Publications of NIPGR Scientists
Permanent URI for this communityhttps://ndkr-library.nipgr.ac.in/handle/123456789/1
Browse
7 results
Search Results
Item The Mediator complex subunit, OsMED26_2, modulates plant growth, seed set and seed traits related to starch quality in rice(Elsevier B.V., 2026) Prusty, Ankita; Malik, Naveen; Ranjan, Rajeev; Agarwal, Pinky; Parida, Swarup K.; Kapoor, Sanjay; Tyagi, Akhilesh K.The Mediator (MED) complex is a multi-subunit structure crucial for RNA polymerase II-dependent transcription in eukaryotes. In this study, we investigated the function of a seed-preferential subunit of the rice Mediator complex, namely, OsMED26_2, for the first time. Knockdown of OsMED26_2 in rice reduced plant height and altered panicle morphology with shorter panicles, lesser branching, and fewer seeds per panicle. OsMED26_2 knockdown also led to shorter grains with shorter length and chalky endosperm. A significantly higher percentage of grains with chalkiness (PGWC) and degree of chalky endosperm (DCE) was observed in OsMED26_2 knockdown lines. OsMED26_2-knockdown seeds contained lower starch levels and altered proportions of amylose and amylopectin. Scanning electron microscopy further showed that these changes caused irregular, round, and loosely packed starch granules in the endosperm, contributing to the chalky phenotype. Decreased amylose content and increased grain chalkiness were corroborated by the downregulation of the Waxy (Wx) gene, which is involved in amylose synthesis, and altered expression of AMY3A, CHALK5, FLO4, GPA3, and SUSY3 genes, which regulate grain chalkiness. Our findings demonstrate that OsMED26_2 is critical in regulating panicle architecture, impacting yield, and modulating starch level and composition to control grain chalkiness and thereby suggesting its functional significance especially in manipulating yield attributing grain cooking quality traits of rice.Item OsCPK29 interacts with MADS68 to regulate pollen development in rice(Elsevier B.V., 2022) Ranjan, Rajeev; Malik, Naveen; Sharma, Shivam; Agarwal, Pinky; Kapoor, Sanjay; Tyagi, Akhilesh K.Pollen development and its germination are obligatory for the reproductive success of flowering plants. Calcium-dependent protein kinases (CPKs, also known as CDPKs) regulate diverse signaling pathways controlling plant growth and development. Here, we report the functional characterization of a novel OsCPK29 from rice, which is mainly expressed during pollen maturation stages of the anther. OsCPK29 exclusively localizes in the nucleus, and its N-terminal variable domain is responsible for retaining it in the nucleus. OsCPK29 knockdown rice plants exhibit reduced fertility, set fewer seeds, and produce collapsed non-viable pollen grains that do not germinate. Cytological analysis of anther semi-thin sections during different developmental stages suggested that pollen abnormalities appear after the vacuolated pollen stage. Detailed microscopic study of pollen grains further revealed that they were lacking the functional intine layer although exine layer was present. Consistent with that, downregulation of known intine development-related rice genes was also observed in OsCPK29 silenced anthers. Furthermore, it has been demonstrated that OsCPK29 interacts in vitro as well as in vivo with the MADS68 transcription factor which is a known regulator of pollen development. Therefore, phenotypic observations and molecular studies suggest that OsCPK29 is an important regulator of pollen development in rice.Item Rice improvement through genome-based functional analysis and molecular breeding in India(Springer, 2016) Agarwal, Pinky; Parida, Swarup K.; Raghuvanshi, Saurabh; Kapoor, Sanjay; Khurana, Paramjit; Khurana, Jitendra P.; Tyagi, Akhilesh K.Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.Item Comprehensive genomic analysis and expression profiling of phospholipase C gene family during abiotic stresses and development in rice(PLOS, 2013) Singh, Amarjeet; Kanwar, Poonam; Pandey, Amita; Tyagi, Akhilesh K.; Sopory, Sudhir K.; Kapoor, Sanjay; Pandey, Girdhar K.BACKGROUND: Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. METHODOLOGY/PRINCIPAL FINDINGS: An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. CONCLUSION/SIGNIFICANCE: The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future.Item A 286 bp upstream regulatory region of a rice anther-specific gene, OSIPP3, confers pollen-specific expression in Arabidopsis(Springer, 2013) Khurana, Reema; Kathuria, Hitesh; Mukhopadhyay, Arnab; Kapoor, Sanjay; Tyagi, Akhilesh K.OSIPP3 gene (coding for pectin methylesterase inhibitor protein) was isolated from a pre-pollinated inflorescence-specific cDNA library by differential screening of stage-specific libraries from Oryza sativa. OSIPP3 is present in the genome of rice as a single copy gene. OSIPP3 gene was expressed exclusively in the pre-pollinated spikelets of rice. Upstream regulatory region (URR) of OSIPP3 was isolated and a series of 5'-deletions were cloned upstream of GUS reporter gene and were used to transform Arabidopsis. OSIPP3_del1 and del2 transgenic plants showed GUS expression in root, anther and silique, while OSIPP3_del3 showed GUS activity only in anthers and siliques. Pollen-specific expression was observed in case of plants harboring OSIPP3_del4 construct. It can, therefore, be concluded that the OSIPP3 URR between -178 and +108 bp is necessary for conferring pollen-specific expression in Arabidopsis.Item Spatial and temporal activity of upstream regulatory regions of rice anther-specific genes in transgenic rice and Arabidopsis(Springer, 2013) Khurana, Reema; Kapoor, Sanjay; Tyagi, Akhilesh K.Upstream regulatory regions (URRs) of rice anther-specific genes, namely OSbHLH (coding for basic helix-loop-helix-containing protein) and OSFbox (F-box protein encoding gene), selected from the microarray data have been cloned to control expression of GUS and GFP reporter genes in stably transformed rice. Quantitative real time PCR analysis shows maximum transcript accumulation of these two genes in the meiotic anthers. Analysis of OSbHLH and OSFbox URRs by PLACE database reveal the presence of known pollen-specific cis elements. The URRs of both OSbHLH and OSFbox genes have maximum activity in the meiotic anther stage in rice, but confer constitutive expression in the heterologous dicot system, Arabidopsis, indicative of monocot specificity. Another rice gene (OSIPK; with homology to genes encoding calcium-dependent protein kinases) URR already reported to have anther-specific activity in Arabidopsis and tobacco also confers anther-specific expression in rice and is active in the pollen tubes, suggesting it belongs to the category of late expressed genes. The spatial activity of three URRs has also been analysed by histochemical evaluation of GUS activity in different anther cells/tissues. The activity of OSIPK URR in rice is strongest among the three URRs.Item Rice genomics moves ahead(Springer, 2010) Raghuvanshi, Saurabh; Kapoor, Meenu; Tyagi, Shashi; Kapoor, Sanjay; Khurana, Paramjit; Khurana, Jitendra; Tyagi, Akhilesh K.Rice is one of the pillars of world-wide food security. Improvement in its yield is necessary to mitigate hunger of millions of people who depend on rice as a staple. Decoding rice genome sequence is expected to complement efforts being made to improve rice and its yield. The information about more than 32,000 genes, regulatory elements, repeat DNA, and DNA markers opens-up new horizons for molecular analysis and genetic enhancement not only for rice but also for other cereal crops. In the post-genomic era, significant progress has been made on defining transcriptome and epigenome as well as gene discovery by way of forward and reverse genetic approaches. Efforts are on to fill the gap between the genome and the phenotype. This may lead to regular practice of genomics-assisted breeding of rice.