OsGDPD2 led to decreased GDPD activity and Pi content. Notably, most of the P‐containing metabolites and fatty acids were elevated in transgenic lines. Further, quantitative analysis of polar lipids revealed higher accumulation of several classes of phospholipids and galactolipids in overexpression lines indicating a potential role of OsGDPD2 in de novo glycerolipid biosynthesis. Thus, present study provides insights into novel physiological roles of OsGDPD2 in low Pi acclimation in rice.
OsJAZ11 regulates phosphate starvation responses in rice
(Springer Nature Publishing AG, 2021) Pandey, Bipin K.; Verma, Lokesh; Prusty, Ankita; Singh, Ajit Pal; Bennett, Malcolm J.; Tyagi, Akhilesh K.; Giri, Jitender; Mehra, Poonam
Jasmonic Acid (JA) is a key plant signaling molecule which negatively regulates growth processes including root elongation. JAZ (JASMONATE ZIM-DOMAIN) proteins function as transcriptional repressors of JA signaling. Therefore, targeting JA signaling by deploying JAZ repressors may enhance root length in crops. In this study, we overexpressed JAZ repressor OsJAZ11 in rice to alleviate the root growth inhibitory action of JA. OsJAZ11 is a low phosphate (Pi) responsive gene which is transcriptionally regulated by OsPHR2. We report that OsJAZ11 overexpression promoted primary and seminal root elongation which enhanced Pi foraging. Expression studies revealed that overexpression of OsJAZ11 also reduced Pi starvation response (PSR) under Pi limiting conditions. Moreover, OsJAZ11 overexpression also suppressed JA signaling and biosynthesis as compared to wild type (WT). We further demonstrated that the C-terminal region of OsJAZ11 was crucial for stimulating root elongation in overexpression lines. Rice transgenics overexpressing truncated OsJAZ11ΔC transgene (i.e., missing C-terminal region) exhibited reduced root length and Pi uptake. Interestingly, OsJAZ11 also regulates Pi homeostasis via physical interaction with a key Pi sensing protein, OsSPX1. Our study highlights the functional connections between JA and Pi signaling and reveals JAZ repressors as a promising candidate for improving low Pi tolerance of elite rice genotypes.
OsJAZ11 regulates spikelet and seed development in rice
(John Wiley & Sons, 2022) Mehra, Poonam; Pandey, Bipin K.; Verma, Lokesh; Prusty, Ankita; Singh, Ajit Pal; Sharma, Shivam; Malik, Naveen; Bennett, Malcolm J.; Parida, Swarup K.; Giri, Jitender; Tyagi, Akhilesh K.
Seed size is one of the major determinants of seed weight and eventually, crop yield. As the global population is increasing beyond the capacity of current food production, enhancing seed size is a key target for crop breeders. Despite the identification of several genes and QTLs, current understanding about the molecular regulation of seed size/weight remains fragmentary. In the present study, we report novel role of a jasmonic acid (JA) signaling repressor, OsJAZ11 controlling rice seed width and weight. Transgenic rice lines overexpressing OsJAZ11 exhibited up to a 14% increase in seed width and ~30% increase in seed weight compared to wild type (WT). Constitutive expression of OsJAZ11 dramatically influenced spikelet morphogenesis leading to extra glume-like structures, open hull, and abnormal numbers of floral organs. Furthermore, overexpression lines accumulated higher JA levels in spikelets and developing seeds. Expression studies uncovered altered expression of JA biosynthesis/signaling and MADS box genes in overexpression lines compared to WT. Yeast two-hybrid and pull-down assays revealed that OsJAZ11 interacts with OsMADS29 and OsMADS68. Remarkably, expression of OsGW7, a key negative regulator of grain size, was significantly reduced in overexpression lines. We propose that OsJAZ11 participates in the regulation of seed size and spikelet development by coordinating the expression of JA-related, OsGW7 and MADS genes.
