Sreerekha, MV , Venu, RC , Nobuta, Kan , Meyers, Blake , Wang, Guo-liang .
Analysis of Developing Seed Transcriptomes of Rice Using Massively Parallel Signature Sequencing.
Milling yield and taste are the most important aspects of rice grain quality. To identify the genes involved in grain quality, a deep transcriptional analysis of developing seeds was performed using Massively Parallel Signature Sequencing (MPSS). Five MPSS libraries were constructed from 6 day old developing seeds representing Cypress (high milling), LaGrue (low milling), Ilpumbyeo (high taste), YR15965 (low taste) and Nipponbare (control) cultivars. Significant and reliable tags ranging between 9,721 to 13,560 were identified and matched to TIGR ESTs, KOME FL-cDNAs, annotated genes and rice genomic sequence to identify sense, antisense, alternate and novel transcripts expressed in these libraries. About 90% and 85% of the tags from grain quality libraries matched to the japonica and indica genomes, respectively. Of these, nearly 78% of the tags matched to TIGR-annotated genes. Clustering analysis showed specific and commonly expressed tags/genes among milling and taste libraries. Since transcription factors (TFs) play a major role during seed development, specific and commonly expressed transcription factors for milling and taste libraries were also identified. The antisense and alternate transcripts identified in this study were further supported by public rice expression databases (KOME and TIGR). Numerous novel transcripts/genes were also identified as expressed in these libraries. A functional classification of genes using KEGG analysis showed expression and suppression of several biochemical pathways related to carbohydrate metabolism, vitamins and cofactors, and nucleotide metabolism. Some of the genes related to starch biosynthesis, a seed storage protein family, and aspartate family amino acid proteins were further evaluated by RT-PCR. A time course study of genes involved in seed development is also being conducted. Our comprehensive and deep survey of the developing seed transcriptome in five rice cultivars provide a rich genomic resource for further elucidating the molecular basis of grain quality in rice.
Acknowledgements: We thank Dr. Gynheung An for providing seeds of Ilpumbyeo and YR15965 and Robert Fjellstrom for seeds of Cypress and LaGrue. This project is funded by the NSF Plant Genome Program (#0321437) and USDA-CSREES RiceCAP Program.
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1 - The Ohio State University, Department of Plant Pathology, 2021 Coffey Rd. #201, Kottman Hall,, Columbus, OH, 43210, United States of America
2 - The Ohio State University, Department of Plant Pathology
3 - University of Delaware, Department of Plant and Soil Sciences
Presentation Type: Plant Biology Abstract
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM