Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

Publication Overview
TitleDevelopment and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)
AuthorsBianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen J, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M
TypeJournal Article
Journal NamePloS one
Volume9
Issue10
Year2014
Page(s)e110377
CitationBianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen J, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M. Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh). PloS one. 2014; 9(10):e110377.

Abstract

High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

Features
This publication contains information about 18,019 features:
Feature NameUniquenameType
CONS61CONS61genetic_marker
AFL2AFL2genetic_marker
GDsnp00152GDsnp00152genetic_marker
RosBREEDSNP_SNP_AC_18695269_Lg1_00183_MAF20_MDP0000404072_exon1RosBREEDSNP_SNP_AC_18695269_Lg1_00183_MAF20_MDP0000404072_exon1genetic_marker
RosBREEDSNP_SNP_AG_14154922_Lg1_01058_MAF30_1682312_exon1RosBREEDSNP_SNP_AG_14154922_Lg1_01058_MAF30_1682312_exon1genetic_marker
RosBREEDSNP_SNP_AG_34453757_Lg1_02371_MAF20_MDP0000286439_exon1RosBREEDSNP_SNP_AG_34453757_Lg1_02371_MAF20_MDP0000286439_exon1genetic_marker
RosBREEDSNP_SNP_CT_26229758_Lg1_00674_MAF50_74609_exon1RosBREEDSNP_SNP_CT_26229758_Lg1_00674_MAF50_74609_exon1genetic_marker
RosBREEDSNP_SNP_GA_16501559_Lg1_00107_MAF30_1618955_exon2RosBREEDSNP_SNP_GA_16501559_Lg1_00107_MAF30_1618955_exon2genetic_marker
RosBREEDSNP_SNP_GA_30217061_Lg1_CXE4_MAF40_MDP0000318149_exon1RosBREEDSNP_SNP_GA_30217061_Lg1_CXE4_MAF40_MDP0000318149_exon1genetic_marker
RosBREEDSNP_SNP_GT_16455193_Lg1_00107_MAF30_475684_exon1RosBREEDSNP_SNP_GT_16455193_Lg1_00107_MAF30_475684_exon1genetic_marker
RosBREEDSNP_SNP_TC_14798027_Lg1_01500_MAF50_67147_exon1RosBREEDSNP_SNP_TC_14798027_Lg1_01500_MAF50_67147_exon1genetic_marker
RosBREEDSNP_SNP_TC_16504943_Lg1_00107_MAF40_883912_exon1RosBREEDSNP_SNP_TC_16504943_Lg1_00107_MAF40_883912_exon1genetic_marker
RosBREEDSNP_SNP_TC_21289759_Lg1_02518_MAF20_1636950_exon6RosBREEDSNP_SNP_TC_21289759_Lg1_02518_MAF20_1636950_exon6genetic_marker
RosBREEDSNP_SNP_TC_35468899_Lg1_02092_MAF50_138030_exon2RosBREEDSNP_SNP_TC_35468899_Lg1_02092_MAF50_138030_exon2genetic_marker
RosBREEDSNP_SNP_CT_12148172_Lg1_00420_MAF50_MDP0000130704_exon1RosBREEDSNP_SNP_CT_12148172_Lg1_00420_MAF50_MDP0000130704_exon1genetic_marker
GDsnp01500GDsnp01500genetic_marker
RosBREEDSNP_SNP_AG_21291785_Lg1_02518_MAF30_1687981_exon1RosBREEDSNP_SNP_AG_21291785_Lg1_02518_MAF30_1687981_exon1genetic_marker
GDsnp00056GDsnp00056genetic_marker
GDsnp01264GDsnp01264genetic_marker
RosBREEDSNP_SNP_AG_16680919_Lg10_01710_MAF30_MDP0000226923_exon1RosBREEDSNP_SNP_AG_16680919_Lg10_01710_MAF30_MDP0000226923_exon1genetic_marker
RosBREEDSNP_SNP_AG_36033324_Lg10_186429_MAF30_186429_exon1RosBREEDSNP_SNP_AG_36033324_Lg10_186429_MAF30_186429_exon1genetic_marker
RosBREEDSNP_SNP_CA_2705271_Lg10_00056_MAF20_MDP0000183449_exon2RosBREEDSNP_SNP_CA_2705271_Lg10_00056_MAF20_MDP0000183449_exon2genetic_marker
RosBREEDSNP_SNP_CT_34936228_Lg10_00258_MAF20_MDP0000311107_exon7RosBREEDSNP_SNP_CT_34936228_Lg10_00258_MAF20_MDP0000311107_exon7genetic_marker
RosBREEDSNP_SNP_GT_20013910_Lg10_00869_MAF50_924537_exon1RosBREEDSNP_SNP_GT_20013910_Lg10_00869_MAF50_924537_exon1genetic_marker
RosBREEDSNP_SNP_GT_26641840_Lg10_00812_MAF50_MDP0000280037_exon1RosBREEDSNP_SNP_GT_26641840_Lg10_00812_MAF50_MDP0000280037_exon1genetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic-eCollection
ISSN1932-6203
eISSN1932-6203
Publication Date2014
Journal AbbreviationPLoS ONE
DOI10.1371/journal.pone.0110377
Elocation10.1371/journal.pone.0110377
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryUnited States
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:25303088