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_0566646FB_AFFY_0566646genetic_marker
FB_AFFY_0566656FB_AFFY_0566656genetic_marker
FB_AFFY_0566666FB_AFFY_0566666genetic_marker
FB_AFFY_0566937FB_AFFY_0566937genetic_marker
FB_AFFY_0567237FB_AFFY_0567237genetic_marker
FB_AFFY_0567295FB_AFFY_0567295genetic_marker
FB_AFFY_0567336FB_AFFY_0567336genetic_marker
FB_AFFY_0567459FB_AFFY_0567459genetic_marker
FB_AFFY_0567464FB_AFFY_0567464genetic_marker
FB_AFFY_0567477FB_AFFY_0567477genetic_marker
FB_AFFY_0567491FB_AFFY_0567491genetic_marker
FB_AFFY_0567501FB_AFFY_0567501genetic_marker
FB_AFFY_0567506FB_AFFY_0567506genetic_marker
FB_AFFY_0567533FB_AFFY_0567533genetic_marker
FB_AFFY_0567536FB_AFFY_0567536genetic_marker
FB_AFFY_0567573FB_AFFY_0567573genetic_marker
FB_AFFY_0567581FB_AFFY_0567581genetic_marker
FB_AFFY_0567587FB_AFFY_0567587genetic_marker
FB_AFFY_0567605FB_AFFY_0567605genetic_marker
FB_AFFY_0567619FB_AFFY_0567619genetic_marker
FB_AFFY_0567663FB_AFFY_0567663genetic_marker
FB_AFFY_0567669FB_AFFY_0567669genetic_marker
FB_AFFY_0567709FB_AFFY_0567709genetic_marker
FB_AFFY_0567716FB_AFFY_0567716genetic_marker
FB_AFFY_0567719FB_AFFY_0567719genetic_marker

Pages