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_1648883FB_AFFY_1648883genetic_marker
FB_AFFY_1648950FB_AFFY_1648950genetic_marker
FB_AFFY_1648953FB_AFFY_1648953genetic_marker
FB_AFFY_1649265FB_AFFY_1649265genetic_marker
FB_AFFY_1649272FB_AFFY_1649272genetic_marker
FB_AFFY_1649299FB_AFFY_1649299genetic_marker
FB_AFFY_1649322FB_AFFY_1649322genetic_marker
FB_AFFY_1649328FB_AFFY_1649328genetic_marker
FB_AFFY_1649339FB_AFFY_1649339genetic_marker
FB_AFFY_1649364FB_AFFY_1649364genetic_marker
FB_AFFY_1649665FB_AFFY_1649665genetic_marker
FB_AFFY_1649714FB_AFFY_1649714genetic_marker
FB_AFFY_1649746FB_AFFY_1649746genetic_marker
FB_AFFY_1649753FB_AFFY_1649753genetic_marker
FB_AFFY_1649754FB_AFFY_1649754genetic_marker
FB_AFFY_1649811FB_AFFY_1649811genetic_marker
FB_AFFY_1649823FB_AFFY_1649823genetic_marker
FB_AFFY_1650027FB_AFFY_1650027genetic_marker
FB_AFFY_1650029FB_AFFY_1650029genetic_marker
FB_AFFY_1650035FB_AFFY_1650035genetic_marker
FB_AFFY_1650132FB_AFFY_1650132genetic_marker
FB_AFFY_1650287FB_AFFY_1650287genetic_marker
FB_AFFY_1650326FB_AFFY_1650326genetic_marker
FB_AFFY_1650336FB_AFFY_1650336genetic_marker
FB_AFFY_1650375FB_AFFY_1650375genetic_marker

Pages