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_0386517FB_AFFY_0386517genetic_marker
FB_AFFY_0386522FB_AFFY_0386522genetic_marker
FB_AFFY_0386534FB_AFFY_0386534genetic_marker
FB_AFFY_0386538FB_AFFY_0386538genetic_marker
FB_AFFY_0386549FB_AFFY_0386549genetic_marker
FB_AFFY_0386550FB_AFFY_0386550genetic_marker
FB_AFFY_0386556FB_AFFY_0386556genetic_marker
FB_AFFY_0386559FB_AFFY_0386559genetic_marker
FB_AFFY_0386562FB_AFFY_0386562genetic_marker
FB_AFFY_0386619FB_AFFY_0386619genetic_marker
FB_AFFY_0386734FB_AFFY_0386734genetic_marker
FB_AFFY_0386838FB_AFFY_0386838genetic_marker
FB_AFFY_0386844FB_AFFY_0386844genetic_marker
FB_AFFY_0386847FB_AFFY_0386847genetic_marker
FB_AFFY_0386850FB_AFFY_0386850genetic_marker
FB_AFFY_0386920FB_AFFY_0386920genetic_marker
FB_AFFY_0386934FB_AFFY_0386934genetic_marker
FB_AFFY_0386952FB_AFFY_0386952genetic_marker
FB_AFFY_0387063FB_AFFY_0387063genetic_marker
FB_AFFY_0387066FB_AFFY_0387066genetic_marker
FB_AFFY_0387075FB_AFFY_0387075genetic_marker
FB_AFFY_0387176FB_AFFY_0387176genetic_marker
FB_AFFY_0387180FB_AFFY_0387180genetic_marker
FB_AFFY_0387202FB_AFFY_0387202genetic_marker
FB_AFFY_0387208FB_AFFY_0387208genetic_marker

Pages