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
RosBREEDSNP_SNP_GA_49174_Lg17_00091_MAF20_1640662_exon1RosBREEDSNP_SNP_GA_49174_Lg17_00091_MAF20_1640662_exon1genetic_marker
FB_AFFY_2622548FB_AFFY_2622548genetic_marker
FB_AFFY_9648863FB_AFFY_9648863genetic_marker
GDsnp02437GDsnp02437genetic_marker
FB_AFFY_0195750FB_AFFY_0195750genetic_marker
FB_AFFY_5606764FB_AFFY_5606764genetic_marker
RosBREEDSNP_SNP_AC_10935478_Lg17_00918_MAF40_MDP0000500222_exon1RosBREEDSNP_SNP_AC_10935478_Lg17_00918_MAF40_MDP0000500222_exon1genetic_marker
FB_AFFY_6205214FB_AFFY_6205214genetic_marker
FB_AFFY_9395547FB_AFFY_9395547genetic_marker
FB_AFFY_9105017FB_AFFY_9105017genetic_marker
FB_AFFY_4584203FB_AFFY_4584203genetic_marker
FB_AFFY_5193389FB_AFFY_5193389genetic_marker
RosBREEDSNP_SNP_TC_26007783_Lg6_01682_MAF40_604254_exon1RosBREEDSNP_SNP_TC_26007783_Lg6_01682_MAF40_604254_exon1genetic_marker
GDsnp00947GDsnp00947genetic_marker
FB_AFFY_9115994FB_AFFY_9115994genetic_marker
FB_AFFY_1506603FB_AFFY_1506603genetic_marker
FB_AFFY_3594884FB_AFFY_3594884genetic_marker
FB_AFFY_6864260FB_AFFY_6864260genetic_marker
RosBREEDSNP_SNP_GA_19977586_Lg9_02100_MAF40_MDP0000137341_exon4RosBREEDSNP_SNP_GA_19977586_Lg9_02100_MAF40_MDP0000137341_exon4genetic_marker
RosBREEDSNP_SNP_GA_5159668_Lg8_01378_MAF10_MDP0000150374_exon1RosBREEDSNP_SNP_GA_5159668_Lg8_01378_MAF10_MDP0000150374_exon1genetic_marker
RosBREEDSNP_SNP_CT_50036156_Lg15_01778_MAF30_224068_exon1RosBREEDSNP_SNP_CT_50036156_Lg15_01778_MAF30_224068_exon1genetic_marker
RosBREEDSNP_SNP_GA_6007512_Lg16_01003_MAF50_MDP0000188823_exon2RosBREEDSNP_SNP_GA_6007512_Lg16_01003_MAF50_MDP0000188823_exon2genetic_marker
FB_AFFY_0717545FB_AFFY_0717545genetic_marker
FB_AFFY_3549872FB_AFFY_3549872genetic_marker
FB_AFFY_6942004FB_AFFY_6942004genetic_marker

Pages