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_1603000FB_AFFY_1603000genetic_marker
FB_AFFY_1603020FB_AFFY_1603020genetic_marker
FB_AFFY_1603056FB_AFFY_1603056genetic_marker
FB_AFFY_1603062FB_AFFY_1603062genetic_marker
FB_AFFY_1603063FB_AFFY_1603063genetic_marker
FB_AFFY_1603064FB_AFFY_1603064genetic_marker
FB_AFFY_1603066FB_AFFY_1603066genetic_marker
FB_AFFY_1603068FB_AFFY_1603068genetic_marker
FB_AFFY_1603089FB_AFFY_1603089genetic_marker
FB_AFFY_1603168FB_AFFY_1603168genetic_marker
FB_AFFY_1603172FB_AFFY_1603172genetic_marker
FB_AFFY_1603218FB_AFFY_1603218genetic_marker
FB_AFFY_1603223FB_AFFY_1603223genetic_marker
FB_AFFY_1603233FB_AFFY_1603233genetic_marker
FB_AFFY_1603292FB_AFFY_1603292genetic_marker
FB_AFFY_1603342FB_AFFY_1603342genetic_marker
FB_AFFY_1603474FB_AFFY_1603474genetic_marker
FB_AFFY_1603577FB_AFFY_1603577genetic_marker
FB_AFFY_1603603FB_AFFY_1603603genetic_marker
FB_AFFY_1603635FB_AFFY_1603635genetic_marker
FB_AFFY_1603640FB_AFFY_1603640genetic_marker
FB_AFFY_1603650FB_AFFY_1603650genetic_marker
FB_AFFY_1603668FB_AFFY_1603668genetic_marker
FB_AFFY_1603722FB_AFFY_1603722genetic_marker
FB_AFFY_1603761FB_AFFY_1603761genetic_marker

Pages