Publications of NIPGR Scientists

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Author: search.filters.author.Giri, JitenderSubject: search.filters.subject.Root

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    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.
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    MEDIATOR SUBUNIT17 is required for transcriptional optimization of root system architecture in Arabidopsis
    (Oxford University Press, 2023) Agrawal, Rekha; Singh, Amrita; Giri, Jitender; Magyar, Zoltan; Thakur, Jitendra K.
    Sucrose and auxin are well-known determinants of root system architecture (RSA). However, the factors that connect the signaling pathways evoked by these two critical factors during root development are poorly understood. In this study, we report the role of MEDIATOR SUBUNIT17 (MED17) in RSA and its involvement in the transcriptional integration of sugar and auxin signaling pathways in Arabidopsis (Arabidopsis thaliana). Sucrose regulates root meristem activation through the TARGET OF RAPAMYCIN-E2 PROMOTER BINDING FACTOR A TOR-E2FA pathway, and auxin regulates lateral root (LR) development through AUXIN RESPONSE FACTOR-LATERAL ORGAN BOUNDARIES DOMAIN ARF-LBDs. Both sucrose and auxin play a vital role during primary and LR development. However, there is no clarity on how sucrose is involved in the ARF-dependent regulation of auxin-responsive genes. This study establishes MED17 as a nodal point to connect sucrose and auxin signaling. Transcription of MED17 was induced by sucrose in an E2FA/B-dependent manner. Moreover, E2FA/B interacted with MED17, which can aid in the recruitment of the Mediator complex on the target promoters. Interestingly, E2FA/B and MED17 also occupied the promoter of ARF7, but not ARF19, leading to ARF7 expression, which then activates auxin signaling and thus initiates LR development. MED17 also activated cell division in the root meristem by occupying the promoters of cell-cycle genes, thus regulating their transcription. Thus, MED17 plays an important role in relaying the transcriptional signal from sucrose to auxin-responsive and cell-cycle genes to regulate primary and lateral root development, highlighting the role of the Mediator as the transcriptional processor for optimal root system architecture in Arabidopsis.
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    Reference gene identification for gene expression analysis in rice under different metal stress
    (Elsevier B.V., 2021) Soni, Praveen; Shivhare, Radha; Kaur, Amandeep; Bansal, Sakshi; Sonah, Humira; Deshmukh, Rupesh; Giri, Jitender; Lata, Charu; Ram, Hasthi
    Real-time quantitative polymerase chain reaction (RT-qPCR) is the most common approach to quantify changes in gene expression. Appropriate internal reference genes are essential for normalization of data of RT-qPCR. In the present study, we identified suitable reference genes for gene expression analysis in rice seedlings subjected to different heavy metal stresses such as deficiencies of iron and zinc and toxicities of cobalt, cadmium and nickel. First, from publically available RNA-Seq data we identified 10 candidate genes having stable expression. We also included commonly used house-keeping gene OsUBQ5 (Ubiquitin 5) in our analysis. Expression stability of all the 11 genes was determined by two independent tools, NormFinder and geNorm. Our results show that selected candidate reference genes have higher stability in their expression compared to that of OsUBQ5. Genes with locus ID LOC_Os03g16690, encoding an oxysterol-binding protein (OsOBP) and LOC_Os01g56580, encoding Casein Kinase_1a.3 (OsCK1a.3) were identified to be the most stably expressed reference genes under most of the conditions tested. Finally, the study reveals that it is better to use a specific reference gene for a specific heavy metal stress condition rather than using a common reference gene for multiple heavy metal stress conditions. The reference genes identified here would be very useful for gene expression studies under heavy metal stresses in rice.
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    Morpho-physiological and transcriptome profiling reveal novel zinc deficiency-responsive genes in rice
    (Springer, 2017) Bandyopadhyay, Tirthankar; Mehra, Poonam; Hairat, Suboot; Giri, Jitender
    Intensive farming has depleted the soil zinc (Zn) availability resulting in decreased crop productivity. Here, we attempt to understand the Zn deficiency response in rice through temporal transcriptome analysis. For this, rice seedlings were raised under Zn-deficient conditions up to 4 weeks followed by Zn re-supply for 3 days. Zn-deficient plants developed characteristic deficiency symptoms such as leaf bronzing, decrease in biomass, total chlorophyll, PSII efficiency, decreased carbonic anhydrase activity and increased ROS production. Interestingly, severe alterations in root system architecture were also observed. Comprehensive transcriptome analyses of rice seedlings were carried out after 2 (DEF2W) and 4 weeks (DEF4W) of Zn deficiency with respect to transcriptome profiles of corresponding Zn sufficient conditions (SUF2W, SUF4W). Additionally, to detect the potential Zn-responsive genes, transcriptome profile of Zn-recovered seedlings was compared with DEF4W. All differentially expressed Zn-responsive genes were categorized into early and late Zn deficiency response, and a set of 77 genes, induced and repressed on Zn deficiency and re-supply, respectively, was identified. These genes could be used as low Zn-responsive marker genes. Further, genes involved in membrane transport, phytosiderophore activity and organic acid biosynthesis showed high differential expression. Additionally, the present study unravelled several genes putatively associated with alterations in root system architecture under Zn deficiency and provides novel insights into the interpretation of morpho-physiological, biochemical and molecular regulation of zinc deficiency responses in rice.
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    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.