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_3881601FB_AFFY_3881601genetic_marker
FB_AFFY_0485264FB_AFFY_0485264genetic_marker
FB_AFFY_6771230FB_AFFY_6771230genetic_marker
RosBREEDSNP_SNP_GA_15230080_Lg2_00222_MAF40_1630459_exon1RosBREEDSNP_SNP_GA_15230080_Lg2_00222_MAF40_1630459_exon1genetic_marker
RosBREEDSNP_SNP_CA_22652840_Lg12_01150_MAF40_713737_exon1RosBREEDSNP_SNP_CA_22652840_Lg12_01150_MAF40_713737_exon1genetic_marker
RosBREEDSNP_SNP_CT_22247625_Lg6_02165_MAF20_1627766_exon9RosBREEDSNP_SNP_CT_22247625_Lg6_02165_MAF20_1627766_exon9genetic_marker
FB_AFFY_5477072FB_AFFY_5477072genetic_marker
RosBREEDSNP_SNP_AG_22536388_Lg10_RosCOS139_MAF20_MDP0000298812_exon1RosBREEDSNP_SNP_AG_22536388_Lg10_RosCOS139_MAF20_MDP0000298812_exon1genetic_marker
RosBREEDSNP_SNP_GA_12380727_Lg11_00441_MAF30_1688374_exon1RosBREEDSNP_SNP_GA_12380727_Lg11_00441_MAF30_1688374_exon1genetic_marker
RosBREEDSNP_SNP_TC_6133421_Lg14_02706_MAF50_MDP0000320229_exon3RosBREEDSNP_SNP_TC_6133421_Lg14_02706_MAF50_MDP0000320229_exon3genetic_marker
FB_AFFY_6057641FB_AFFY_6057641genetic_marker
FB_AFFY_6169457FB_AFFY_6169457genetic_marker
FB_AFFY_1287109FB_AFFY_1287109genetic_marker
FB_AFFY_2259939FB_AFFY_2259939genetic_marker
FB_AFFY_4690638FB_AFFY_4690638genetic_marker
FB_AFFY_7389405FB_AFFY_7389405genetic_marker
RosBREEDSNP_SNP_TG_3891842_Lg6_01747_MAF20_451241_exon1RosBREEDSNP_SNP_TG_3891842_Lg6_01747_MAF20_451241_exon1genetic_marker
RosBREEDSNP_SNP_GA_8652481_Lg13_RosCOS2067_MAF20_1646188_exon2RosBREEDSNP_SNP_GA_8652481_Lg13_RosCOS2067_MAF20_1646188_exon2genetic_marker
RosBREEDSNP_SNP_CA_23409284_Lg6_01556_MAF40_441066_exon1RosBREEDSNP_SNP_CA_23409284_Lg6_01556_MAF40_441066_exon1genetic_marker
FB_AFFY_9430695FB_AFFY_9430695genetic_marker
GDsnp00286GDsnp00286genetic_marker
FB_AFFY_2818286FB_AFFY_2818286genetic_marker
FB_AFFY_9802776FB_AFFY_9802776genetic_marker
FB_AFFY_5495225FB_AFFY_5495225genetic_marker
FB_AFFY_4350057FB_AFFY_4350057genetic_marker

Pages