Development and validation of the Axiom(®) Apple480K SNP genotyping array

Area of Science:

• Plant genetics
• Genomics
• Agricultural science

Background:

• Cultivated apple (Malus × domestica) is a vital temperate fruit crop with significant economic and cultural importance.
• The apple genome's high heterozygosity and recent duplication, coupled with rapid linkage disequilibrium decay, complicate genome-wide association (GWA) studies.
• Single nucleotide polymorphism (SNP) arrays offer a cost-effective, high-throughput method for marker identification in complex genomes.

Purpose of the Study:

• To develop and validate a high-density SNP genotyping array for cultivated apple.
• To assess the array's effectiveness for genetic studies in apple germplasm.
• To provide a robust tool for future GWA studies in apple.

Main Methods:

• Development of a 487K SNP Affymetrix Axiom array using high-depth resequencing data from 63 diverse apple cultivars.
• SNP selection focused on enriching genic regions and ensuring uniform coverage of non-genic regions.
• Genotyping of 1324 apple accessions, including two mapping populations, to validate the array's performance.

Main Results:

• The Axiom® Apple480K array successfully genotyped a large number of apple accessions.
• A significant majority of SNPs (74%) met stringent polymorphism criteria (poly high resolution).
• A subset of 275K highly reliable markers was identified for germplasm surveys.

Conclusions:

• The Axiom® Apple480K array is a validated and effective tool for apple genetic research.
• The array facilitates robust germplasm surveys and is expected to be a key resource for GWA studies in apple.
• Commercial availability of the array will advance genetic research and breeding in cultivated apple.