title: Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice.
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.
authors.affiliation: Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
authors.forename: Rita
authors.initials: R
authors.lastname: Sharma
authors.forename: Pinky
authors.initials: P
authors.lastname: Agarwal
authors.forename: Swatismita
authors.initials: S
authors.lastname: Ray
authors.forename: Priyanka
authors.initials: P
authors.lastname: Deveshwar
authors.forename: Pooja
authors.initials: P
authors.lastname: Sharma
authors.forename: Niharika
authors.initials: N
authors.lastname: Sharma
authors.forename: Aashima
authors.initials: A
authors.lastname: Nijhawan
authors.forename: Mukesh
authors.initials: M
authors.lastname: Jain
authors.forename: Ashok Kumar
authors.initials: AK
authors.lastname: Singh
authors.forename: Vijay Pal
authors.initials: VP
authors.lastname: Singh
authors.forename: Jitendra Paul
authors.initials: JP
authors.lastname: Khurana
authors.forename: Akhilesh Kumar
authors.initials: AK
authors.lastname: Tyagi
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kapoor
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056626:Inflorescence / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D012098:Reproduction / Q000235:genetics; D012639:Seeds / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant