Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin

Publication Overview
TitleEvaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin
AuthorsTroggio M, Surbanovski N, Bianco L, Moretto M, Giongo L, Banchi E, Viola R, Fernández FF, Costa F, Velasco R, Cestaro A, Sargent DJ
TypeJournal Article
Journal NamePloS one
Volume8
Issue6
Year2013
Page(s)e67407
CitationTroggio M, Surbanovski N, Bianco L, Moretto M, Giongo L, Banchi E, Viola R, Fernández FF, Costa F, Velasco R, Cestaro A, Sargent DJ. Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin. PloS one. 2013; 8(6):e67407.

Abstract

High throughput arrays for the simultaneous genotyping of thousands of single-nucleotide polymorphisms (SNPs) have made the rapid genetic characterisation of plant genomes and the development of saturated linkage maps a realistic prospect for many plant species of agronomic importance. However, the correct calling of SNP genotypes in divergent polyploid genomes using array technology can be problematic due to paralogy, and to divergence in probe sequences causing changes in probe binding efficiencies. An Illumina Infinium II whole-genome genotyping array was recently developed for the cultivated apple and used to develop a molecular linkage map for an apple rootstock progeny (M432), but a large proportion of segregating SNPs were not mapped in the progeny, due to unexpected genotype clustering patterns. To investigate the causes of this unexpected clustering we performed BLAST analysis of all probe sequences against the 'Golden Delicious' genome sequence and discovered evidence for paralogous annealing sites and probe sequence divergence for a high proportion of probes contained on the array. Following visual re-evaluation of the genotyping data generated for 8,788 SNPs for the M432 progeny using the array, we manually re-scored genotypes at 818 loci and mapped a further 797 markers to the M432 linkage map. The newly mapped markers included the majority of those that could not be mapped previously, as well as loci that were previously scored as monomorphic, but which segregated due to divergence leading to heterozygosity in probe annealing sites. An evaluation of the 8,788 probes in a diverse collection of Malus germplasm showed that more than half the probes returned genotype clustering patterns that were difficult or impossible to interpret reliably, highlighting implications for the use of the array in genome-wide association studies.

