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_11268600_Lg8_RosCOS936_MAF40_MDP0000124989_exon2RosBREEDSNP_SNP_GA_11268600_Lg8_RosCOS936_MAF40_MDP0000124989_exon2genetic_marker
RosBREEDSNP_SNP_GA_9698192_Lg8_RosCOS2185_MAF40_MDP0000200579_exon1RosBREEDSNP_SNP_GA_9698192_Lg8_RosCOS2185_MAF40_MDP0000200579_exon1genetic_marker
RosBREEDSNP_SNP_TC_8606832_Lg10_RosCOS1766_MAF30_158573_exon2RosBREEDSNP_SNP_TC_8606832_Lg10_RosCOS1766_MAF30_158573_exon2genetic_marker
RosBREEDSNP_SNP_GT_27677928_Lg5_01601_MAF30_1623480_exon4RosBREEDSNP_SNP_GT_27677928_Lg5_01601_MAF30_1623480_exon4genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_CT_418_5139542Pear_Bartlett_RosBREEDSNP_SNP_CT_418_5139542genetic_marker
RosBREEDSNP_SNP_AC_25884621_Lg5_MDP0000155074_MAF10_MDP0000155074_exon8RosBREEDSNP_SNP_AC_25884621_Lg5_MDP0000155074_MAF10_MDP0000155074_exon8genetic_marker
RosBREEDSNP_SNP_CA_27011691_Lg5_02251_MAF40_1631728_exon2RosBREEDSNP_SNP_CA_27011691_Lg5_02251_MAF40_1631728_exon2genetic_marker
RosBREEDSNP_SNP_TC_14548205_Lg2_00987_MAF20_1687368_exon5RosBREEDSNP_SNP_TC_14548205_Lg2_00987_MAF20_1687368_exon5genetic_marker
RosBREEDSNP_SNP_TC_6905364_Lg17_01927_MAF30_MDP0000301145_exon1RosBREEDSNP_SNP_TC_6905364_Lg17_01927_MAF30_MDP0000301145_exon1genetic_marker
RosBREEDSNP_SNP_TC_27907615_Lg5_01859_MAF40_1663610_exon1RosBREEDSNP_SNP_TC_27907615_Lg5_01859_MAF40_1663610_exon1genetic_marker
RosBREEDSNP_SNP_GA_6022220_Lg5_139135_MAF10_139135_exon1RosBREEDSNP_SNP_GA_6022220_Lg5_139135_MAF10_139135_exon1genetic_marker
RosBREEDSNP_SNP_CT_35001874_Lg13_01899_MAF40_MDP0000667911_exon1RosBREEDSNP_SNP_CT_35001874_Lg13_01899_MAF40_MDP0000667911_exon1genetic_marker
RosBREEDSNP_SNP_GT_15408956_Lg16_02207_MAF20_1681603_exon1RosBREEDSNP_SNP_GT_15408956_Lg16_02207_MAF20_1681603_exon1genetic_marker
RosBREEDSNP_SNP_TG_36495464_Lg5_00100_MAF30_MDP0000217948_exon16RosBREEDSNP_SNP_TG_36495464_Lg5_00100_MAF30_MDP0000217948_exon16genetic_marker
RosBREEDSNP_SNP_GT_36503731_Lg5_00100_MAF10_MDP0000217948_exon33RosBREEDSNP_SNP_GT_36503731_Lg5_00100_MAF10_MDP0000217948_exon33genetic_marker
RosBREEDSNP_SNP_AG_36508128_Lg5_00100_MAF20_1632791_exon9RosBREEDSNP_SNP_AG_36508128_Lg5_00100_MAF20_1632791_exon9genetic_marker
RosBREEDSNP_SNP_CT_36510795_Lg5_00100_MAF20_MDP0000232589_exon4RosBREEDSNP_SNP_CT_36510795_Lg5_00100_MAF20_MDP0000232589_exon4genetic_marker
RosBREEDSNP_SNP_CT_6990147_Lg10_127967_MAF50_127967_exon1RosBREEDSNP_SNP_CT_6990147_Lg10_127967_MAF50_127967_exon1genetic_marker
Pear_Bartlett_RosBREEDSNP_SNP_CA_182_5111327Pear_Bartlett_RosBREEDSNP_SNP_CA_182_5111327genetic_marker
RosBREEDSNP_SNP_AG_36493426_Lg5_00100_MAF10_1654983_exon1RosBREEDSNP_SNP_AG_36493426_Lg5_00100_MAF10_1654983_exon1genetic_marker
RosBREEDSNP_SNP_AC_13750342_Lg5_01505_MAF20_350318_exon3RosBREEDSNP_SNP_AC_13750342_Lg5_01505_MAF20_350318_exon3genetic_marker
RosBREEDSNP_SNP_TC_20176551_Lg6_01831_MAF50_MDP0000218928_exon1RosBREEDSNP_SNP_TC_20176551_Lg6_01831_MAF50_MDP0000218928_exon1genetic_marker
RosBREEDSNP_SNP_TC_11852022_Lg7_4338_MAF40_4338_exon1RosBREEDSNP_SNP_TC_11852022_Lg7_4338_MAF40_4338_exon1genetic_marker
RosBREEDSNP_SNP_TG_11852053_Lg7_4338_MAF20_4338_exon1RosBREEDSNP_SNP_TG_11852053_Lg7_4338_MAF20_4338_exon1genetic_marker
RosBREEDSNP_SNP_TG_11852172_Lg7_85261_MAF40_85261_exon1RosBREEDSNP_SNP_TG_11852172_Lg7_85261_MAF40_85261_exon1genetic_marker

Pages

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