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_1614684FB_AFFY_1614684genetic_marker
FB_AFFY_1615299FB_AFFY_1615299genetic_marker
FB_AFFY_1615305FB_AFFY_1615305genetic_marker
FB_AFFY_1615324FB_AFFY_1615324genetic_marker
FB_AFFY_1615450FB_AFFY_1615450genetic_marker
FB_AFFY_1615502FB_AFFY_1615502genetic_marker
FB_AFFY_1615852FB_AFFY_1615852genetic_marker
FB_AFFY_1615897FB_AFFY_1615897genetic_marker
FB_AFFY_1615916FB_AFFY_1615916genetic_marker
FB_AFFY_1616000FB_AFFY_1616000genetic_marker
FB_AFFY_1616614FB_AFFY_1616614genetic_marker
FB_AFFY_1616677FB_AFFY_1616677genetic_marker
FB_AFFY_1616712FB_AFFY_1616712genetic_marker
FB_AFFY_1616718FB_AFFY_1616718genetic_marker
FB_AFFY_1616754FB_AFFY_1616754genetic_marker
FB_AFFY_1616812FB_AFFY_1616812genetic_marker
FB_AFFY_1616830FB_AFFY_1616830genetic_marker
FB_AFFY_1616845FB_AFFY_1616845genetic_marker
FB_AFFY_1616853FB_AFFY_1616853genetic_marker
FB_AFFY_1616856FB_AFFY_1616856genetic_marker
FB_AFFY_1616936FB_AFFY_1616936genetic_marker
FB_AFFY_1616948FB_AFFY_1616948genetic_marker
FB_AFFY_1616958FB_AFFY_1616958genetic_marker
FB_AFFY_1616986FB_AFFY_1616986genetic_marker
FB_AFFY_1617029FB_AFFY_1617029genetic_marker

Pages