|Title||Development and validation of the Axiom®Apple480K SNP genotyping array|
|Author(s)||Bianco, Luca; Cestaro, Alessandro; Linsmith, Gareth; Muranty, Hélène; Denancé, Caroline; Théron, Anthony; Poncet, Charles; Micheletti, Diego; Kerschbamer, Emanuela; Pierro, Erica A. Di; Larger, Simone; Pindo, Massimo; De Weg, Eric Van; Davassi, Alessandro; Laurens, François; Velasco, Riccardo; Durel, Charles Eric; Troggio, Michela|
|Source||The Plant Journal 86 (2016)1. - ISSN 0960-7412 - p. 62 - 74.|
WUR Plant Breeding
WUR PB Biodiversiteit en Genetische Variatie
|Publication type||Refereed Article in a scientific journal|
|Keyword(s)||genome-wide association study - genotyping - linkage mapping - Malus × domestica Borkh. - SNP chip - validation|
Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium 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. The SNPs were 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 1324 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 or 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.