title: Development and validation of the Axiom(®) Apple480K SNP genotyping array.
abstract: 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.
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Bianco
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Cestaro
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Gareth
authors.initials: G
authors.lastname: Linsmith
authors.affiliation: Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Muranty
authors.affiliation: Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Denancé
authors.affiliation: Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039, Clermont-Ferrand, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Théron
authors.affiliation: Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039, Clermont-Ferrand, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Poncet
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Diego
authors.initials: D
authors.lastname: Micheletti
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Emanuela
authors.initials: E
authors.lastname: Kerschbamer
authors.affiliation: Department of Biosciences, University of Milan, via Celoria 26, 20133, Milano, Italy.
authors.forename: Erica A
authors.initials: EA
authors.lastname: Di Pierro
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Larger
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Pindo
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 16, 6700 AA, Wageningen, The Netherlands.
authors.forename: Eric
authors.initials: E
authors.lastname: Van de Weg
authors.affiliation: Affymetrix UK Ltd, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe, HP10 0HH, UK.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Davassi
authors.affiliation: Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France.
authors.forename: François
authors.initials: F
authors.lastname: Laurens
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Velasco
authors.affiliation: Institut de Recherche en Horticulture et Semences - UMR1345, Institut National de la Recherche Agronomique (INRA), SFR 4207 QUASAV, 42 Rue Georges Morel, F-49071, Beaucouzé, France.
authors.forename: Charles-Eric
authors.initials: CE
authors.lastname: Durel
authors.affiliation: Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy.
authors.forename: Michela
authors.initials: M
authors.lastname: Troggio
mesh_terms: D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D015810:Linkage Disequilibrium; D027845:Malus / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
keywords: Malus × domestica Borkh.; SNP chip; genome-wide association study; genotyping; linkage mapping; validation