Polyploid and aneuploid detection in apple using a single nucleotide polymorphism array

Polyploidisation is a common mechanism underlying genome evolution in plants. Both polyploid and aneuploid individuals occur naturally at low frequency in diploid species because of unbalanced or unreduced gamete formation during meiosis. We evaluated the Illumina Infinium® II FruitBreedomics 20K apple single nucleotide polymorphism (SNP) array for its ability to detect polyploid and aneuploid individuals in an apple germplasm collection comprising 663 genotypes. The set of SNPs employed to perform the analysis consisted of 6733 high-quality polymorphic markers spanning the entire apple genome at an average density of one SNP every 85.6 kb. The method we used to detect chromosomal aberrations is based on analysis of the B allele frequency (BAF) at each SNP position. We have demonstrated that this simple method can be used successfully to detect triploid, tetraploid and aneuploid accessions of apple and validated our findings using flow cytometry analysis