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_9484757FB_AFFY_9484757genetic_marker
FB_AFFY_9484762FB_AFFY_9484762genetic_marker
FB_AFFY_9484770FB_AFFY_9484770genetic_marker
FB_AFFY_9484790FB_AFFY_9484790genetic_marker
FB_AFFY_9484794FB_AFFY_9484794genetic_marker
FB_AFFY_9484800FB_AFFY_9484800genetic_marker
FB_AFFY_9484802FB_AFFY_9484802genetic_marker
FB_AFFY_9484804FB_AFFY_9484804genetic_marker
FB_AFFY_9484806FB_AFFY_9484806genetic_marker
FB_AFFY_9484837FB_AFFY_9484837genetic_marker
FB_AFFY_9484856FB_AFFY_9484856genetic_marker
FB_AFFY_9484890FB_AFFY_9484890genetic_marker
FB_AFFY_9484914FB_AFFY_9484914genetic_marker
FB_AFFY_9484932FB_AFFY_9484932genetic_marker
FB_AFFY_9485306FB_AFFY_9485306genetic_marker
FB_AFFY_9485341FB_AFFY_9485341genetic_marker
FB_AFFY_9485236FB_AFFY_9485236genetic_marker
FB_AFFY_9485271FB_AFFY_9485271genetic_marker
FB_AFFY_9485289FB_AFFY_9485289genetic_marker
FB_AFFY_9485292FB_AFFY_9485292genetic_marker
FB_AFFY_9486130FB_AFFY_9486130genetic_marker
FB_AFFY_9486164FB_AFFY_9486164genetic_marker
FB_AFFY_9486183FB_AFFY_9486183genetic_marker
FB_AFFY_9486211FB_AFFY_9486211genetic_marker
FB_AFFY_9486221FB_AFFY_9486221genetic_marker

Pages