Publications of NIPGR Scientists

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    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.
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    Seed's Awakening: Unveiling the MKK3-MPK7-ERF4 module in dormancy-to-germination transition
    (Elsevier B.V., 2023) Varshney, Vishal; Majee, Manoj
    Seed dormancy is nature's strategic pause in the plant life cycle, a purposeful interlude during which a seed, poised on the cusp of potential growth, bides its time in a state of quiescence. This period of dormancy is a crucial adaptation, allowing the seed to withstand unfavorable environmental conditions and synchronize germination with optimal circumstances for growth and survival (Née et al., 2017). Dormancy is orchestrated by a complex interplay of genetic, physiological, and environmental factors, including phytohormones like abscisic acid (ABA) and gibberellins (GA), as well as specific regulators like DELAY OF GERMINATION1 (DOG1) and others (Née et al., 2017; Liu et al., 2020)
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    The developmental dynamics in cool season legumes with focus on chickpea
    (Springer Nature Publishing AG, 2023) Basu, Udita; Parida, Swarup K.
    Chickpea is one of the most widely consumed grain legume world-wide. Advances in next-generation sequencing and genomics tools have led to genetic dissection and identification of potential candidate genes regulating agronomic traits in chickpea. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored. Studies in crops such as rice, maize, tomato and pea have highlighted the contribution of key regulator of developmental events in yield related traits. A comprehensive knowledge on the development aspects of a crop can pave way for new vistas to explore. Pea and Medicago are the close relatives of genus Cicer and the basic developmental events in these legumes are similar. However, there are some distinct developmental features in chickpea which hold potential for future crop improvement endeavours. The global chickpea germplasm encompasses wide range of diversities in terms of morphology at both vegetative and reproductive stages. There is an immediate need for understanding the genetic and molecular basis of this diversity and utilizing them for the yield contributing trait improvement. The review discusses some of the key developmental events which have potential in yield enhancement and the lessons which can be learnt from model legumes in this regard.
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    Biochemical analysis of anthocyanin and proanthocyanidin and their regulation in determining chickpea flower and seed coat colours
    (Oxford University Press, 2023) Pal, Lalita; Dwivedi, Vikas; Gupta, Santosh Kumar; Saxena, Samiksha; Pandey, Ashutosh; Chattopadhyay, Debasis
    Flower and seed coat colour are important agronomic traits in chickpea (Cicer arietinum L.). Cultivated chickpeas are of two types namely, desi (dark seeded, purple flower) and kabuli (light colour seeded, white flower). There has been limited information about the molecular mechanism underlying the colour variation of flower and seed coats in desi and kabuli chickpea. We profiled the anthocyanin and proanthocyanidin (PA) contents in chickpea flowers and seed coats. Tissue-specific silencing of two genes encoding a basic helix-loop-helix (CabHLH) protein and a tonoplast-localized multidrug and toxic compound extrusion (CaMATE1) transporter in a desi genotype resulted in the reduction in expressions of anthocyanin and PA biosynthetic genes and anthocyanin and PA contents in the flower and seed coat and produced flowers and seeds with kabuli characteristics. Transcriptional regulation of a subset of anthocyanin and PA biosynthetic genes by a natural CabHLH variant and transport assay of a natural CaMATE1 variant explained the association of these alleles with the kabuli phenotype. We carried out a detailed molecular characterization of these genes, and provided evidences that kabuli chickpea flower and seed colour phenotype can be derived by manipulation of single genes in a desi chickpea background.
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    Identification and molecular characterization of rice bran-specific lipases
    (Springer Nature Publishing AG, 2021) Bansal, Sakshi; Sardar, Shaswati; Sinha, Kshitija; Bhunia, Rupam Kumar; Katoch, Megha; Sonah, Humira; Deshmukh, Rupesh; Ram, Hasthi
    Key message Among the 113 lipases present in rice genome, bran and endosperm-specifc lipases were identifed and lipase activity for one of the selected lipase gene is demonstrated in yeast. Abstract: Rice bran is nutritionally superior than endosperm as it has major reservoirs of various minerals, vitamins, essential mineral oils and other bioactive compounds, however it is often under-utilized as a food product due to bran instability after milling. Various hydrolytic enzymes, such as lipases, present in bran causes degradation of the lipids present and are responsible for the bran instability. Here, in this study, we have systematically analyzed the 113 lipase genes present in rice genome, and identifed 21 seed-specifc lipases. By analyzing the expression of these genes in diferent seed tissues during seed development, we have identifed three bran-specifc and three endosperm-specifc lipases, and one lipase which expresses in both bran and endosperm tissues. Further analysis of these genes during seed maturation and seed germination revealed that their expression increases during seed maturation and decreases during seed germination. Finally, we have shown the lipase activity for one of the selected genes, LOC_Os05g30900, in heterologous system yeast. The bran-specifc lipases identifed in this study would be very valuable for engineering designer rice varieties having increased bran stability in post-milling.
