Genome-wide SNP detection, validation, and development of an 8K SNP array for apple.

Publication Overview
TitleGenome-wide SNP detection, validation, and development of an 8K SNP array for apple
AuthorsChagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C
TypeJournal Article
Journal NamePloS one
Volume7
Issue2
Year2012
Page(s)e31745
CitationChagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PloS one. 2012; 7(2):e31745.

Abstract

As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of 'Golden Delicious', SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.

Features
This publication contains information about 456 features:
Feature NameUniquenameType
RosBREEDSNP_SNP_AC_35393262_Lg12_01793_MAF40_MDP0000288367_exon4RosBREEDSNP_SNP_AC_35393262_Lg12_01793_MAF40_MDP0000288367_exon4genetic_marker
RosBREEDSNP_SNP_AC_784801_Lg5_00460_MAF20_1670871_exon1RosBREEDSNP_SNP_AC_784801_Lg5_00460_MAF20_1670871_exon1genetic_marker
RosBREEDSNP_SNP_AG_11389245_Lg14_02214_MAF30_MDP0000172694_exon1RosBREEDSNP_SNP_AG_11389245_Lg14_02214_MAF30_MDP0000172694_exon1genetic_marker
RosBREEDSNP_SNP_AG_12614663_Lg17_01904_MAF10_1685619_exon6RosBREEDSNP_SNP_AG_12614663_Lg17_01904_MAF10_1685619_exon6genetic_marker
RosBREEDSNP_SNP_AG_1633077_Lg16_01734_MAF50_1642541_exon2RosBREEDSNP_SNP_AG_1633077_Lg16_01734_MAF50_1642541_exon2genetic_marker
RosBREEDSNP_SNP_AG_17041443_Lg9_01648_MAF30_MDP0000272132_exon3RosBREEDSNP_SNP_AG_17041443_Lg9_01648_MAF30_MDP0000272132_exon3genetic_marker
RosBREEDSNP_SNP_AG_18816224_Lg1_02731_MAF20_834968_exon2RosBREEDSNP_SNP_AG_18816224_Lg1_02731_MAF20_834968_exon2genetic_marker
RosBREEDSNP_SNP_AG_20356248_Lg1_328561_MAF40_328561_exon1RosBREEDSNP_SNP_AG_20356248_Lg1_328561_MAF40_328561_exon1genetic_marker
RosBREEDSNP_SNP_AG_21320047_Lg15_MDP0000677258_MAF50_MDP0000677258_exon1RosBREEDSNP_SNP_AG_21320047_Lg15_MDP0000677258_MAF50_MDP0000677258_exon1genetic_marker
RosBREEDSNP_SNP_AG_21429305_Lg13_119422_MAF20_119422_exon1RosBREEDSNP_SNP_AG_21429305_Lg13_119422_MAF20_119422_exon1genetic_marker
RosBREEDSNP_SNP_AG_21538144_Lg3_261364_MAF30_261364_exon1RosBREEDSNP_SNP_AG_21538144_Lg3_261364_MAF30_261364_exon1genetic_marker
RosBREEDSNP_SNP_AG_2264123_Lg7_01946_MAF30_MDP0000181886_exon4RosBREEDSNP_SNP_AG_2264123_Lg7_01946_MAF30_MDP0000181886_exon4genetic_marker
RosBREEDSNP_SNP_AG_22846134_Lg1_MdExp7_MAF40_1635125_exon1RosBREEDSNP_SNP_AG_22846134_Lg1_MdExp7_MAF40_1635125_exon1genetic_marker
RosBREEDSNP_SNP_AG_23078001_Lg2_RosCOS292_MAF50_MDP0000407787_exon1RosBREEDSNP_SNP_AG_23078001_Lg2_RosCOS292_MAF50_MDP0000407787_exon1genetic_marker
RosBREEDSNP_SNP_AG_24245886_Lg10_RosCOS3104_MAF40_54464_exon1RosBREEDSNP_SNP_AG_24245886_Lg10_RosCOS3104_MAF40_54464_exon1genetic_marker
RosBREEDSNP_SNP_AG_25120947_Lg5_00373_MAF40_25601_exon2RosBREEDSNP_SNP_AG_25120947_Lg5_00373_MAF40_25601_exon2genetic_marker
RosBREEDSNP_SNP_AG_2627039_Lg3_02300_MAF20_MDP0000206447_exon4RosBREEDSNP_SNP_AG_2627039_Lg3_02300_MAF20_MDP0000206447_exon4genetic_marker
RosBREEDSNP_SNP_AG_26743462_Lg1_01228_MAF20_477610_exon1RosBREEDSNP_SNP_AG_26743462_Lg1_01228_MAF20_477610_exon1genetic_marker
RosBREEDSNP_SNP_AG_27286399_Lg2_02271_MAF50_MDP0000291692_exon7RosBREEDSNP_SNP_AG_27286399_Lg2_02271_MAF50_MDP0000291692_exon7genetic_marker
RosBREEDSNP_SNP_AG_27536555_Lg14_00052_MAF40_1639446_exon1RosBREEDSNP_SNP_AG_27536555_Lg14_00052_MAF40_1639446_exon1genetic_marker
RosBREEDSNP_SNP_AG_30481224_Lg14_RosCOS2457_MAF30_122969_exon1RosBREEDSNP_SNP_AG_30481224_Lg14_RosCOS2457_MAF30_122969_exon1genetic_marker
RosBREEDSNP_SNP_AG_31359569_Lg1_327822__327822_exon5RosBREEDSNP_SNP_AG_31359569_Lg1_327822__327822_exon5genetic_marker
RosBREEDSNP_SNP_AG_32112556_Lg2_00022_MAF20_1651674_exon1RosBREEDSNP_SNP_AG_32112556_Lg2_00022_MAF20_1651674_exon1genetic_marker
RosBREEDSNP_SNP_AG_32138210_Lg12_00762_MAF20_1638638_exon5RosBREEDSNP_SNP_AG_32138210_Lg12_00762_MAF20_1638638_exon5genetic_marker
RosBREEDSNP_SNP_AG_32422411_Lg2_327917_MAF30_327917_exon1RosBREEDSNP_SNP_AG_32422411_Lg2_327917_MAF30_327917_exon1genetic_marker

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