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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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Title Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice
 
Creator 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
 
Subject Development
Expression
Meta-analysis
Metabolic pathways
Panicle
Promoter
Seed
Transcription factors
 
Description Accepted date: 6 March 2012
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.
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 Re-
search (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.
 
Date 2015-10-29T07:03:32Z
2015-10-29T07:03:32Z
2012
 
Type Article
 
Identifier Funct. Integr. Genomics, 12(2): 229-248
1438-7948
http://link.springer.com/article/10.1007%2Fs10142-012-0274-3
http://172.16.0.77:8080/jspui/handle/123456789/279
 
Language en_US
 
Publisher Springer