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_CA_27011620_Lg15_02084_MAF40_MDP0000179991_exon5RosBREEDSNP_SNP_CA_27011620_Lg15_02084_MAF40_MDP0000179991_exon5genetic_marker
FB_AFFY_1861786FB_AFFY_1861786genetic_marker
RosBREEDSNP_SNP_TG_12744729_Lg3_02020_MAF20_1619446_exon9RosBREEDSNP_SNP_TG_12744729_Lg3_02020_MAF20_1619446_exon9genetic_marker
GDsnp01575GDsnp01575genetic_marker
FB_AFFY_8941038FB_AFFY_8941038genetic_marker
RosBREEDSNP_SNP_AG_1318292_Lg17_00864_MAF30_1643044_exon1RosBREEDSNP_SNP_AG_1318292_Lg17_00864_MAF30_1643044_exon1genetic_marker
FB_AFFY_2119832FB_AFFY_2119832genetic_marker
GDsnp02853GDsnp02853genetic_marker
FB_AFFY_6928587FB_AFFY_6928587genetic_marker
FB_AFFY_3480186FB_AFFY_3480186genetic_marker
GDsnp00213GDsnp00213genetic_marker
FB_AFFY_6829749FB_AFFY_6829749genetic_marker
RosBREEDSNP_SNP_GA_27497747_Lg6_RosCOS1040_MAF20_1658681_exon1RosBREEDSNP_SNP_GA_27497747_Lg6_RosCOS1040_MAF20_1658681_exon1genetic_marker
RosBREEDSNP_SNP_CT_14350830_Lg9_02046_MAF20_MDP0000159004_exon2RosBREEDSNP_SNP_CT_14350830_Lg9_02046_MAF20_MDP0000159004_exon2genetic_marker
RosBREEDSNP_SNP_CA_9088223_Lg16_01730_MAF40_MDP0000265949_exon11RosBREEDSNP_SNP_CA_9088223_Lg16_01730_MAF40_MDP0000265949_exon11genetic_marker
RosBREEDSNP_SNP_TG_5372070_Lg9_00514_MAF20_1646977_exon3RosBREEDSNP_SNP_TG_5372070_Lg9_00514_MAF20_1646977_exon3genetic_marker
FB_AFFY_1588892FB_AFFY_1588892genetic_marker
RosBREEDSNP_SNP_CT_12072463_Lg17_00682_MAF50_MDP0000266161_exon6RosBREEDSNP_SNP_CT_12072463_Lg17_00682_MAF50_MDP0000266161_exon6marker_locus
FB_AFFY_8072203FB_AFFY_8072203genetic_marker
FB_AFFY_0256954FB_AFFY_0256954genetic_marker
RosBREEDSNP_SNP_GA_6845933_Lg16_02194_MAF50_390497_exon1RosBREEDSNP_SNP_GA_6845933_Lg16_02194_MAF50_390497_exon1genetic_marker
FB_AFFY_6431480FB_AFFY_6431480genetic_marker
FB_AFFY_5152130FB_AFFY_5152130genetic_marker
FB_AFFY_1357515FB_AFFY_1357515genetic_marker
FB_AFFY_1084377FB_AFFY_1084377genetic_marker

Pages