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
GDsnp01597GDsnp01597genetic_marker
GDsnp01601GDsnp01601genetic_marker
GDsnp01614GDsnp01614genetic_marker
GDsnp01615GDsnp01615genetic_marker
GDsnp01623GDsnp01623genetic_marker
GDsnp01627GDsnp01627genetic_marker
GDsnp01639GDsnp01639genetic_marker
GDsnp01641GDsnp01641genetic_marker
GDsnp01642GDsnp01642genetic_marker
GDsnp01681GDsnp01681genetic_marker
GDsnp01682GDsnp01682genetic_marker
GDsnp01693GDsnp01693genetic_marker
GDsnp01694GDsnp01694genetic_marker
GDsnp01697GDsnp01697genetic_marker
GDsnp01704GDsnp01704genetic_marker
GDsnp01706GDsnp01706genetic_marker
GDsnp01713GDsnp01713genetic_marker
GDsnp01717GDsnp01717genetic_marker
GDsnp01728GDsnp01728genetic_marker
GDsnp01730GDsnp01730genetic_marker
GDsnp01734GDsnp01734genetic_marker
GDsnp01747GDsnp01747genetic_marker
GDsnp01751GDsnp01751genetic_marker
GDsnp01761GDsnp01761genetic_marker
GDsnp01769GDsnp01769genetic_marker

Pages

Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:25303088