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_GA_4471268_Lg11_01165_MAF50_MDP0000136407_exon3RosBREEDSNP_SNP_GA_4471268_Lg11_01165_MAF50_MDP0000136407_exon3genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_GA_173_5148102Pear_Bartlett_RosBREEDSNP_SNP_GA_173_5148102genetic_marker
RosBREEDSNP_SNP_CA_4828642_Lg3_00276_MAF10_1650518_exon1RosBREEDSNP_SNP_CA_4828642_Lg3_00276_MAF10_1650518_exon1genetic_marker
RosBREEDSNP_SNP_TG_6555653_Lg11_00621_MAF10_MDP0000568382_exon1RosBREEDSNP_SNP_TG_6555653_Lg11_00621_MAF10_MDP0000568382_exon1genetic_marker
RosBREEDSNP_SNP_CT_6749212_Lg11_01788_MAF10_1680903_exon1RosBREEDSNP_SNP_CT_6749212_Lg11_01788_MAF10_1680903_exon1genetic_marker
RosBREEDSNP_SNP_TC_6507628_Lg11_00621_MAF50_529455_exon1RosBREEDSNP_SNP_TC_6507628_Lg11_00621_MAF50_529455_exon1genetic_marker
RosBREEDSNP_SNP_AG_6697510_Lg11_01788_MAF30_1668595_exon1RosBREEDSNP_SNP_AG_6697510_Lg11_01788_MAF30_1668595_exon1genetic_marker
GDsnp01921GDsnp01921genetic_marker
RosBREEDSNP_SNP_TG_6690536_Lg11_01788_MAF30_339902_exon2RosBREEDSNP_SNP_TG_6690536_Lg11_01788_MAF30_339902_exon2genetic_marker
GDsnp01483GDsnp01483genetic_marker
RosBREEDSNP_SNP_CT_11790983_Lg2_00614_MAF10_247328_exon1RosBREEDSNP_SNP_CT_11790983_Lg2_00614_MAF10_247328_exon1genetic_marker
GDsnp00185GDsnp00185genetic_marker
RosBREEDSNP_SNP_AG_8451493_Lg11_00185_MAF50_1646131_exon1RosBREEDSNP_SNP_AG_8451493_Lg11_00185_MAF50_1646131_exon1genetic_marker
RosBREEDSNP_SNP_AG_14065734_Lg10_ERS1_MAF30_1641299_exon1RosBREEDSNP_SNP_AG_14065734_Lg10_ERS1_MAF30_1641299_exon1genetic_marker
RosBREEDSNP_SNP_AG_10421935_Lg1_RosCOS3195_MAF20_411069_exon1RosBREEDSNP_SNP_AG_10421935_Lg1_RosCOS3195_MAF20_411069_exon1genetic_marker
RosBREEDSNP_SNP_TC_9976495_Lg11_RosCOS3333_MAF20_1653958_exon1RosBREEDSNP_SNP_TC_9976495_Lg11_RosCOS3333_MAF20_1653958_exon1genetic_marker
RosBREEDSNP_SNP_CT_9957437_Lg3_01990_MAF20_372091_exon1RosBREEDSNP_SNP_CT_9957437_Lg3_01990_MAF20_372091_exon1genetic_marker
RosBREEDSNP_SNP_GA_10602307_Lg11_00254_MAF10_MDP0000591409_exon1RosBREEDSNP_SNP_GA_10602307_Lg11_00254_MAF10_MDP0000591409_exon1genetic_marker
RosBREEDSNP_SNP_GT_11567504_Lg11_02309_MAF40_915969_exon1RosBREEDSNP_SNP_GT_11567504_Lg11_02309_MAF40_915969_exon1genetic_marker
RosBREEDSNP_SNP_CT_11585696_Lg11_02309_MAF30_1668440_exon2RosBREEDSNP_SNP_CT_11585696_Lg11_02309_MAF30_1668440_exon2genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_CT_401_5133492Pear_Bartlett_RosBREEDSNP_SNP_CT_401_5133492genetic_marker
RosBREEDSNP_SNP_CT_13676595_Lg11_RosCOS2909_MAF40_1653132_exon3RosBREEDSNP_SNP_CT_13676595_Lg11_RosCOS2909_MAF40_1653132_exon3genetic_marker
RosBREEDSNP_SNP_TC_26252739_Lg13_02452_MAF30_MDP0000212353_exon6RosBREEDSNP_SNP_TC_26252739_Lg13_02452_MAF30_MDP0000212353_exon6genetic_marker
RosBREEDSNP_SNP_TC_26256422_Lg13_02452_MAF20_MDP0000212353_exon3RosBREEDSNP_SNP_TC_26256422_Lg13_02452_MAF20_MDP0000212353_exon3genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_TC_242_5090421Pear_Bartlett_RosBREEDSNP_SNP_TC_242_5090421genetic_marker

Pages

Featuremaps
This publication contains information about 2 maps:
Map Name
Apple-M432-2013
Apple-M432-2013-physical-Malus-domestica