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GENOME ANALYSIS

Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars^1,[w]

Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China (J.B., C.C., X.Z., Y.Z., S.L., J.W., H.Y., J.Y.); Graduate School of the Chinese Academy of Sciences, Beijing 100039, China (J.B., C.C., Y.Z.); James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China (S.L., J.W., H.Y., J.Y.); Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (J.B.); Department of Medicine, University of Chicago, Chicago, Illinois 60637 (S.L.); Electrical Engineering and Computer Science Department, University of Kansas, Lawrence, Kansas 66045–7621 (T.C.); Center for Functional Genomics, Evanston Northwestern Healthcare Research Institute, Northwestern University, Evanston, Illinois 60201 (S.M.W.); and National Hybrid Rice Research and Development Center, Changsha 410125, China (M.C.)

Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P < 0.01), we identified 595 up-regulated (22 tags in panicles, 228 in leaves, and 345 in roots) and 25 down-regulated (seven tags in panicles, 15 in leaves, and three in roots) in LYP9. Most of the tag-identified and up-regulated genes were found related to enhancing carbon- and nitrogen-assimilation, including photosynthesis in leaves, nitrogen uptake in roots, and rapid growth in both roots and panicles. Among the down-regulated genes in LYP9, there is an essential enzyme in photorespiration, alanine:glyoxylate aminotransferase 1. Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice.

^[w] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.060988.

^* Corresponding author; e-mail junyu{at}genomics.org.cn; fax 86–10–80494969.

Received February 11, 2005; returned for revision April 15, 2005; accepted April 17, 2005.

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