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
SNP_FB_0193345SNP_FB_0193345genetic_marker
SNP_FB_0193353SNP_FB_0193353genetic_marker
SNP_FB_0193367SNP_FB_0193367genetic_marker
SNP_FB_0193901SNP_FB_0193901genetic_marker
SNP_FB_0193903SNP_FB_0193903genetic_marker
SNP_FB_0193904SNP_FB_0193904genetic_marker
SNP_FB_0193910SNP_FB_0193910genetic_marker
SNP_FB_0193918SNP_FB_0193918genetic_marker
SNP_FB_0193919SNP_FB_0193919genetic_marker
SNP_FB_0193921SNP_FB_0193921genetic_marker
SNP_FB_0193923SNP_FB_0193923genetic_marker
SNP_FB_0194112SNP_FB_0194112genetic_marker
SNP_FB_0194114SNP_FB_0194114genetic_marker
SNP_FB_0194118SNP_FB_0194118genetic_marker
SNP_FB_0194121SNP_FB_0194121genetic_marker
SNP_FB_0194123SNP_FB_0194123genetic_marker
SNP_FB_0194131SNP_FB_0194131genetic_marker
SNP_FB_0194139SNP_FB_0194139genetic_marker
SNP_FB_1065410SNP_FB_1065410genetic_marker
SNP_FB_1065411SNP_FB_1065411genetic_marker
SNP_FB_1065416SNP_FB_1065416genetic_marker
SNP_FB_1065438SNP_FB_1065438genetic_marker
SNP_FB_1065440SNP_FB_1065440genetic_marker
SNP_FB_0194999SNP_FB_0194999genetic_marker
SNP_FB_0195017SNP_FB_0195017genetic_marker

Pages