Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)

Publication Overview
TitleDevelopment and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)
AuthorsBianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen J, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M
TypeJournal Article
Journal NamePloS one
Volume9
Issue10
Year2014
Page(s)e110377
CitationBianco L, Cestaro A, Sargent DJ, Banchi E, Derdak S, Di Guardo M, Salvi S, Jansen J, Viola R, Gut I, Laurens F, Chagné D, Velasco R, van de Weg E, Troggio M. Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh). PloS one. 2014; 9(10):e110377.

Abstract

High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

Features
This publication contains information about 18,019 features:
Feature NameUniquenameType
RosBREEDSNP_SNP_CT_51280174_Lg15_00236_MAF10_602999_exon1RosBREEDSNP_SNP_CT_51280174_Lg15_00236_MAF10_602999_exon1genetic_marker
GDsnp00626GDsnp00626genetic_marker
GDsnp01186GDsnp01186genetic_marker
GDsnp01715GDsnp01715genetic_marker
GDsnp02207GDsnp02207genetic_marker
RosBREEDSNP_SNP_AC_18500686_Lg16_134900__134900_exon3RosBREEDSNP_SNP_AC_18500686_Lg16_134900__134900_exon3genetic_marker
RosBREEDSNP_SNP_CT_5434935_Lg16_00030_MAF40_1618450_exon11RosBREEDSNP_SNP_CT_5434935_Lg16_00030_MAF40_1618450_exon11genetic_marker
RosBREEDSNP_SNP_CT_5601568_Lg16_SquamosaTF_MAF50_1632712_exon1RosBREEDSNP_SNP_CT_5601568_Lg16_SquamosaTF_MAF50_1632712_exon1genetic_marker
RosBREEDSNP_SNP_GA_15461670_Lg16_02207_MAF10_1624116_exon5RosBREEDSNP_SNP_GA_15461670_Lg16_02207_MAF10_1624116_exon5genetic_marker
RosBREEDSNP_SNP_GA_3978947_Lg16_01179_MAF10_MDP0000589715_exon4RosBREEDSNP_SNP_GA_3978947_Lg16_01179_MAF10_MDP0000589715_exon4genetic_marker
RosBREEDSNP_SNP_GA_5652449_Lg16_SquamosaTF_MAF30_1653768_exon1RosBREEDSNP_SNP_GA_5652449_Lg16_SquamosaTF_MAF30_1653768_exon1genetic_marker
RosBREEDSNP_SNP_GA_5655538_Lg16_SquamosaTF_MAF20_MDP0000182386_exon3RosBREEDSNP_SNP_GA_5655538_Lg16_SquamosaTF_MAF20_MDP0000182386_exon3genetic_marker
RosBREEDSNP_SNP_GT_18500461_Lg16_134900_MAF10_134900_exon3RosBREEDSNP_SNP_GT_18500461_Lg16_134900_MAF10_134900_exon3genetic_marker
RosBREEDSNP_SNP_GT_5603911_Lg16_SquamosaTF_MAF40_MDP0000319890_exon3RosBREEDSNP_SNP_GT_5603911_Lg16_SquamosaTF_MAF40_MDP0000319890_exon3genetic_marker
RosBREEDSNP_SNP_TC_14053916_Lg16_117494_MAF20_117494_exon3RosBREEDSNP_SNP_TC_14053916_Lg16_117494_MAF20_117494_exon3genetic_marker
RosBREEDSNP_SNP_CT_6021220_Lg16_01003_MAF20_1631279_exon2RosBREEDSNP_SNP_CT_6021220_Lg16_01003_MAF20_1631279_exon2genetic_marker
RosBREEDSNP_SNP_TC_15467926_Lg16_02207_MAF50_MDP0000155786_exon2RosBREEDSNP_SNP_TC_15467926_Lg16_02207_MAF50_MDP0000155786_exon2genetic_marker
RosBREEDSNP_SNP_TG_14113138_Lg16_01624_MAF50_MDP0000280459_exon2RosBREEDSNP_SNP_TG_14113138_Lg16_01624_MAF50_MDP0000280459_exon2genetic_marker
RosBREEDSNP_SNP_CT_5665967_Lg16_SquamosaTF_MAF40_765776_exon1RosBREEDSNP_SNP_CT_5665967_Lg16_SquamosaTF_MAF40_765776_exon1genetic_marker
RosBREEDSNP_SNP_CA_21262086_Lg17_00423_MAF50_MDP0000218450_exon3RosBREEDSNP_SNP_CA_21262086_Lg17_00423_MAF50_MDP0000218450_exon3genetic_marker
RosBREEDSNP_SNP_CT_26729916_Lg17_snpEB140474_MAF50_MDP0000754706_exon2RosBREEDSNP_SNP_CT_26729916_Lg17_snpEB140474_MAF50_MDP0000754706_exon2genetic_marker
RosBREEDSNP_SNP_GA_772407_Lg17_RosCOS659_MAF20_1675105_exon1RosBREEDSNP_SNP_GA_772407_Lg17_RosCOS659_MAF20_1675105_exon1genetic_marker
RosBREEDSNP_SNP_GT_12671458_Lg17_01904_MAF10_1684596_exon3RosBREEDSNP_SNP_GT_12671458_Lg17_01904_MAF10_1684596_exon3genetic_marker
RosBREEDSNP_SNP_TC_5737459_Lg17_00606_MAF20_896868_exon1RosBREEDSNP_SNP_TC_5737459_Lg17_00606_MAF20_896868_exon1genetic_marker
RosBREEDSNP_SNP_GA_1149469_Lg17_01241_MAF40_MDP0000131695_exon12RosBREEDSNP_SNP_GA_1149469_Lg17_01241_MAF40_MDP0000131695_exon12genetic_marker

Pages