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_GT_29342518_Lg3_02463_MAF50_MDP0000798662_exon2RosBREEDSNP_SNP_GT_29342518_Lg3_02463_MAF50_MDP0000798662_exon2genetic_marker
RosBREEDSNP_SNP_GT_29441767_Lg14_01811_MAF20_107955_exon1RosBREEDSNP_SNP_GT_29441767_Lg14_01811_MAF20_107955_exon1genetic_marker
RosBREEDSNP_SNP_GT_29809045_Lg11_00662_MAF20_1633056_exon3RosBREEDSNP_SNP_GT_29809045_Lg11_00662_MAF20_1633056_exon3genetic_marker
RosBREEDSNP_SNP_GT_36335353_Lg2_01322_MAF30_MDP0000707672_exon3RosBREEDSNP_SNP_GT_36335353_Lg2_01322_MAF30_MDP0000707672_exon3genetic_marker
RosBREEDSNP_SNP_GT_4015212_Lg2_01476_MAF20_795360_exon1RosBREEDSNP_SNP_GT_4015212_Lg2_01476_MAF20_795360_exon1genetic_marker
RosBREEDSNP_SNP_GT_4854431_Lg2_RosCOS3565_MAF10_MDP0000222804_exon4RosBREEDSNP_SNP_GT_4854431_Lg2_RosCOS3565_MAF10_MDP0000222804_exon4genetic_marker
RosBREEDSNP_SNP_GT_4959350_Lg15_RosCOS2117_MAF30_776823_exon1RosBREEDSNP_SNP_GT_4959350_Lg15_RosCOS2117_MAF30_776823_exon1genetic_marker
RosBREEDSNP_SNP_GT_6130026_Lg14_02706_MAF30_1663732_exon1RosBREEDSNP_SNP_GT_6130026_Lg14_02706_MAF30_1663732_exon1genetic_marker
RosBREEDSNP_SNP_GT_706809_Lg14_01902_MAF20_MDP0000136426_exon3RosBREEDSNP_SNP_GT_706809_Lg14_01902_MAF20_MDP0000136426_exon3genetic_marker
RosBREEDSNP_SNP_GT_8977648_Lg2_00407_MAF50_1662497_exon2RosBREEDSNP_SNP_GT_8977648_Lg2_00407_MAF50_1662497_exon2genetic_marker
RosBREEDSNP_SNP_TC_11173563_Lg9_00947_MAF20_7234_exon1RosBREEDSNP_SNP_TC_11173563_Lg9_00947_MAF20_7234_exon1genetic_marker
RosBREEDSNP_SNP_TC_11509973_Lg2_01005_MAF30_504806_exon3RosBREEDSNP_SNP_TC_11509973_Lg2_01005_MAF30_504806_exon3genetic_marker
RosBREEDSNP_SNP_TC_11991962_Lg6_01366_MAF40_1642277_exon2RosBREEDSNP_SNP_TC_11991962_Lg6_01366_MAF40_1642277_exon2genetic_marker
RosBREEDSNP_SNP_TC_1215786_Lg12_RosCOS3293_MAF40_404415_exon1RosBREEDSNP_SNP_TC_1215786_Lg12_RosCOS3293_MAF40_404415_exon1genetic_marker
RosBREEDSNP_SNP_TC_12849756_Lg9_00331_MAF20_267702_exon1RosBREEDSNP_SNP_TC_12849756_Lg9_00331_MAF20_267702_exon1genetic_marker
RosBREEDSNP_SNP_TC_13038857_Lg10_RosCOS724_MAF40_MDP0000688434_exon2RosBREEDSNP_SNP_TC_13038857_Lg10_RosCOS724_MAF40_MDP0000688434_exon2genetic_marker
RosBREEDSNP_SNP_TC_14006533_Lg1_01889_MAF20_MDP0000263325_exon3RosBREEDSNP_SNP_TC_14006533_Lg1_01889_MAF20_MDP0000263325_exon3genetic_marker
RosBREEDSNP_SNP_TC_1451208_Lg15_MDP0000227096_MAF50_MDP0000227096_exon6RosBREEDSNP_SNP_TC_1451208_Lg15_MDP0000227096_MAF50_MDP0000227096_exon6genetic_marker
RosBREEDSNP_SNP_TC_16628559_Lg1_02538_MAF40_MDP0000495165_exon1RosBREEDSNP_SNP_TC_16628559_Lg1_02538_MAF40_MDP0000495165_exon1genetic_marker
RosBREEDSNP_SNP_TC_1741931_Lg3_EB140229_MAF40_MDP0000190972_exon3RosBREEDSNP_SNP_TC_1741931_Lg3_EB140229_MAF40_MDP0000190972_exon3genetic_marker
RosBREEDSNP_SNP_TC_18855907_Lg4_00324_MAF50_1671602_exon1RosBREEDSNP_SNP_TC_18855907_Lg4_00324_MAF50_1671602_exon1genetic_marker
RosBREEDSNP_SNP_TC_19307229_Lg12_01357_MAF50_MDP0000159673_exon2RosBREEDSNP_SNP_TC_19307229_Lg12_01357_MAF50_MDP0000159673_exon2genetic_marker
RosBREEDSNP_SNP_TC_1993488_Lg9_01573_MAF30_MDP0000231545_exon1RosBREEDSNP_SNP_TC_1993488_Lg9_01573_MAF30_MDP0000231545_exon1genetic_marker
RosBREEDSNP_SNP_TC_20670206_Lg2_RosCOS358_MAF20_MDP0000185281_exon4RosBREEDSNP_SNP_TC_20670206_Lg2_RosCOS358_MAF20_MDP0000185281_exon4genetic_marker
RosBREEDSNP_SNP_TC_2260844_Lg7_01946_MAF10_684526_exon1RosBREEDSNP_SNP_TC_2260844_Lg7_01946_MAF10_684526_exon1genetic_marker

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