Array-comparative genome hybridization reveals genome variations between a citrus bud mutant and its parental cultivar

Distinguishing a bud mutant from its parental genotype using conventional molecular markers is extremely difficult because they are thought to be genetically near-identical owing to the nature of somatic mutations that give rise to the bud mutant phenotype. In this study, array-comparative genome hybridization (array-CGH) was used to investigate the genetic variation between a sweet orange bud mutant “Hong Anliu” and its parental type “Anliu”. Surprisingly, 25 candidate genes were shown to exhibit gene dosage variations, with 18 being underrepresented and 7 overrepresented in the bud mutant in comparison with the parental type. These gene dosage variations were validated by quantitative PCR. Interestingly, however, the transcription levels of some of the corresponding genes were not significantly different between the two genotypes. The detection of gene dosage variations in at least 25 candidate genes between “Hong Anliu” and “Anliu” may explain in part the genetic difference responsible for the phenotypic deviation of the bud mutant from its parental cultivar. Our findings also suggest that array-CGH is a powerful technology that can be used for detection of genome-wide variations among near-identical genotypes such as bud mutants and their parental cultivars.