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    Integrated seed proteome and phosphoproteome analyses reveal interplay of nutrient dynamics, carbon-nitrogen partitioning and oxidative signaling in chickpea
    (John Wiley & Sons, 2020) Sinha, Arunima; Haider, Toshiba; Narula, Kanika; Ghosh, Sudip; Chakraborty, Niranjan; Chakraborty, Subhra
    Nutrient dynamics in storage organs is a complex developmental process that requires coordinated interactions of environmental, biochemical, and genetic factors. Although sink organ developmental events have been identified, our understanding of translational and post‐translational regulation of reserve synthesis, accumulation and utilization in legume crops is limited. To understand nutrient dynamics during embryonic and cotyledonary photoheterotrophic transition to mature and germinating autotrophic seeds, an integrated proteomics and phosphoproteomics study in six sequential seed developmental stages in chickpea was performed. MS/MS analyses identified 109 unique nutrient‐associated proteins (NAPs) involved in metabolism, storage and biogenesis, and protein turnover. Differences and similarities in 60 nutrient‐associated phosphoproteins (NAPPs) containing 93 phosphosites were compared with NAPs. Data revealed accumulation of carbon‐nitrogen metabolic and photosynthetic proteoforms during seed filling. Furthermore, enrichment of storage proteoforms and protease inhibitors was associated with cell expansion and seed maturation. Finally, combined proteoforms network analysis identified three significant modules, centered around malate dehydrogenase, HSP70, triose phosphate isomerase and vicilin. Novel clues suggest that ubiquitin‐proteasome pathway regulates nutrient reallocation. Second, increased abundance of NAPs/NAPPs related to oxidative and serine/threonine signalling indicate direct interface between redox sensing and signaling during seed development. Taken together, nutrient signals act as metabolic and differentiation determinant governing storage organ reprogramming.
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    PHYTOCHROME INTERACTING FACTOR1 interactions leading to the completion or prolongation of seed germination
    (Taylor & Francis Group, 2018) Dirk, Lynnette M. A.; Kumar, Santosh; Majee, Manoj; Downie, A. Bruce
    In Arabidopsis thaliana, the basic Helix Loop Helix transcription factor, PHYTOCHROME INTERACTING FACTOR1 (PIF1) is known to orchestrate the seed transcriptome such that, ultimately, proteins repressing the completion of germination are produced in darkness. While PIF1-mediated control of abscisic acid (ABA) and gibberellic acid (GA) anabolism/catabolism is indirect, PIF1 action favors ABA while discriminating against GA, firmly establishing ABA’s repressive influence on the completion of germination. The result is tissue that is more sensitive to and producing more ABA; and is less responsive to and deficient in GA. Illumination of the appropriate wavelength activates phytochrome which enters the nucleus, and binds to PIF1, initiating PIF1’s phosphorylation by diverse kinases, subsequent polyubiquitination, and hydrolysis. One mechanism by which phosphorylated PIF1 is eliminated from the cells of the seed upon illumination involves an F-BOX protein, COLD TEMPERATURE GERMINATING10 (CTG10). Discovered in an unbiased screen of activation tagged lines hastening the completion of seed germination at 10°C, one indirect consequence of CTG10 action in reducing PIF1 titer, should be to enhance the transcription of genes whose products work to increase bioactive GA titer, shifting the intracellular milieu from one that is repressive to, toward one conducive to, the completion of seed germination. We have tested this hypothesis using a variety of Arabidopsis lines altered in CTG10 amounts. Here we demonstrate using bimolecular fluorescence complementation that PIF1 interacts with CTG10 and show that, in light exposed seeds, PIF1 is more persistent in ctg10 relative to WT seeds while it is less stable in seeds over-expressing CTG10. These results are congruent with the relative transcript abundance from three genes whose products are involved in bioactive GA accumulation. We put forth a model of how PIF1 interactions in imbibed seeds change during germination and how a permissive light signal influences these changes, leading to the completion of germination of these positively photoblastic propagules.