OsJAZ9 overexpression modulates jasmonic acid biosynthesis and potassium deficiency responses in rice
(Springer Nature Publishing AG, 2020) Singh, Ajit Pal; Pandey, Bipin K.; Mehra, Poonam; Heitz, Thierry; Giri, Jitender
Potassium (K) represents up to 10% of the plant’s total dry biomass, and its deficiency makes plants highly susceptible to both abiotic and biotic stresses. K shortage results in the inhibition of root and shoots growth, but the underlying mechanism of this response is unclear. Our RNA-Seq and qPCR analysis suggested leading roles for JA pathway genes under K deficiency in rice. Notably, K deficiency and JA application produced similar phenotypic and transcriptional responses. Here, we integrated molecular, physiological and morphological studies to analyze the role of OsJAZ9 in JA homeostasis and K deficiency responses. We raised OsJAZ9 over-expression, knockdown, transcriptional reporter, translational reporter and C-terminal deleted translational reporter lines in rice to establish the role of JA signaling in K ion homeostasis. JA profiling revealed significantly increased JA-Ile levels in OsJAZ9 OE lines under K deficiency. Furthermore, we established that OsJAZ9 overexpression and knockdown result in K deficiency tolerance and sensitivity, respectively, by modulating various K transporters and root system architecture. Our data provide evidence on the crucial roles of OsJAZ9 for improving K deficiency tolerance in rice by altering JA levels and JA responses.
Phosphorus starvation response in plants and opportunities for crop improvement
(Wiley, 2013) Pandey, Bipin K.; Mehra, Poonam; Giri, Jitender
Phosphorus (P) is one of the most essential nutrients for the adequate growth and development of plants as well as a crucial component of all life forms. Plants absorb P only in the inorganic form of orthophosphate (Pi). The availability of soluble Pi in most of the world's soil is poor as compared to its requirement for optimum growth and crop yield. Application of P fertilizers is a common practice to grow crop plants in P-poor soils. However, highly reactive Pi easily forms insoluble complexes in soil and a large fraction of applied Pi fertilizer becomes unavailable to plants. This problem is further compounded as the source of P fertilizers (i.e., P rocks) may be exhausted in the near future. Plants have evolved physiologically, biochemically, and morphologically to cope with Pi starvation through modification of the root system architecture for better Pi uptake and remobilize the internal Pi content. Genetic regulation of these adaptations has been explored to some extent and thus provides the resource for crop improvement using transgenics or plant breeding approaches. This complex network is regulated by transcription factors, microRNAs, membrane transporters, kinases/phosphatases, ubiquitin conjugase, and various hormones. Sugars have also been shown to play important roles in Pi starvation-mediated gene expression. Here, we review the recent progress made in delineating the functions of genetic elements in terms of modulating the Pi starvation response in plants. We further explore the possible strategies for crop improvement using available resources.
Rice actin binding protein RMD controls crown root angle in response to external phosphate
(Springer Nature, 2018) Huang, Guoqiang; Liang, Wanqi; Sturrock, Craig J.; Pandey, Bipin K.; Giri, Jitender; Mairhofer, Stefan; Wang, Daoyang; Muller, Lukas; Tan, Hexin; York, Larry M.; Yang, Jing; Song, Yu; Kim, Yu-Jin; Qiao, Yang; Xu, Jian; Kepinski, Stefan; Bennett, Malcolm J.; Zhang, Dabing
Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topsoil and in many species; low phosphate induces shallower root growth as an adaptive response. Identifying genes and mechanisms controlling root angle is therefore of paramount importance to plant breeding. Here we show that the actin-binding protein Rice Morphology Determinant (RMD) controls root growth angle by linking actin filaments and gravity-sensing organelles termed statoliths. RMD is upregulated in response to low external phosphate and mutants lacking of RMD have steeper crown root growth angles that are unresponsive to phosphate levels. RMD protein localizes to the surface of statoliths, and rmd mutants exhibit faster gravitropic response owing to more rapid statoliths movement. We conclude that adaptive changes to root angle in response to external phosphate availability are RMD dependent, providing a potential target for breeders.
Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate
(Nature Publishing Group, 2018) Giri, Jitender; Bhosale, Rahul; Huang, Guoqiang; Pandey, Bipin K.; Parker, Helen; Zappala, Susan; Yang, Jing; Dievart, Anne; Bureau, Charlotte; Ljung, Karin; Price, Adam; Rose, Terry; Larrieu, Antoine; Mairhofer, Stefan; Sturrock, Craig J.; White, Philip; Dupuy, Lionel; Hawkesford, Malcolm; Perin, Christophe; Liang, Wanqi; Peret, Benjamin; Hodgman, Charlie T.; Lynch, Jonathan; Wissuwa, Matthias; Zhang, Dabing; Pridmore, Tony; Mooney, Sacha J.; Guiderdoni, Emmanuel; Swarup, Ranjan; Bennett, Malcolm J.
Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice.
Unearthing root response mechanisms to soil compaction in legumes
(John Wiley & Sons, 2026) Ganotra, Jahanvi; Pandey, Mandavi; Pandey, Bipin K.; Giri, Jitender
Roots 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.