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Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice

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Abstract

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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Acknowledgements

This work was supported by Department of Biotechnology, Ministry of Science & Technology, Government of India (Project No. BT/AB/FG-I(PH-II)(4)/2009). We acknowledge Dr. Ramesh Hariharan and his team at Strand LS Bengaluru, India for their help in microarray data analysis and Ms. Manupriya for providing the list of transcription factor family genes in rice. Senior Research fellowship by the Council for Scientific and Industrial Research (CSIR) to R.S., S.R., P.D, M.J., A.N., and P.S. and University Grants Commissions (UGC) fellowship to P.A. are acknowledged.

Microarray data used in this study have been deposited in the Gene Expression Omnibus database at the National Center for Biotechnology Information under the accession nos. GSE6893 and GSE6901. All the datasets shortlisted in this manuscript including list of panicle or seed-specific genes, differentially expressed genes during panicle or seed development with respect to all four vegetative stages and unique genes upregulated with respect to preceding stage of development are given in Supplementary Table S3.

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Author notes

  1. Rita Sharma

    Present address: Department of Plant Pathology, University of California, Davis, CA, 95616, USA

  2. Pinky Agarwal, Mukesh Jain & Akhilesh Kumar Tyagi

    Present address: National Institute for Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India

  3. Swatismita Ray

    Present address: Biotechnology and Bioresources Management Division, Tata Energy Research Institute, Lodhi Road, New Delhi, 110003, India

  4. Niharika Sharma

    Present address: Plant Molecular Biology and Biotechnology Group, Melbourne School of Land and Environment, University of Melbourne, Parkville, 3010, Victoria, Australia

Authors and Affiliations

  1. Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India

    Rita Sharma, Pinky Agarwal, Swatismita Ray, Priyanka Deveshwar, Pooja Sharma, Niharika Sharma, Aashima Nijhawan, Mukesh Jain, Jitendra Paul Khurana, Akhilesh Kumar Tyagi & Sanjay Kapoor

  2. Division of Genetics, Indian Agriculture Research Institute, New Delhi, 110012, India

    Ashok Kumar Singh & Vijay Pal Singh

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The authors Rita Sharma and Pinky Agarwal contributed equally to this work.

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Table S1

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Table S2

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Table S3

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Table S4

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Table S5

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Table S6

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Table S7

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Table S8

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Sharma, R., Agarwal, P., Ray, S. et al. Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics 12, 229–248 (2012). https://doi.org/10.1007/s10142-012-0274-3

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