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_1568876FB_AFFY_1568876genetic_marker
FB_AFFY_1568883FB_AFFY_1568883genetic_marker
FB_AFFY_1568888FB_AFFY_1568888genetic_marker
FB_AFFY_1568889FB_AFFY_1568889genetic_marker
FB_AFFY_1568912FB_AFFY_1568912genetic_marker
FB_AFFY_1569039FB_AFFY_1569039genetic_marker
FB_AFFY_1569086FB_AFFY_1569086genetic_marker
FB_AFFY_1569093FB_AFFY_1569093genetic_marker
FB_AFFY_1569108FB_AFFY_1569108genetic_marker
FB_AFFY_1569133FB_AFFY_1569133genetic_marker
FB_AFFY_1569134FB_AFFY_1569134genetic_marker
FB_AFFY_1569138FB_AFFY_1569138genetic_marker
FB_AFFY_1569167FB_AFFY_1569167genetic_marker
FB_AFFY_1569191FB_AFFY_1569191genetic_marker
FB_AFFY_1570218FB_AFFY_1570218genetic_marker
FB_AFFY_1570229FB_AFFY_1570229genetic_marker
FB_AFFY_1570241FB_AFFY_1570241genetic_marker
FB_AFFY_1570243FB_AFFY_1570243genetic_marker
FB_AFFY_1570244FB_AFFY_1570244genetic_marker
FB_AFFY_1570252FB_AFFY_1570252genetic_marker
FB_AFFY_1570254FB_AFFY_1570254genetic_marker
FB_AFFY_1570295FB_AFFY_1570295genetic_marker
FB_AFFY_1570302FB_AFFY_1570302genetic_marker
FB_AFFY_1570321FB_AFFY_1570321genetic_marker
FB_AFFY_1570322FB_AFFY_1570322genetic_marker

Pages