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
GDsnp01773GDsnp01773genetic_marker
GDsnp01778GDsnp01778genetic_marker
GDsnp01779GDsnp01779genetic_marker
GDsnp01780GDsnp01780genetic_marker
GDsnp01781GDsnp01781genetic_marker
GDsnp01783GDsnp01783genetic_marker
GDsnp01786GDsnp01786genetic_marker
GDsnp01788GDsnp01788genetic_marker
GDsnp01797GDsnp01797genetic_marker
GDsnp01800GDsnp01800genetic_marker
GDsnp01805GDsnp01805genetic_marker
GDsnp01810GDsnp01810genetic_marker
GDsnp01811GDsnp01811genetic_marker
GDsnp01813GDsnp01813genetic_marker
GDsnp01815GDsnp01815genetic_marker
GDsnp01822GDsnp01822genetic_marker
GDsnp01831GDsnp01831genetic_marker
GDsnp01846GDsnp01846genetic_marker
GDsnp01853GDsnp01853genetic_marker
GDsnp01855GDsnp01855genetic_marker
GDsnp01867GDsnp01867genetic_marker
GDsnp01872GDsnp01872genetic_marker
GDsnp01874GDsnp01874genetic_marker
GDsnp01882GDsnp01882genetic_marker
GDsnp01885GDsnp01885genetic_marker

Pages