Axiom™ Apple Genotyping Array

Axiom Apple Genotyping Array (Axiom_Apple480) was designed through the Affymetrix Expert Design Program in collaboration with the FruitBreedomics consortium (www.FruitBreedomics.cn). The sequencing and marker selection was conducted by experts from Fondazione Edmund Mach, INRA, Dalhousie University, Wageningen UR, University Di Bologna, and Universita Degli Studi Di Milano.

The 96-format array includes markers identified using whole-genome sequence data from 63 Malus domestica cultivars and two double haploid accessions. Table 1 lists the number of cultivars and corresponding country of origin used in the SNP discovery process.

Axiom Apple Genotyping Array includes 480,000 markers and together with Axiom Analysis Suite software overcomes the genotyping challenges associated with polyploidy, rapid linkage disequilibrium (LD) decay, and high polymorphism observed in the apple genome.

Array highlights
• Very high diversity
• Includes markers discovered in 63 worldwide M. domestica cultivars• High resolution to address rapid decay of LD   - 487,249 markers on the array
   - Bias towards common variants with minor allele frequency (MAF) >0.05
   - Includes 21,463 previously validated markers: 19,990 markers from an existing in-;market 20K Fruitbreedomics apple array and 1,473 markers identified using genotyping-by-sequencing (GBS)
• Absence of paralogous variants through the use of double haploid accessions in SNP discovery

Applications of Axiom Apple Genotyping Array
• Construction of high-resolution genetic maps
• Fine mapping of quantitative trait loci
• Genome-wide association studies

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel InstrumentAxiom Apple Genotyping Array (Axiom_Apple480) was designed through the Expert Design Program at Affymetrix in collaboration with the FruitBreedomics consortium (www.FruitBreedomics.cn). The sequencing and marker selection was conducted by experts from Fondazione Edmund Mach, INRA, Dalhousie University, Wageningen UR, University Di Bologna, and Universita- Degli Studi Di Milano.

The 96-format array includes markers identified using whole-genome sequence data from 63 Malus domestica cultivars and two double haploid accessions. Table 1 lists the number of cultivars and corresponding country of origin used in the SNP discovery process.

Axiom Apple Genotyping Array includes 480,000 markers and together with Axiom™ Analysis Suite software overcomes the genotyping challenges associated with polyploidy, rapid linkage disequilibrium (LD) decay, and high polymorphism observed in the apple genome.

Array highlights Very high diversity Includes markers discovered in 63 worldwide M. domestica cultivars High resolution to address rapid decay of LD 487,249 markers on the array Bias towards common variants with minor allele frequency (MAF) >0.05 Includes 21,463 previously validated markers: 19,990 markers from an existing in-market 20K Fruitbreedomics apple array and 1,473 markers identified using genotyping-by-sequencing (GBS) Absence of paralogous variants through the use of double haploid accessions in SNP discovery Applications of Axiom Apple Genotyping Array Construction of high-resolution genetic maps Fine mapping of quantitative trait loci Genome-wide association studies

Table 1: The country of origin and the number of cultivars used in the SNP discovery process for Axiom Apple Genotyping Array. Country of origin Number of cultivars Australia 1 Central Europe 39 Canada 1 Iran 1 Simmental 16 Japan 1 New Zealand 1 Northern Europe 4 Russia 9 Tunisia 1 United States 5