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_8016939FB_AFFY_8016939genetic_marker
FB_AFFY_9314689FB_AFFY_9314689genetic_marker
FB_AFFY_6970449FB_AFFY_6970449genetic_marker
FB_AFFY_3479956FB_AFFY_3479956genetic_marker
FB_AFFY_0254748FB_AFFY_0254748genetic_marker
FB_AFFY_6790737FB_AFFY_6790737genetic_marker
FB_AFFY_9351914FB_AFFY_9351914genetic_marker
GDsnp01299GDsnp01299genetic_marker
FB_AFFY_3387657FB_AFFY_3387657genetic_marker
RosBREEDSNP_SNP_TC_14053916_Lg16_117494_MAF20_117494_exon3RosBREEDSNP_SNP_TC_14053916_Lg16_117494_MAF20_117494_exon3genetic_marker
RosBREEDSNP_SNP_TG_33478372_Lg11_02576_MAF30_1661869_exon1RosBREEDSNP_SNP_TG_33478372_Lg11_02576_MAF30_1661869_exon1genetic_marker
FB_AFFY_3214141FB_AFFY_3214141genetic_marker
RosBREEDSNP_SNP_TC_13528560_Lg4_RosCOS2954_MAF50_524827_exon1RosBREEDSNP_SNP_TC_13528560_Lg4_RosCOS2954_MAF50_524827_exon1genetic_marker
FB_AFFY_8102871FB_AFFY_8102871genetic_marker
RosBREEDSNP_SNP_CT_13512352_Lg3_57248__57248_exon1RosBREEDSNP_SNP_CT_13512352_Lg3_57248__57248_exon1genetic_marker
RosBREEDSNP_SNP_TG_71128_Lg17_00091_MAF40_1678954_exon1RosBREEDSNP_SNP_TG_71128_Lg17_00091_MAF40_1678954_exon1genetic_marker
FB_AFFY_3588808FB_AFFY_3588808genetic_marker
FB_AFFY_8114959FB_AFFY_8114959genetic_marker
FB_AFFY_6142395FB_AFFY_6142395genetic_marker
FB_AFFY_4780198FB_AFFY_4780198genetic_marker
FB_AFFY_0045109FB_AFFY_0045109genetic_marker
FB_AFFY_1099320FB_AFFY_1099320genetic_marker
FB_AFFY_4449280FB_AFFY_4449280genetic_marker
FB_AFFY_0255910FB_AFFY_0255910genetic_marker
FB_AFFY_9799155FB_AFFY_9799155genetic_marker

Pages