Publications of NIPGR Scientists

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Author: search.filters.author.Jaiswal, Priya

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    Decoding rice seed storage proteins: From gene identification to structural prediction
    (Oxford University Press, 2026) Yadav, Antima; Jaiswal, Priya; Mathew, Iny Elizebeth; Panwar, Akanksha; Agarwal, Pinky
    Background and Aims: Rice seed storage proteins (SSPs) are major determinants of grain nutritional quality, serving as primary sources of dietary protein, energy, and essential nutrients. However, limited understanding of their diversity, evolution, and regulation constrains efforts to improve grain quality. This study aimed to perform a comprehensive genome-wide characterization of SSPs in rice. Methods: A combined homology- and domain-based approach was employed to identify SSP-encoding genes in the rice genome. These proteins were further analysed through phylogenetic reconstruction, domain and motif characterization, promoter cis-element analysis, expression profiling across seed developmental stages, and three-dimensional structural modelling. Key Results: A total of 65 SSP genes were identified, including 19 previously uncharacterized members. Phylogenetic and domain analyses revealed evolutionary relationships between albumins and prolamins, and between globulins and glutelins. Tandem clustering of albumins, glutelins, and prolamins suggested gene duplication as a major driver of SSP family expansion. Expression profiling indicated that albumins, globulins, and glutelins were transcriptionally active from the S2 stage, whereas prolamins were predominantly expressed from the S3 stage onwards. Promoter analysis identified several seed-specific cis-regulatory elements, including CAATBOX1, EBOXBNNAPA, and DOFCOREZM. Structural modelling showed that albumins and prolamins are primarily composed of α-helices, while globulins and glutelins are enriched in β-strands and coils. Conclusions: This integrative analysis provides comprehensive insights into the classification, evolution, regulatory mechanisms, and structural features of rice SSPs. The findings establish a valuable resource for future functional studies and offer a foundation for strategies aimed at improving grain nutritional quality.
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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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    SUPER STARCHY1/ONAC025 participates in rice grain filling
    (American Society of Plant Biologists, 2020) Mathew, Iny Elizebeth; Priyadarshini, Richa; Mahto, Arunima; Jaiswal, Priya; Parida, Swarup K.; Agarwal, Pinky
    NAC transcription factors (TFs) are known for their role in development and stress. This article attempts to functionally validate the role of rice SS1/ ONAC025 (LOC_ Os11g31330) during seed development. The gene is seed-specific and its promoter directs reporter expression in the developing endosperm and embryo in rice transgenic plants. Furthermore, rice transgenic plants ectopically expressing SS1/ ONAC025 have a plantlet lethal phenotype with hampered vegetative growth, but increased tillers and an altered shoot apical meristem structure. The vegetative cells of these plantlets are filled with distinct starch granules. RNAseq analysis of two independent plantlets reveals the differential expression of reproductive and photosynthetic genes. A comparison with seed development transcriptome indicates differential regulation of many seed-related genes by SS1/ ONAC025. Genes involved in starch biosynthesis, especially amylopectin and those encoding seed storage proteins, and regulating seed size are also differentially expressed. In conjunction, SS1/ ONAC025 shows highest expression in japonica rice. As a TF, SS1/ ONAC025 is a transcriptional repressor localized to endoplasmic reticulum and nucleus. The article shows that SS1/ ONAC025 is a seed-specific gene promoting grain filling in rice, and negatively affecting vegetative growth.