NATIONL CENTER OF PLANT GENE RESEARCH(WUHAN)
Comparative analysis of gene expression at early ....
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Comparative analysis of gene expression at early seedling stage between a rice hybrid and its parents using a cDNA microarray of 9198 uni-sequences HUANG Yi, LI Lihua, CHEN Ying, LI Xianghua, XU Caiguo, WANG Shiping & ZHANG Qifa National Key Laboratory of Crop Genetic Improveme- nt, National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070, China Correspondence should be addressed to Zhang Qifa (email: qifazh@mail.hzau.edu.cn) Received March 17, 2006; accepted June 20, 2006 Abstract Using a cDNA microarray consisting of 9198 expressed sequence tags, we surveyed the gene expression profiles in shoots and roots of a rice hybrid, Liangyoupei 9 and its parents Peiai 64s and 93-11 at 72 h after germination. A total of 8587 sequences had detectable signals in both shoots and roots of the three genotypes. A total of 1571 sequences exhibited significant (P<0.01) expression differences in hoots or roots among the three genotypes, of which 121 showed expression poly-morphisms in both shoots and roots, and 870 revealed significant expression differences between the hybrid and one of the parents. The expression polymorphism of the sequences was associated with the functional categories of the sequences. They occurred more frequently in categories of carbohy-drate, energy and lipid metabolisms and stress response than expected, while less frequently in categories of amino acid metabolism, transcription and translation regulation, and signal transduction. A total of 214 sequences exhibited significant (P<0.05) mid-parent heterosis in expression, of which 117 had homology to genes with known functions, assigned in the categories of basic metabolism, genetic information processing, cell growth and death, signal transduction, transportation and stress response. The results may provide useful information for exploring the relationship between gene expression polymorphism and phenotypic variation, and for characterizing the molecular mechanism of seedling development and heterosis in rice. Keywords: Oryza sativa shoots, roots, gene expression, microarray, heterosis.