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
SNP_FB_0933298SNP_FB_0933298genetic_marker
SNP_FB_0385336SNP_FB_0385336genetic_marker
SNP_FB_0385352SNP_FB_0385352genetic_marker
SNP_FB_0933501SNP_FB_0933501genetic_marker
SNP_FB_0933502SNP_FB_0933502genetic_marker
SNP_FB_0933527SNP_FB_0933527genetic_marker
SNP_FB_0933528SNP_FB_0933528genetic_marker
SNP_FB_0933530SNP_FB_0933530genetic_marker
SNP_FB_0933540SNP_FB_0933540genetic_marker
SNP_FB_0385970SNP_FB_0385970genetic_marker
SNP_FB_0385972SNP_FB_0385972genetic_marker
SNP_FB_0385974SNP_FB_0385974genetic_marker
SNP_FB_0385975SNP_FB_0385975genetic_marker
RosBREEDSNP_SNP_CT_10388012_Lg17_01044_MAF30_672362_exon2RosBREEDSNP_SNP_CT_10388012_Lg17_01044_MAF30_672362_exon2genetic_marker
SNP_FB_0386775SNP_FB_0386775genetic_marker
SNP_FB_0387348SNP_FB_0387348genetic_marker
SNP_FB_0387349SNP_FB_0387349genetic_marker
SNP_FB_0387361SNP_FB_0387361genetic_marker
SNP_FB_0387366SNP_FB_0387366genetic_marker
SNP_FB_0387753SNP_FB_0387753genetic_marker
SNP_FB_0387775SNP_FB_0387775genetic_marker
SNP_FB_0387786SNP_FB_0387786genetic_marker
SNP_FB_0387793SNP_FB_0387793genetic_marker
SNP_FB_0388791SNP_FB_0388791genetic_marker
SNP_FB_0388797SNP_FB_0388797genetic_marker

Pages