Serial Analysis of Gene Expression Study of a Hybrid Rice Strain (LYP9) and Its Parental Cultivars

• Published in: Plant physiology (Bethesda) Vol. 138; no. 3; pp. 1216 - 1231
• Main Authors: Bao, JingYue, Lee, Sanggyu, Chen, Chen, Zhang, XiuQing, Zhang, Yu, Liu, SiQi, Clark, Terry, Wang, Jian, Cao, MengLiang, Yang, HuanMing, Wang, San Ming, Yu, Jun
• Format: Journal Article
• Language: English
• Published: Rockville, MD American Society of Plant Biologists 01.07.2005; American Society of Plant Physiologists
• Subjects: Agronomy. Soil science and plant productions; Biological and medical sciences; Chromosome Mapping; Chromosomes, Plant; Classical and quantitative genetics. Population genetics. Molecular genetics; Complementary DNA; Datasets; Expressed Sequence Tags; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling - methods; gene expression regulation; Gene Expression Regulation, Plant; Generalities. Genetics. Plant material; Genes; Genetics and breeding of economic plants; genome; Genome Analysis; Genome, Plant; Genomes; grain crops; Hybridity; Hybridization, Genetic; hybrids; Libraries; Molecular genetics; molecular sequence data; nucleotide sequences; Oryza - classification; Oryza - genetics; Oryza sativa; Panicles; plant genetics; Plants; Rice; Species Specificity; transcriptome; Assimilation; Monocotyledones; Root; Enzyme; Alanine-glyoxylate transaminase; Growth; Transferases; Plant leaf; Gene expression; Heterosis; Oryza sativa; Complementary DNA; Gene; Gramineae; Photorespiration; Transaminases; Angiospermae; Spermatophyta; Photosynthesis
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.105.060988

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.