Publications of NIPGR Scientists

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    Zinc finger transcriptional repressor ZOS5-09 regulates grain filling and development in rice
    (John Wiley & Sons, 2025) Jaiswal, Priya; Qasim, Falah; Mahto, Arunima; Vichitra, Ankur; Das, Upasana; Tyagi, Akhilesh K.; Agarwal, Pinky
    Grain size is one of the key determinants of grain yield. Our study focuses on a novel seed-preferential C2H2 zinc finger transcription factor, ZOS5-09 (LOC_Os05g38600) that plays an important role in regulating rice grain traits. Rice plants with the ZOS5-09 promoter::GUS construct showed high expression of ZOS5-09 in rice endosperm. In planta reporter effector assays and localization studies showed that ZOS5-09 is a nuclear-localized transcriptional repressor. It has two C2H2 zinc finger domains and a C-terminal NoRS (nucleolar retention signal). Ectopic and seed-preferential overexpression of ZOS5-09 resulted in lethality. Seed-preferential overexpression without NoRS was detrimental to grain filling. Rice plants with knock-down or CRISPR-based knock-out of ZOS5-09 displayed reduced grain length and weight but increased grain width. Grain size change was due to lower cell proliferation and increased cell size in the transverse direction because of downregulation of cell cycle-related genes and increased expression of expansins. Decreased expression of ZOS5-09 also resulted in reduced total starch and protein content and higher endosperm chalkiness, thus negatively affecting grain quality. ZOS5-09 directly bound to a zinc finger–binding site and regulated a seed storage protein-encoding gene, GLU6. It acted as a repressor by promoting deacetylation upon interaction with a histone deacetylase. In summary, our results indicate that an optimum expression of ZOS5-09 is essential for proper rice grain development. Our study highlights the role of a transcriptional repressor in regulating rice grain traits and improves our understanding of the transcriptional regulatory networks affecting grain size.
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    Genome-wide strategies for genetic enhancement of rice
    (2011) Kapoor, S; Khurana, R; Baranwal, V; Agarwal, Pinky; Ray, S; Tyagi, Akhilesh K.
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    Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice
    (Wiley-Blackwell, 2009) Jain, Mukesh; Khurana, Jitendra P.
    Auxin influences growth and development in plants by altering gene expression. Many auxin-responsive genes have been characterized in Arabidopsis in detail, but not in crop plants. Earlier, we reported the identification and characterization of the members of the GH3, Aux/IAA and SAUR gene families in rice. In this study, whole genome microarray analysis of auxin-responsive genes in rice was performed, with the aim of gaining some insight into the mechanism of auxin action. A comparison of expression profiles of untreated and auxin-treated rice seedlings identified 315 probe sets representing 298 (225 upregulated and 73 downregulated) unique genes as auxin-responsive. Functional categorization revealed that genes involved in various biological processes, including metabolism, transcription, signal transduction, and transport, are regulated by auxin. The expression profiles of auxin-responsive genes identified in this study and those of the members of the GH3, Aux/IAA, SAUR and ARF gene families were analyzed during various stages of vegetative and reproductive (panicle and seed) development by employing microarray analysis. Many of these genes are, indeed, expressed in a tissue-specific or developmental stage-specific manner, and the expression profiles of some of the representative genes were confirmed by real-time PCR. The differential expression of auxin-responsive genes during various stages of panicle and seed development implies their involvement in diverse developmental processes. Moreover, several auxin-responsive genes were differentially expressed under various abiotic stress conditions, indicating crosstalk between auxin and abiotic stress signaling.