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

Publication Overview
TitleDevelopment and validation of the Axiom(®) Apple480K SNP genotyping array
AuthorsBianco 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
TypeJournal Article
Journal NameThe Plant journal : for cell and molecular biology
Year2016
CitationBianco 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.

Abstract

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. This article is protected by copyright. All rights reserved.

Features
This publication contains information about 487,249 features:
Feature NameUniquenameType
FB_AFFY_1682579FB_AFFY_1682579genetic_marker
FB_AFFY_1682653FB_AFFY_1682653genetic_marker
FB_AFFY_1682666FB_AFFY_1682666genetic_marker
FB_AFFY_1682667FB_AFFY_1682667genetic_marker
FB_AFFY_1682677FB_AFFY_1682677genetic_marker
FB_AFFY_1682680FB_AFFY_1682680genetic_marker
FB_AFFY_1682686FB_AFFY_1682686genetic_marker
FB_AFFY_1682702FB_AFFY_1682702genetic_marker
FB_AFFY_1682710FB_AFFY_1682710genetic_marker
FB_AFFY_1682711FB_AFFY_1682711genetic_marker
FB_AFFY_1682712FB_AFFY_1682712genetic_marker
FB_AFFY_1682722FB_AFFY_1682722genetic_marker
FB_AFFY_1682723FB_AFFY_1682723genetic_marker
FB_AFFY_1683190FB_AFFY_1683190genetic_marker
FB_AFFY_1683196FB_AFFY_1683196genetic_marker
FB_AFFY_1683199FB_AFFY_1683199genetic_marker
FB_AFFY_1683212FB_AFFY_1683212genetic_marker
FB_AFFY_1683234FB_AFFY_1683234genetic_marker
FB_AFFY_1683253FB_AFFY_1683253genetic_marker
FB_AFFY_1683287FB_AFFY_1683287genetic_marker
FB_AFFY_1683292FB_AFFY_1683292genetic_marker
FB_AFFY_1683427FB_AFFY_1683427genetic_marker
FB_AFFY_1683611FB_AFFY_1683611genetic_marker
FB_AFFY_1683657FB_AFFY_1683657genetic_marker
FB_AFFY_1683658FB_AFFY_1683658genetic_marker

Pages