Publications of NIPGR Scientists

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Author: search.filters.author.Sharma, RitaSubject: search.filters.subject.Development

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    Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice
    (Springer, 2012) Sharma, Rita; Agarwal, Pinky; Ray, Swatismita; Deveshwar, Priyanka; Sharma, Pooja; Sharma, Niharika; Nijhawan, Aashima; Jain, Mukesh; Singh, Ashok Kumar; Singh, Vijay Pal; Khurana, Jitendra Paul; Tyagi, Akhilesh K.; Kapoor, Sanjay
    Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.
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    Comparative transcript profiling of TCP family genes provide insight into gene functions and diversification in rice and Arabidopsis
    (Academy Journals, 2010) Sharma, Rita; Kapoor, Meenu; Tyagi, Akhilesh K.; Kapoor, Sanjay
    Plant-specific TCP transcription factor family has been implicated in diverse aspects of growth and development. Rice and Arabidopsis genomes encode 26 and 24 TCP family genes, respectively. In this study, we have performed an inclusive analysis of their expression during 21 and 18 stages of development in rice and Arabidopsis, respectively. The assorted patterns of expression, exhibited by TCP family genes, provide an evidence for spatiotemporal regulation of their relative abundance throughout plant development. Further profiling of rice genes in three sub-stages of early panicle development revealed differential accumulation of nine genes during panicle initiation and organ development. QPCR-based expression profiling of selected rice genes, during four stages of anther, suggested their involvement in early anther development as well. Eleven genes of rice and seven of Arabidopsis were differentially expressed in response to three abiotic stress treatments viz., cold, dehydration and salt. In silico analysis of 5' regulatory regions of differentially expressed genes revealed the presence of previously characterized cis-regulatory elements. Duplications seem to have played major role in diversification of TCP family genes with 14 genes of rice and 10 of Arabidopsis lying on duplicated segments of the respective genomes. Most of the duplicated genes exhibited varied expression patterns. The knowledge obtained in this study will be useful for selection and assessment of the functions of individual genes using reverse genetics approaches.
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    Identification, phylogeny and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato
    (Springer, 2010) Sharma, Manoj K.; Kumar, Rahul; Solanke, Amolkumar U.; Sharma, Rita; Tyagi, Akhilesh K.; Sharma, Arun K.
    Ethylene responsive transcription factors have been shown to be intimately connected to plant development, defense responses and stress signaling pathways and in order to use them for plant improvement, we need to have better understanding of these proteins. In this study, 85 ERF genes have been identified from tomato using raw EST data in various public repositories. Phylogenetic analysis with tomato ERF domains revealed their distribution in all the groups, previously identified in model systems. MEME motif analysis resulted in identification of conserved domains, characteristic to member of each clade, in addition to ERF domain. Expression analysis during vegetative and reproductive stages of development using QPCR and tomato GeneChip arrays, revealed their tissue-specific/preferential accumulation. In total, 57 genes were found to be differentially expressed during temporal stages of tomato fruit development. The expression analysis of 23 ERF family genes representing each clade in response to seven abiotic stress treatments revealed their differential expression in response to more than one abiotic stress treatments. Results suggest that ERF genes play diverse roles in plant's life and comprehensive data generated will be helpful in conducting functional genomics studies to understand their precise role during plant development and stress response.