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_1645090FB_AFFY_1645090genetic_marker
FB_AFFY_1645136FB_AFFY_1645136genetic_marker
FB_AFFY_1645512FB_AFFY_1645512genetic_marker
FB_AFFY_1645524FB_AFFY_1645524genetic_marker
FB_AFFY_1645545FB_AFFY_1645545genetic_marker
FB_AFFY_1645557FB_AFFY_1645557genetic_marker
FB_AFFY_1645575FB_AFFY_1645575genetic_marker
FB_AFFY_1645630FB_AFFY_1645630genetic_marker
FB_AFFY_1645652FB_AFFY_1645652genetic_marker
FB_AFFY_1645662FB_AFFY_1645662genetic_marker
FB_AFFY_1645759FB_AFFY_1645759genetic_marker
FB_AFFY_1645789FB_AFFY_1645789genetic_marker
FB_AFFY_1645874FB_AFFY_1645874genetic_marker
FB_AFFY_1646028FB_AFFY_1646028genetic_marker
FB_AFFY_1646035FB_AFFY_1646035genetic_marker
FB_AFFY_1646037FB_AFFY_1646037genetic_marker
FB_AFFY_1646270FB_AFFY_1646270genetic_marker
FB_AFFY_1646276FB_AFFY_1646276genetic_marker
FB_AFFY_1646287FB_AFFY_1646287genetic_marker
FB_AFFY_1646586FB_AFFY_1646586genetic_marker
FB_AFFY_1647009FB_AFFY_1647009genetic_marker
FB_AFFY_1647045FB_AFFY_1647045genetic_marker
FB_AFFY_1647052FB_AFFY_1647052genetic_marker
FB_AFFY_1647053FB_AFFY_1647053genetic_marker
FB_AFFY_1647105FB_AFFY_1647105genetic_marker

Pages