Genetic variation takes many forms, from large chromosomal anomalies to individual base pair changes. Copy number variants (CNVs) are generally considered to be gains or losses of DNA segments larger than 1 kb. In humans CNVs are a factor in determining phenotype, as they provide rapid genetic response to a changing environment and have been associated with risk of disease. Preliminary analyses of plant genomes have indicated that CNVs are important to the evolution of plant genomes which have been under strong selection. Surprisingly, CNVs have been an untapped source of genomic variation, compared with SNPs, for understanding the genetic control of key traits in plants and as tools to improve selection efficiency of new varieties. Domesticated apples first appeared in the Near East around 4,000 years ago and it seems pertinent to investigate the CNV of apple varieties, as many CNVs may have emerged since its domestication. We have performed a genome-wide analysis of CNV using low coverage genome re-sequencing of 34 apple varieties using the R package CNVrd2. CNVs were detected across the apple genome. CNVs associated with candidate genes for aroma, and pest and disease resistance were identified.
