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_34926642_Lg12_01647_MAF30_1639248_exon2RosBREEDSNP_SNP_AG_34926642_Lg12_01647_MAF30_1639248_exon2genetic_marker
RosBREEDSNP_SNP_AG_34977942_Lg13_01899_MAF20_973055_exon1RosBREEDSNP_SNP_AG_34977942_Lg13_01899_MAF20_973055_exon1genetic_marker
RosBREEDSNP_SNP_AG_3503210_Lg17_02049_MAF50_478011_exon1RosBREEDSNP_SNP_AG_3503210_Lg17_02049_MAF50_478011_exon1genetic_marker
RosBREEDSNP_SNP_AG_35171763_Lg12_01665_MAF10_1643807_exon3RosBREEDSNP_SNP_AG_35171763_Lg12_01665_MAF10_1643807_exon3genetic_marker
RosBREEDSNP_SNP_AG_3529973_Lg17_02049_MAF10_MDP0000321089_exon5RosBREEDSNP_SNP_AG_3529973_Lg17_02049_MAF10_MDP0000321089_exon5genetic_marker
RosBREEDSNP_SNP_AG_35422934_Lg1_02092_MAF20_7047_exon1RosBREEDSNP_SNP_AG_35422934_Lg1_02092_MAF20_7047_exon1genetic_marker
RosBREEDSNP_SNP_AG_3543730_Lg17_02049_MAF50_10410_exon1RosBREEDSNP_SNP_AG_3543730_Lg17_02049_MAF50_10410_exon1genetic_marker
RosBREEDSNP_SNP_AG_35490042_Lg2_00267_MAF50_MDP0000189931_exon3RosBREEDSNP_SNP_AG_35490042_Lg2_00267_MAF50_MDP0000189931_exon3genetic_marker
RosBREEDSNP_SNP_AG_35612232_Lg12_01855_MAF30_1629962_exon5RosBREEDSNP_SNP_AG_35612232_Lg12_01855_MAF30_1629962_exon5genetic_marker
RosBREEDSNP_SNP_AG_35835624_Lg12_MDP0000375826_MAF50_MDP0000375826_exon1RosBREEDSNP_SNP_AG_35835624_Lg12_MDP0000375826_MAF50_MDP0000375826_exon1genetic_marker
RosBREEDSNP_SNP_AG_35850734_Lg11_00795_MAF20_1627584_exon6RosBREEDSNP_SNP_AG_35850734_Lg11_00795_MAF20_1627584_exon6genetic_marker
RosBREEDSNP_SNP_AG_35958135_Lg11_RosCOS372_MAF20_725038_exon1RosBREEDSNP_SNP_AG_35958135_Lg11_RosCOS372_MAF20_725038_exon1genetic_marker
RosBREEDSNP_SNP_AG_36008454_Lg11_RosCOS372_MAF40_1686532_exon1RosBREEDSNP_SNP_AG_36008454_Lg11_RosCOS372_MAF40_1686532_exon1genetic_marker
RosBREEDSNP_SNP_AG_3601270_Lg14_01767_MAF50_1619222_exon11RosBREEDSNP_SNP_AG_3601270_Lg14_01767_MAF50_1619222_exon11genetic_marker
RosBREEDSNP_SNP_AG_3603469_Lg15_01047_MAF10_MDP0000283970_exon1RosBREEDSNP_SNP_AG_3603469_Lg15_01047_MAF10_MDP0000283970_exon1genetic_marker
RosBREEDSNP_SNP_AG_36091067_Lg10_RosCOS2135_MAF40_474692_exon1RosBREEDSNP_SNP_AG_36091067_Lg10_RosCOS2135_MAF40_474692_exon1genetic_marker
RosBREEDSNP_SNP_AG_36448217_Lg2_00669_MAF20_1626696_exon1RosBREEDSNP_SNP_AG_36448217_Lg2_00669_MAF20_1626696_exon1genetic_marker
RosBREEDSNP_SNP_AG_36493426_Lg5_00100_MAF10_1654983_exon1RosBREEDSNP_SNP_AG_36493426_Lg5_00100_MAF10_1654983_exon1genetic_marker
RosBREEDSNP_SNP_AG_36508128_Lg5_00100_MAF20_1632791_exon9RosBREEDSNP_SNP_AG_36508128_Lg5_00100_MAF20_1632791_exon9genetic_marker
RosBREEDSNP_SNP_AG_36898184_Lg10_00405_MAF10_MDP0000131371_exon5RosBREEDSNP_SNP_AG_36898184_Lg10_00405_MAF10_MDP0000131371_exon5genetic_marker
RosBREEDSNP_SNP_AG_37110581_Lg3_00664_MAF50_497449_exon2RosBREEDSNP_SNP_AG_37110581_Lg3_00664_MAF50_497449_exon2genetic_marker
RosBREEDSNP_SNP_AG_371869_Lg13_00368_MAF40_577826_exon3RosBREEDSNP_SNP_AG_371869_Lg13_00368_MAF40_577826_exon3genetic_marker
RosBREEDSNP_SNP_AG_3725831_Lg12_00430_MAF40_488031_exon2RosBREEDSNP_SNP_AG_3725831_Lg12_00430_MAF40_488031_exon2genetic_marker
RosBREEDSNP_SNP_AG_3730213_Lg9_00605_MAF50_MDP0000205248_exon4RosBREEDSNP_SNP_AG_3730213_Lg9_00605_MAF50_MDP0000205248_exon4genetic_marker
RosBREEDSNP_SNP_AG_3741785_Lg16_01186_MAF40_529707_exon3RosBREEDSNP_SNP_AG_3741785_Lg16_01186_MAF40_529707_exon3genetic_marker

Pages

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