Comparative genomic hybridization analysis of rice dwarf mutants induced by gamma irradiation.
Comparative genomic hybridization (CGH) is a powerful tool used to analyze changes in copy number, polymorphisms, and structural variations in the genome. Gene copy number variation (CNV) is a common form of natural diversity in the genome, which can create new genes and alter gene structure. Thus, CNVs may influence phenotypic variation and gene expression. In this study, to detect CNVs, we irradiated rice seeds with gamma rays (300 Gy) and selected two dwarf mutagenized plants, GA III 189 and 1052, in the M3 generation. These plants were subjected to CGH analysis using Agilent's RICE CGH array. Most of the CNVs identified were less than 10 kb in length. We detected 90 amplified and 18 deleted regions in GA III 189, and 99 amplified and 11 deleted regions in GA III 1052. Of note, CNVs were located on chromosome 12 in both GA III 189 and 1052, which contained 39 commonly amplified regions in 29 genes. The commonly amplified genes included six genes encoding F box domain containing proteins. Alterations in these F box domain containing genes were confirmed by quantitative RT PCR. Integration of CGH and gene expression data identified copy number aberrations and novel genes potentially involved in the dwarf phenotype. These CGH and gene expression data may be useful for uncovering the mechanisms underlying the dwarf phenotype.
Genetics and molecular research GMR