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_TC_1682643_Lg3_EB140229_MAF30_145018_exon1RosBREEDSNP_SNP_TC_1682643_Lg3_EB140229_MAF30_145018_exon1genetic_marker
RosBREEDSNP_SNP_GA_1636499_Lg3_EH034548_MAF10_MDP0000448299_exon2RosBREEDSNP_SNP_GA_1636499_Lg3_EH034548_MAF10_MDP0000448299_exon2genetic_marker
RosBREEDSNP_SNP_CT_1611891_Lg3_EH034548_MAF30_1687561_exon1RosBREEDSNP_SNP_CT_1611891_Lg3_EH034548_MAF30_1687561_exon1genetic_marker
RosBREEDSNP_SNP_CT_2449342_Lg3_RosCOS1398_MAF20_MDP0000188698_exon9RosBREEDSNP_SNP_CT_2449342_Lg3_RosCOS1398_MAF20_MDP0000188698_exon9genetic_marker
RosBREEDSNP_SNP_AC_2646455_Lg3_02300_MAF40_1630359_exon1RosBREEDSNP_SNP_AC_2646455_Lg3_02300_MAF40_1630359_exon1genetic_marker
RosBREEDSNP_SNP_CT_23845634_Lg11_10010_MAF10_MDP0000268864_exon1RosBREEDSNP_SNP_CT_23845634_Lg11_10010_MAF10_MDP0000268864_exon1genetic_marker
RosBREEDSNP_SNP_CA_2618360_Lg3_02300_MAF20_428644_exon2RosBREEDSNP_SNP_CA_2618360_Lg3_02300_MAF20_428644_exon2genetic_marker
RosBREEDSNP_SNP_CT_18477507_Lg3_00955_MAF10_MDP0000225878_exon1RosBREEDSNP_SNP_CT_18477507_Lg3_00955_MAF10_MDP0000225878_exon1genetic_marker
RosBREEDSNP_SNP_TC_17886905_Lg1_00440_MAF20_MDP0000319069_exon4RosBREEDSNP_SNP_TC_17886905_Lg1_00440_MAF20_MDP0000319069_exon4genetic_marker
RosBREEDSNP_SNP_GA_2615242_Lg3_02300_MAF30_368029_exon1RosBREEDSNP_SNP_GA_2615242_Lg3_02300_MAF30_368029_exon1genetic_marker
RosBREEDSNP_SNP_AG_2627039_Lg3_02300_MAF20_MDP0000206447_exon4RosBREEDSNP_SNP_AG_2627039_Lg3_02300_MAF20_MDP0000206447_exon4genetic_marker
RosBREEDSNP_SNP_AG_5194078_Lg3_01957_MAF30_502326_exon1RosBREEDSNP_SNP_AG_5194078_Lg3_01957_MAF30_502326_exon1genetic_marker
RosBREEDSNP_SNP_AC_5035350_Lg11_RosCOS2981_MAF30_343989_exon1RosBREEDSNP_SNP_AC_5035350_Lg11_RosCOS2981_MAF30_343989_exon1genetic_marker
RosBREEDSNP_SNP_CT_5945674_Lg11_MDP0000163230_MAF30_MDP0000163230_exon2RosBREEDSNP_SNP_CT_5945674_Lg11_MDP0000163230_MAF30_MDP0000163230_exon2genetic_marker
RosBREEDSNP_SNP_CT_5939110_Lg3_01263_MAF10_MDP0000319303_exon11RosBREEDSNP_SNP_CT_5939110_Lg3_01263_MAF10_MDP0000319303_exon11genetic_marker
RosBREEDSNP_SNP_CT_7138274_Lg3_01493_MAF10_MDP0000137959_exon3RosBREEDSNP_SNP_CT_7138274_Lg3_01493_MAF10_MDP0000137959_exon3genetic_marker
RosBREEDSNP_SNP_TC_6563127_Lg3_01921_MAF20_1676724_exon4RosBREEDSNP_SNP_TC_6563127_Lg3_01921_MAF20_1676724_exon4genetic_marker
RosBREEDSNP_SNP_AC_40130375_Lg2_02535_MAF50_MDP0000389749_exon1RosBREEDSNP_SNP_AC_40130375_Lg2_02535_MAF50_MDP0000389749_exon1genetic_marker
RosBREEDSNP_SNP_CT_9499478_Lg3_02195_MAF40_256975_exon2RosBREEDSNP_SNP_CT_9499478_Lg3_02195_MAF40_256975_exon2genetic_marker
RosBREEDSNP_SNP_TC_25729269_Lg1_00087_MAF10_MDP0000374392_exon1RosBREEDSNP_SNP_TC_25729269_Lg1_00087_MAF10_MDP0000374392_exon1genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_AC_231_5149441Pear_Bartlett_RosBREEDSNP_SNP_AC_231_5149441genetic_marker
RosBREEDSNP_SNP_AC_10674505_Lg3_00874_MAF10_1678678_exon2RosBREEDSNP_SNP_AC_10674505_Lg3_00874_MAF10_1678678_exon2genetic_marker
RosBREEDSNP_SNP_AG_11529315_Lg3_02220_MAF30_MDP0000370572_exon5RosBREEDSNP_SNP_AG_11529315_Lg3_02220_MAF30_MDP0000370572_exon5genetic_marker
RosBREEDSNP_SNP_TC_11533385_Lg3_02220_MAF30_10439_exon1RosBREEDSNP_SNP_TC_11533385_Lg3_02220_MAF30_10439_exon1genetic_marker
RosBREEDSNP_SNP_GA_14489555_Lg3_01124_MAF20_MDP0000452675_exon1RosBREEDSNP_SNP_GA_14489555_Lg3_01124_MAF20_MDP0000452675_exon1genetic_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