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_AC_34196762_Lg11_02910_MAF30_MDP0000718803_exon2RosBREEDSNP_SNP_AC_34196762_Lg11_02910_MAF30_MDP0000718803_exon2genetic_marker
RosBREEDSNP_SNP_AG_13793112_Lg10_snpEG631376_MAF30_MDP0000252318_exon4RosBREEDSNP_SNP_AG_13793112_Lg10_snpEG631376_MAF30_MDP0000252318_exon4genetic_marker
RosBREEDSNP_SNP_TC_14692206_Lg10_01267_MAF50_MDP0000639673_exon3RosBREEDSNP_SNP_TC_14692206_Lg10_01267_MAF50_MDP0000639673_exon3genetic_marker
GDsnp01710GDsnp01710genetic_marker
RosBREEDSNP_SNP_CT_34251015_Lg1_01678_MAF30_MDP0000189607_exon2RosBREEDSNP_SNP_CT_34251015_Lg1_01678_MAF30_MDP0000189607_exon2genetic_marker
RosBREEDSNP_SNP_CA_18510791_Lg10_01832_MAF30_1622972_exon5RosBREEDSNP_SNP_CA_18510791_Lg10_01832_MAF30_1622972_exon5genetic_marker
RosBREEDSNP_SNP_CA_20822717_Lg10_PG_MAF30_1667167_exon2RosBREEDSNP_SNP_CA_20822717_Lg10_PG_MAF30_1667167_exon2genetic_marker
RosBREEDSNP_SNP_AG_36033314_Lg10_186429_MAF40_186429_exon1RosBREEDSNP_SNP_AG_36033314_Lg10_186429_MAF40_186429_exon1genetic_marker
GDsnp00346GDsnp00346genetic_marker
RosBREEDSNP_SNP_CT_6795870_Lg5_00238_MAF30_1682361_exon4RosBREEDSNP_SNP_CT_6795870_Lg5_00238_MAF30_1682361_exon4genetic_marker
RosBREEDSNP_SNP_GA_30214912_Lg10_00734_MAF20_1651709_exon1RosBREEDSNP_SNP_GA_30214912_Lg10_00734_MAF20_1651709_exon1genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_GA_283_5101708Pear_Bartlett_RosBREEDSNP_SNP_GA_283_5101708genetic_marker
RosBREEDSNP_SNP_TC_13051232_Lg10_RosCOS724_MAF10_806797_exon1RosBREEDSNP_SNP_TC_13051232_Lg10_RosCOS724_MAF10_806797_exon1genetic_marker
RosBREEDSNP_SNP_AC_34958317_Lg10_00258_MAF20_MDP0000125820_exon3RosBREEDSNP_SNP_AC_34958317_Lg10_00258_MAF20_MDP0000125820_exon3genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_CA_491_5113807Pear_Bartlett_RosBREEDSNP_SNP_CA_491_5113807genetic_marker
RosBREEDSNP_SNP_CT_2409387_Lg5_02457_MAF40_1665658_exon2RosBREEDSNP_SNP_CT_2409387_Lg5_02457_MAF40_1665658_exon2genetic_marker
RosBREEDSNP_SNP_TC_27687938_Lg3_00607_MAF30_605396_exon1RosBREEDSNP_SNP_TC_27687938_Lg3_00607_MAF30_605396_exon1genetic_marker
RosBREEDSNP_SNP_GA_27691074_Lg3_00607_MAF50_380398_exon1RosBREEDSNP_SNP_GA_27691074_Lg3_00607_MAF50_380398_exon1genetic_marker
RosBREEDSNP_SNP_CA_480323_Lg11_01480_MAF40_1652429_exon1RosBREEDSNP_SNP_CA_480323_Lg11_01480_MAF40_1652429_exon1genetic_marker
RosBREEDSNP_SNP_GT_30978430_Lg15_RosCOS444_MAF10_MDP0000263390_exon6RosBREEDSNP_SNP_GT_30978430_Lg15_RosCOS444_MAF10_MDP0000263390_exon6genetic_marker
RosBREEDSNP_SNP_GT_30914007_Lg15_RosCOS444_MAF30_MDP0000611785_exon1RosBREEDSNP_SNP_GT_30914007_Lg15_RosCOS444_MAF30_MDP0000611785_exon1genetic_marker
RosBREEDSNP_SNP_TC_28678775_Lg15_02592_MAF20_MDP0000161195_exon1RosBREEDSNP_SNP_TC_28678775_Lg15_02592_MAF20_MDP0000161195_exon1genetic_marker
RosBREEDSNP_SNP_GA_3433852_Lg11_01167_MAF40_42738_exon1RosBREEDSNP_SNP_GA_3433852_Lg11_01167_MAF40_42738_exon1genetic_marker
RosBREEDSNP_SNP_AG_3436048_Lg11_01167_MAF10_476534_exon1RosBREEDSNP_SNP_AG_3436048_Lg11_01167_MAF10_476534_exon1genetic_marker
RosBREEDSNP_SNP_CT_16990033_Lg9_01648_MAF10_MDP0000222742_exon1RosBREEDSNP_SNP_CT_16990033_Lg9_01648_MAF10_MDP0000222742_exon1genetic_marker

Pages

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