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_0403104FB_AFFY_0403104genetic_marker
FB_AFFY_0403195FB_AFFY_0403195genetic_marker
FB_AFFY_0403483FB_AFFY_0403483genetic_marker
FB_AFFY_0403487FB_AFFY_0403487genetic_marker
FB_AFFY_0403533FB_AFFY_0403533genetic_marker
FB_AFFY_0403575FB_AFFY_0403575genetic_marker
FB_AFFY_0403576FB_AFFY_0403576genetic_marker
FB_AFFY_0403588FB_AFFY_0403588genetic_marker
FB_AFFY_0403597FB_AFFY_0403597genetic_marker
FB_AFFY_0403598FB_AFFY_0403598genetic_marker
FB_AFFY_0403599FB_AFFY_0403599genetic_marker
FB_AFFY_0403607FB_AFFY_0403607genetic_marker
FB_AFFY_0403613FB_AFFY_0403613genetic_marker
FB_AFFY_0403618FB_AFFY_0403618genetic_marker
FB_AFFY_0403620FB_AFFY_0403620genetic_marker
FB_AFFY_0403623FB_AFFY_0403623genetic_marker
FB_AFFY_0403624FB_AFFY_0403624genetic_marker
FB_AFFY_0404147FB_AFFY_0404147genetic_marker
FB_AFFY_0404161FB_AFFY_0404161genetic_marker
FB_AFFY_0404205FB_AFFY_0404205genetic_marker
FB_AFFY_0404260FB_AFFY_0404260genetic_marker
FB_AFFY_0404288FB_AFFY_0404288genetic_marker
FB_AFFY_0404359FB_AFFY_0404359genetic_marker
FB_AFFY_0404656FB_AFFY_0404656genetic_marker
FB_AFFY_0404666FB_AFFY_0404666genetic_marker

Pages