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_36587120_Lg10_01761_MAF40_274852_exon1RosBREEDSNP_SNP_TC_36587120_Lg10_01761_MAF40_274852_exon1genetic_marker
RosBREEDSNP_SNP_GT_5292763_Lg6_RosCOS1410_MAF10_MDP0000794927_exon1RosBREEDSNP_SNP_GT_5292763_Lg6_RosCOS1410_MAF10_MDP0000794927_exon1genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_GA_303_5112755Pear_Bartlett_RosBREEDSNP_SNP_GA_303_5112755genetic_marker
RosBREEDSNP_SNP_TC_16551314_Lg8_02022_MAF30_MDP0000568367_exon1RosBREEDSNP_SNP_TC_16551314_Lg8_02022_MAF30_MDP0000568367_exon1genetic_marker
RosBREEDSNP_SNP_TC_16650610_Lg8_01768_MAF50_MDP0000377353_exon2RosBREEDSNP_SNP_TC_16650610_Lg8_01768_MAF50_MDP0000377353_exon2genetic_marker
RosBREEDSNP_SNP_CT_17374441_Lg8_01370_MAF40_MDP0000395942_exon5RosBREEDSNP_SNP_CT_17374441_Lg8_01370_MAF40_MDP0000395942_exon5genetic_marker
RosBREEDSNP_SNP_GA_17359704_Lg8_01370_MAF50_MDP0000284300_exon4RosBREEDSNP_SNP_GA_17359704_Lg8_01370_MAF50_MDP0000284300_exon4genetic_marker
RosBREEDSNP_SNP_AG_13058388_Lg10_RosCOS724_MAF50_MDP0000598951_exon1RosBREEDSNP_SNP_AG_13058388_Lg10_RosCOS724_MAF50_MDP0000598951_exon1genetic_marker
RosBREEDSNP_SNP_GA_19611947_Lg8_00862_MAF20_522521_exon1RosBREEDSNP_SNP_GA_19611947_Lg8_00862_MAF20_522521_exon1genetic_marker
RosBREEDSNP_SNP_GA_25196746_Lg8_01598_MAF50_526504_exon4RosBREEDSNP_SNP_GA_25196746_Lg8_01598_MAF50_526504_exon4genetic_marker
RosBREEDSNP_SNP_GA_22580590_Lg8_01479_MAF50_MDP0000308808_exon1RosBREEDSNP_SNP_GA_22580590_Lg8_01479_MAF50_MDP0000308808_exon1genetic_marker
GDsnp00311GDsnp00311genetic_marker
RosBREEDSNP_SNP_AG_28378785_Lg12_12122_MAF40_12122_exon1RosBREEDSNP_SNP_AG_28378785_Lg12_12122_MAF40_12122_exon1genetic_marker
RosBREEDSNP_SNP_TC_25194345_Lg8_01598_MAF20_521738_exon1RosBREEDSNP_SNP_TC_25194345_Lg8_01598_MAF20_521738_exon1genetic_marker
GDsnp01598GDsnp01598genetic_marker
RosBREEDSNP_SNP_GA_22216481_Lg8_01148_MAF20_MDP0000228182_exon3RosBREEDSNP_SNP_GA_22216481_Lg8_01148_MAF20_MDP0000228182_exon3genetic_marker
RosBREEDSNP_SNP_CT_23774839_Lg8_00157_MAF30_108043_exon1RosBREEDSNP_SNP_CT_23774839_Lg8_00157_MAF30_108043_exon1genetic_marker
RosBREEDSNP_SNP_AG_28743645_Lg12_RosCOS3117_MAF40_MDP0000542342_exon1RosBREEDSNP_SNP_AG_28743645_Lg12_RosCOS3117_MAF40_MDP0000542342_exon1genetic_marker
RosBREEDSNP_SNP_AG_28774744_Lg12_RosCOS3117_MAF30_1648278_exon2RosBREEDSNP_SNP_AG_28774744_Lg12_RosCOS3117_MAF30_1648278_exon2genetic_marker
RosBREEDSNP_SNP_AC_22460510_Lg7_71073__71073_exon1RosBREEDSNP_SNP_AC_22460510_Lg7_71073__71073_exon1genetic_marker
RosBREEDSNP_SNP_CT_22222367_Lg8_01148_MAF20_MDP0000296798_exon10RosBREEDSNP_SNP_CT_22222367_Lg8_01148_MAF20_MDP0000296798_exon10genetic_marker
RosBREEDSNP_SNP_CT_22460297_Lg7_71073_MAF20_71073_exon1RosBREEDSNP_SNP_CT_22460297_Lg7_71073_MAF20_71073_exon1genetic_marker
RosBREEDSNP_SNP_GA_25477462_Lg13_00164_MAF30_MDP0000728942_exon1RosBREEDSNP_SNP_GA_25477462_Lg13_00164_MAF30_MDP0000728942_exon1genetic_marker
RosBREEDSNP_SNP_GA_44311702_Lg15_01687_MAF30_1685405_exon1RosBREEDSNP_SNP_GA_44311702_Lg15_01687_MAF30_1685405_exon1genetic_marker
RosBREEDSNP_SNP_TC_16628559_Lg1_02538_MAF40_MDP0000495165_exon1RosBREEDSNP_SNP_TC_16628559_Lg1_02538_MAF40_MDP0000495165_exon1genetic_marker

Pages

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