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_8896654FB_AFFY_8896654genetic_marker
FB_AFFY_8896659FB_AFFY_8896659genetic_marker
FB_AFFY_8896677FB_AFFY_8896677genetic_marker
FB_AFFY_8896715FB_AFFY_8896715genetic_marker
FB_AFFY_8897408FB_AFFY_8897408genetic_marker
FB_AFFY_8897509FB_AFFY_8897509genetic_marker
FB_AFFY_8897596FB_AFFY_8897596genetic_marker
FB_AFFY_8897632FB_AFFY_8897632genetic_marker
FB_AFFY_8897277FB_AFFY_8897277genetic_marker
FB_AFFY_8897662FB_AFFY_8897662genetic_marker
FB_AFFY_8897663FB_AFFY_8897663genetic_marker
FB_AFFY_8897691FB_AFFY_8897691genetic_marker
FB_AFFY_8897698FB_AFFY_8897698genetic_marker
FB_AFFY_8897699FB_AFFY_8897699genetic_marker
FB_AFFY_8897700FB_AFFY_8897700genetic_marker
FB_AFFY_8897702FB_AFFY_8897702genetic_marker
FB_AFFY_8897855FB_AFFY_8897855genetic_marker
FB_AFFY_8897917FB_AFFY_8897917genetic_marker
FB_AFFY_8897933FB_AFFY_8897933genetic_marker
FB_AFFY_8897934FB_AFFY_8897934genetic_marker
FB_AFFY_8897935FB_AFFY_8897935genetic_marker
FB_AFFY_8897945FB_AFFY_8897945genetic_marker
FB_AFFY_8897947FB_AFFY_8897947genetic_marker
FB_AFFY_8897948FB_AFFY_8897948genetic_marker
FB_AFFY_8897962FB_AFFY_8897962genetic_marker

Pages