480K SNP array for Malus x domestica

Analysis Name480K SNP array for Malus x domestica
MethodA SNP selection pipeline
Sourcehigh-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple
Date performed2016-03-31

Cultivated apple (Malus x domestica Borkh.) is one of the most important fruit crops in temperate regions, with great economic and cultural values. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid LD decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom® genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. SNPs have been chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1,324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom® Apple480K to assess the effectiveness of the array. A large majority of SNPs (359,994; 74%) fell in the stringent class of Poly High Resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom® Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple. 


Bianco L, Cestaro A, Linsmith G, Muranty H, Denance C, Théron A, Poncet C, Micheletti D, Kerschbamer E, Di Pierro EA, Larger S, Pindo M, van de Weg E, Davassi A, Laurens F, Velasco R, Durel CE, Troggio M. Development and validation of the Axiom(®) Apple480K SNP genotyping array. The Plant journal : for cell and molecular biology. 2016 Feb 26.

Download SNP and transcriptome data
File Description File
SNP information. The subset of 275K very robust markers is also reported. tpj13145-sup-0002-TableS1.xlsx
Genotype concordance for SNPs called with the Axiom® Apple480K and high-depth resequencing. tpj13145-sup-0003-TableS2.xlsx
List of SNPs with discordant genotypes. tpj13145-sup-0004-TableS3.xlsx