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_8889970FB_AFFY_8889970genetic_marker
FB_AFFY_8890018FB_AFFY_8890018genetic_marker
FB_AFFY_8890046FB_AFFY_8890046genetic_marker
FB_AFFY_8890051FB_AFFY_8890051genetic_marker
FB_AFFY_8890101FB_AFFY_8890101genetic_marker
FB_AFFY_8890217FB_AFFY_8890217genetic_marker
FB_AFFY_8890255FB_AFFY_8890255genetic_marker
FB_AFFY_8890261FB_AFFY_8890261genetic_marker
FB_AFFY_8890305FB_AFFY_8890305genetic_marker
FB_AFFY_8890306FB_AFFY_8890306genetic_marker
FB_AFFY_8890375FB_AFFY_8890375genetic_marker
FB_AFFY_8890398FB_AFFY_8890398genetic_marker
FB_AFFY_8890426FB_AFFY_8890426genetic_marker
FB_AFFY_8890430FB_AFFY_8890430genetic_marker
FB_AFFY_8890699FB_AFFY_8890699genetic_marker
FB_AFFY_8890752FB_AFFY_8890752genetic_marker
FB_AFFY_8890758FB_AFFY_8890758genetic_marker
FB_AFFY_8890759FB_AFFY_8890759genetic_marker
FB_AFFY_8890784FB_AFFY_8890784genetic_marker
FB_AFFY_8890847FB_AFFY_8890847genetic_marker
FB_AFFY_8890855FB_AFFY_8890855genetic_marker
FB_AFFY_8890856FB_AFFY_8890856genetic_marker
FB_AFFY_8890492FB_AFFY_8890492genetic_marker
FB_AFFY_8890497FB_AFFY_8890497genetic_marker
FB_AFFY_8890622FB_AFFY_8890622genetic_marker

Pages