Features
This publication contains information about 818 features:
Feature NameUniquenameType
RosBREEDSNP_SNP_GT_4854431_Lg2_RosCOS3565_MAF10_MDP0000222804_exon4RosBREEDSNP_SNP_GT_4854431_Lg2_RosCOS3565_MAF10_MDP0000222804_exon4genetic_marker
RosBREEDSNP_SNP_GT_36565723_Lg10_01761_MAF50_MDP0000879133_exon1RosBREEDSNP_SNP_GT_36565723_Lg10_01761_MAF50_MDP0000879133_exon1genetic_marker
RosBREEDSNP_SNP_AG_15349068_Lg3_02546_MAF50_MDP0000454201_exon2RosBREEDSNP_SNP_AG_15349068_Lg3_02546_MAF50_MDP0000454201_exon2genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_CT_461_5136848Pear_Bartlett_RosBREEDSNP_SNP_CT_461_5136848genetic_marker
RosBREEDSNP_SNP_CT_24483289_Lg3_RosCOS430_MAF10_MDP0000425359_exon1RosBREEDSNP_SNP_CT_24483289_Lg3_RosCOS430_MAF10_MDP0000425359_exon1genetic_marker
RosBREEDSNP_SNP_CA_27149833_Lg3_01487_MAF20_MDP0000289672_exon3RosBREEDSNP_SNP_CA_27149833_Lg3_01487_MAF20_MDP0000289672_exon3genetic_marker
RosBREEDSNP_SNP_GT_29342518_Lg3_02463_MAF50_MDP0000798662_exon2RosBREEDSNP_SNP_GT_29342518_Lg3_02463_MAF50_MDP0000798662_exon2genetic_marker
RosBREEDSNP_SNP_CT_29883916_Lg3_01604_MAF40_1685082_exon2RosBREEDSNP_SNP_CT_29883916_Lg3_01604_MAF40_1685082_exon2genetic_marker
RosBREEDSNP_SNP_AG_29943637_Lg3_01937_MAF50_789497_exon1RosBREEDSNP_SNP_AG_29943637_Lg3_01937_MAF50_789497_exon1genetic_marker
RosBREEDSNP_SNP_AC_32704005_Lg3_01329_MAF50_369648_exon1RosBREEDSNP_SNP_AC_32704005_Lg3_01329_MAF50_369648_exon1genetic_marker
RosBREEDSNP_SNP_TC_31098089_Lg3_01779_MAF40_645461_exon2RosBREEDSNP_SNP_TC_31098089_Lg3_01779_MAF40_645461_exon2genetic_marker
RosBREEDSNP_SNP_CT_33672910_Lg3_01014_MAF30_1641420_exon5RosBREEDSNP_SNP_CT_33672910_Lg3_01014_MAF30_1641420_exon5genetic_marker
RosBREEDSNP_SNP_GA_37575211_Lg3_01822_MAF40_MDP0000172036_exon1RosBREEDSNP_SNP_GA_37575211_Lg3_01822_MAF40_MDP0000172036_exon1genetic_marker
RosBREEDSNP_SNP_TC_37585473_Lg3_01822_MAF50_MDP0000247441_exon2RosBREEDSNP_SNP_TC_37585473_Lg3_01822_MAF50_MDP0000247441_exon2genetic_marker
RosBREEDSNP_SNP_TG_33629578_Lg3_01014_MAF20_MDP0000270427_exon2RosBREEDSNP_SNP_TG_33629578_Lg3_01014_MAF20_MDP0000270427_exon2genetic_marker
RosBREEDSNP_SNP_CT_34422352_Lg3_02030_MAF30_MDP0000908766_exon1RosBREEDSNP_SNP_CT_34422352_Lg3_02030_MAF30_MDP0000908766_exon1genetic_marker
RosBREEDSNP_SNP_TC_33291444_Lg3_01667_MAF30_1685466_exon1RosBREEDSNP_SNP_TC_33291444_Lg3_01667_MAF30_1685466_exon1genetic_marker
RosBREEDSNP_SNP_GA_37102564_Lg3_00664_MAF50_795768_exon1RosBREEDSNP_SNP_GA_37102564_Lg3_00664_MAF50_795768_exon1genetic_marker
RosBREEDSNP_SNP_TC_15443131_Lg9_Hi01e10_MAF40_MDP0000624636_exon1RosBREEDSNP_SNP_TC_15443131_Lg9_Hi01e10_MAF40_MDP0000624636_exon1genetic_marker
RosBREEDSNP_SNP_AG_15345285_Lg9_Hi01e10_MAF20_MDP0000229280_exon1RosBREEDSNP_SNP_AG_15345285_Lg9_Hi01e10_MAF20_MDP0000229280_exon1genetic_marker
RosBREEDSNP_SNP_CT_9976748_Lg1_RosCOS404_MAF30_MDP0000188908_exon1RosBREEDSNP_SNP_CT_9976748_Lg1_RosCOS404_MAF30_MDP0000188908_exon1genetic_marker
RosBREEDSNP_SNP_CT_2671029_Lg17_00210_MAF50_MDP0000437795_exon1RosBREEDSNP_SNP_CT_2671029_Lg17_00210_MAF50_MDP0000437795_exon1genetic_marker
RosBREEDSNP_SNP_TG_13048668_Lg10_RosCOS724_MAF30_1638650_exon1RosBREEDSNP_SNP_TG_13048668_Lg10_RosCOS724_MAF30_1638650_exon1genetic_marker
RosBREEDSNP_SNP_TC_7257764_Lg7_snpEB106582_MAF30_485317_exon1RosBREEDSNP_SNP_TC_7257764_Lg7_snpEB106582_MAF30_485317_exon1genetic_marker
RosBREEDSNP_SNP_GT_3881154_Lg4_00966_MAF20_MDP0000183381_exon3RosBREEDSNP_SNP_GT_3881154_Lg4_00966_MAF20_MDP0000183381_exon3genetic_marker

Pages

Featuremaps
This publication contains information about 2 maps:
Map Name
Apple-M432-2013
Apple-M432-2013-physical-Malus-domestica
Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic-Print
ISSN1932-6203
eISSN1932-6203
Publication Date2013
Journal AbbreviationPLoS ONE
LanguageEnglish
Language AbbrENG
Publication TypeJournal Article
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:23826289