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_0943693SNP_FB_0943693genetic_marker
SNP_FB_0434582SNP_FB_0434582genetic_marker
SNP_FB_0945099SNP_FB_0945099genetic_marker
SNP_FB_0945105SNP_FB_0945105genetic_marker
SNP_FB_0945106SNP_FB_0945106genetic_marker
SNP_FB_0945108SNP_FB_0945108genetic_marker
SNP_FB_0945110SNP_FB_0945110genetic_marker
SNP_FB_0944186SNP_FB_0944186genetic_marker
SNP_FB_0944210SNP_FB_0944210genetic_marker
SNP_FB_0945583SNP_FB_0945583genetic_marker
SNP_FB_0945607SNP_FB_0945607genetic_marker
SNP_FB_0945611SNP_FB_0945611genetic_marker
SNP_FB_0945847SNP_FB_0945847genetic_marker
SNP_FB_0945848SNP_FB_0945848genetic_marker
SNP_FB_0945849SNP_FB_0945849genetic_marker
SNP_FB_0945897SNP_FB_0945897genetic_marker
SNP_FB_0945902SNP_FB_0945902genetic_marker
SNP_FB_0945907SNP_FB_0945907genetic_marker
SNP_FB_0436465SNP_FB_0436465genetic_marker
SNP_FB_0436482SNP_FB_0436482genetic_marker
SNP_FB_0436483SNP_FB_0436483genetic_marker
SNP_FB_0436484SNP_FB_0436484genetic_marker
SNP_FB_0436487SNP_FB_0436487genetic_marker
SNP_FB_0436492SNP_FB_0436492genetic_marker
SNP_FB_0436495SNP_FB_0436495genetic_marker

Pages