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
RosBREEDSNP_SNP_AG_7516440_Lg13_AT4_MAF30_1656251_exon1RosBREEDSNP_SNP_AG_7516440_Lg13_AT4_MAF30_1656251_exon1genetic_marker
RosBREEDSNP_SNP_AG_7605137_Lg9_00893_MAF20_1636210_exon1RosBREEDSNP_SNP_AG_7605137_Lg9_00893_MAF20_1636210_exon1genetic_marker
RosBREEDSNP_SNP_AG_7608807_Lg13_02124_MAF40_1660721_exon2RosBREEDSNP_SNP_AG_7608807_Lg13_02124_MAF40_1660721_exon2genetic_marker
RosBREEDSNP_SNP_AG_7685092_Lg9_01858_MAF10_326877_exon1RosBREEDSNP_SNP_AG_7685092_Lg9_01858_MAF10_326877_exon1genetic_marker
RosBREEDSNP_SNP_AG_7699964_Lg9_01858_MAF10_1668945_exon1RosBREEDSNP_SNP_AG_7699964_Lg9_01858_MAF10_1668945_exon1genetic_marker
RosBREEDSNP_SNP_AG_7750385_Lg9_01858_MAF50_1631479_exon6RosBREEDSNP_SNP_AG_7750385_Lg9_01858_MAF50_1631479_exon6genetic_marker
RosBREEDSNP_SNP_AG_788558_Lg5_00460_MAF30_MDP0000297044_exon4RosBREEDSNP_SNP_AG_788558_Lg5_00460_MAF30_MDP0000297044_exon4genetic_marker
RosBREEDSNP_SNP_AG_7904398_Lg6_01954_MAF40_MDP0000479590_exon1RosBREEDSNP_SNP_AG_7904398_Lg6_01954_MAF40_MDP0000479590_exon1genetic_marker
RosBREEDSNP_SNP_AG_8087436_Lg15_00389_MAF50_46141_exon1RosBREEDSNP_SNP_AG_8087436_Lg15_00389_MAF50_46141_exon1genetic_marker
RosBREEDSNP_SNP_AG_810662_Lg17_RosCOS659_MAF40_MDP0000317368_exon10RosBREEDSNP_SNP_AG_810662_Lg17_RosCOS659_MAF40_MDP0000317368_exon10genetic_marker
RosBREEDSNP_SNP_AG_8248084_Lg15_00796_MAF30_1680748_exon1RosBREEDSNP_SNP_AG_8248084_Lg15_00796_MAF30_1680748_exon1genetic_marker
RosBREEDSNP_SNP_AG_830930_Lg4_01597_MAF30_1668681_exon1RosBREEDSNP_SNP_AG_830930_Lg4_01597_MAF30_1668681_exon1genetic_marker
RosBREEDSNP_SNP_AG_831641_Lg7_01172_MAF30_1633901_exon1RosBREEDSNP_SNP_AG_831641_Lg7_01172_MAF30_1633901_exon1genetic_marker
RosBREEDSNP_SNP_AG_8339690_Lg16_RosCOS1090_MAF20_MDP0000149146_exon8RosBREEDSNP_SNP_AG_8339690_Lg16_RosCOS1090_MAF20_MDP0000149146_exon8genetic_marker
RosBREEDSNP_SNP_AG_8342463_Lg16_RosCOS1090_MAF50_MDP0000149147_exon5RosBREEDSNP_SNP_AG_8342463_Lg16_RosCOS1090_MAF50_MDP0000149147_exon5genetic_marker
RosBREEDSNP_SNP_AG_8440063_Lg8_01550_MAF30_MDP0000169265_exon3RosBREEDSNP_SNP_AG_8440063_Lg8_01550_MAF30_MDP0000169265_exon3genetic_marker
RosBREEDSNP_SNP_AG_8507285_Lg3_RosCOS3572_MAF20_793561_exon1RosBREEDSNP_SNP_AG_8507285_Lg3_RosCOS3572_MAF20_793561_exon1genetic_marker
RosBREEDSNP_SNP_AG_8533446_Lg10_00260_MAF20_262836_exon1RosBREEDSNP_SNP_AG_8533446_Lg10_00260_MAF20_262836_exon1genetic_marker
RosBREEDSNP_SNP_AG_8643407_Lg5_01942_MAF20_MDP0000294004_exon2RosBREEDSNP_SNP_AG_8643407_Lg5_01942_MAF20_MDP0000294004_exon2genetic_marker
RosBREEDSNP_SNP_AG_8655302_Lg5_01942_MAF20_MDP0000264936_exon5RosBREEDSNP_SNP_AG_8655302_Lg5_01942_MAF20_MDP0000264936_exon5genetic_marker
RosBREEDSNP_SNP_AG_8666295_Lg5_01942_MAF30_1669212_exon1RosBREEDSNP_SNP_AG_8666295_Lg5_01942_MAF30_1669212_exon1genetic_marker
RosBREEDSNP_SNP_AG_8806260_Lg17_01842_MAF40_MDP0000796893_exon2RosBREEDSNP_SNP_AG_8806260_Lg17_01842_MAF40_MDP0000796893_exon2genetic_marker
RosBREEDSNP_SNP_AG_8810680_Lg12_02857_MAF40_MDP0000064909_exon1RosBREEDSNP_SNP_AG_8810680_Lg12_02857_MAF40_MDP0000064909_exon1genetic_marker
RosBREEDSNP_SNP_AG_8945207_Lg2_00407_MAF30_284458_exon1RosBREEDSNP_SNP_AG_8945207_Lg2_00407_MAF30_284458_exon1genetic_marker
RosBREEDSNP_SNP_AG_9069899_Lg16_01730_MAF20_1637559_exon1RosBREEDSNP_SNP_AG_9069899_Lg16_01730_MAF20_1637559_exon1genetic_marker

Pages