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    Measurement of respiration and internal oxygen in germinating Cicer arietinum L. seeds using optic microsensor
    (Springer, 2017) Pandey, Sonika; Kumari, Aprajita; Bharadwaj, Chellapilla; Gupta, Kapuganti Jagadis
    Internal oxygen concentrations vary in different tissues depending on tissue size, developmental stage, and their location. Respiratory rate of tissue also determines internal oxygen levels. For studying various signaling pathways it is essential to establish a correlation between respiration and internal oxygen. Seed germination is associated with increase in respiration which can dictate the internal oxygen and subsequent production of reactive oxygen species. Using optic oxygen microsensor we made an attempt to measure respiratory rate and internal oxygen. We found that microsensor is able to sense internal oxygen and it is also possible to measure oxygen levels in a close vial that contains seeds. Step-by-step protocol is described here along with illustration.
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    A misannotated locus positively influencing Arabidopsis seed germination is deconvoluted using multiple methods, including surrogate splicing
    (Elsevier B.V., 2017) Majee, Manoj; Wu, Shuiqin; Salaita, Louai; Gingerich, Derek; Dirk, Lynnette M.A.; Chappell, Joseph; Hunt, Art G.; Vierstra, Richard; Downie, A. Bruce
    A screen of activation tagged lines of Arabidopsis thaliana retrieved COLD TEMPERATURE GERMINATING10-D(tag) (CTG10-D(tag)) seeds, capable of radicle protrusion in advance of wild type (WT) at suboptimal- and optimal-temperatures. Genomic walking revealed T-DNA in the intragenic region that upregulates expression of the At4g19330 locus previously predicted to encode an F-BOX protein. A combination of surrogate splicing, primer scanning, RACE, and Illumina PolyAdenylation Tag (PAT) sequencing in petunia (Petunia X hybrida) and Arabidopsis were required to demonstrate that the region around At4g19330 was misannotated and is actually compromised of two separate genes. Even though homologous regions nearby and elsewhere on chromosome 4 are confounding elements in the molecular characterization of the locus, we could determine that the 5′ entity encodes a ribonucleoprotein of unknown function whereas the 3′ gene includes the promoter and full coding region of an F-BOX protein. Although both genes were upregulated, only independently-transformed lines over-expressing the F-Box exhibited enhanced completion of seed germination. We named it CTG10, and a single, poorly penetrant, mutant line of ctg10 manifested the expected reduced completion of seed germination. Whereas CTG10-OE lines are hyposensitive to the gibberellin biosynthetic inhibitor paclobutrazol, the ctg10 mutant line is hypersensitive; a phenotype which could be alleviated when transgenically rescued with CTG10. The F-Box moiety promoted association of CTG10 with ASK proteins in yeast two hybrid assays, indicating that it likely assembles into an SCF-type ubiquitin ligase to promote the ubiquitination of one or more substrates. In this capacity CTG10 might target a protein repressing seed germination for polyubiquitination and subsequent proteasomal degradation.
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    Seed proteomics: An overview
    (Springer, 2016) Narula, Kanika; Sinha, Arunima; Haider, Toshiba; Chakraborty, Niranjan; Chakraborty, Subhra
    Seed is vital for propagation of spermatophytes in biome and as food source for inhabitants of the earth. Studies on seed proteins provide platform for new avenues to explore molecular networks and pathways governing seed filling, maturation, germination, and seedling formation. Protein expression changes of three genetically different sub-regions of angiosperm seeds are reflected in ordered chain of biological events represented from family differences in different taxas. Different families of angiosperm show divergence of seed protein evolution and thus provide insights into seed structure and function. A gamut of information is available on seed proteomic datasets from approximately 3500 proteins that impinge on protein function in diverse plant families. The functional modularity of seed proteins were compared amongst species that span from dicot to moncot and diploid to polyploid. Transitions of protein complement revealed difference between dormancy and germination towards understanding biological check point at translational level. Goal of this chapter is to critically review data available till date on seed proteomic studies and identify family and cross genera knowledge gaps. The information thus obtained would unravel new components and an unparallel understanding of the molecular processes underlying translational and post-translational variations under different conditions that involves histodifferentiation and organogenesis of the seed.