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_CT_4724101_Lg9_RosCOS3253_MAF10_MDP0000291561_exon9RosBREEDSNP_SNP_CT_4724101_Lg9_RosCOS3253_MAF10_MDP0000291561_exon9genetic_marker
RosBREEDSNP_SNP_CT_4924401_Lg15_RosCOS2117_MAF50_MDP0000163464_exon2RosBREEDSNP_SNP_CT_4924401_Lg15_RosCOS2117_MAF50_MDP0000163464_exon2genetic_marker
RosBREEDSNP_SNP_CT_4993274_Lg6_MDP0000075705_MAF10_MDP0000075705_exon1RosBREEDSNP_SNP_CT_4993274_Lg6_MDP0000075705_MAF10_MDP0000075705_exon1genetic_marker
RosBREEDSNP_SNP_CT_54500502_Lg15_01774_MAF20_941405_exon1RosBREEDSNP_SNP_CT_54500502_Lg15_01774_MAF20_941405_exon1genetic_marker
RosBREEDSNP_SNP_CT_5936206_Lg4_02263_MAF30_MDP0000543497_exon1RosBREEDSNP_SNP_CT_5936206_Lg4_02263_MAF30_MDP0000543497_exon1genetic_marker
RosBREEDSNP_SNP_CT_5940163_Lg1_00152_MAF50_1642197_exon1RosBREEDSNP_SNP_CT_5940163_Lg1_00152_MAF50_1642197_exon1genetic_marker
RosBREEDSNP_SNP_CT_6597232_Lg6_RosCOS1869_MAF50_MDP0000739034_exon1RosBREEDSNP_SNP_CT_6597232_Lg6_RosCOS1869_MAF50_MDP0000739034_exon1genetic_marker
RosBREEDSNP_SNP_CT_6742332_Lg2_01549_MAF30_553488_exon3RosBREEDSNP_SNP_CT_6742332_Lg2_01549_MAF30_553488_exon3genetic_marker
RosBREEDSNP_SNP_CT_6947667_Lg17_01927_MAF10_1688280_exon3RosBREEDSNP_SNP_CT_6947667_Lg17_01927_MAF10_1688280_exon3genetic_marker
RosBREEDSNP_SNP_CT_7165677_Lg13_00128_MAF20_1662884_exon1RosBREEDSNP_SNP_CT_7165677_Lg13_00128_MAF20_1662884_exon1genetic_marker
RosBREEDSNP_SNP_CT_741541_Lg14_01902_MAF40_1634998_exon5RosBREEDSNP_SNP_CT_741541_Lg14_01902_MAF40_1634998_exon5genetic_marker
RosBREEDSNP_SNP_CT_7420955_Lg16_RosCOS1166_MAF50_1630221_exon7RosBREEDSNP_SNP_CT_7420955_Lg16_RosCOS1166_MAF50_1630221_exon7genetic_marker
RosBREEDSNP_SNP_CT_7670146_Lg8_MDP0000381531_MAF20_MDP0000381531_exon1RosBREEDSNP_SNP_CT_7670146_Lg8_MDP0000381531_MAF20_MDP0000381531_exon1genetic_marker
RosBREEDSNP_SNP_CT_8429416_Lg8_01550_MAF20_MDP0000306160_exon1RosBREEDSNP_SNP_CT_8429416_Lg8_01550_MAF20_MDP0000306160_exon1genetic_marker
RosBREEDSNP_SNP_CT_8536622_Lg7_01780_MAF20_244415_exon1RosBREEDSNP_SNP_CT_8536622_Lg7_01780_MAF20_244415_exon1genetic_marker
RosBREEDSNP_SNP_CT_856184_Lg10_00106_MAF30_1643657_exon2RosBREEDSNP_SNP_CT_856184_Lg10_00106_MAF30_1643657_exon2genetic_marker
RosBREEDSNP_SNP_CT_8716037_Lg4_02646_MAF20_476635_exon2RosBREEDSNP_SNP_CT_8716037_Lg4_02646_MAF20_476635_exon2genetic_marker
RosBREEDSNP_SNP_CT_9085264_Lg16_01730_MAF50_MDP0000265949_exon17RosBREEDSNP_SNP_CT_9085264_Lg16_01730_MAF50_MDP0000265949_exon17genetic_marker
RosBREEDSNP_SNP_CT_9113098_Lg16_01730_MAF30_112027_exon1RosBREEDSNP_SNP_CT_9113098_Lg16_01730_MAF30_112027_exon1genetic_marker
RosBREEDSNP_SNP_CT_9290123_Lg5_01896_MAF50_139459_exon1RosBREEDSNP_SNP_CT_9290123_Lg5_01896_MAF50_139459_exon1genetic_marker
RosBREEDSNP_SNP_CT_9467430_Lg5_01781_MAF10_1656110_exon1RosBREEDSNP_SNP_CT_9467430_Lg5_01781_MAF10_1656110_exon1genetic_marker
RosBREEDSNP_SNP_GA_12543650_Lg12_MDP0000210506_MAF20_MDP0000210506_exon2RosBREEDSNP_SNP_GA_12543650_Lg12_MDP0000210506_MAF20_MDP0000210506_exon2genetic_marker
RosBREEDSNP_SNP_GA_1310741_Lg10_RosCOS2296_MAF40_1645757_exon1RosBREEDSNP_SNP_GA_1310741_Lg10_RosCOS2296_MAF40_1645757_exon1genetic_marker
RosBREEDSNP_SNP_GA_1316702_Lg8_00487_MAF30_MDP0000392194_exon1RosBREEDSNP_SNP_GA_1316702_Lg8_00487_MAF30_MDP0000392194_exon1genetic_marker
RosBREEDSNP_SNP_GA_14445035_Lg3_01124_MAF50_530134_exon1RosBREEDSNP_SNP_GA_14445035_Lg3_01124_MAF50_530134_exon1genetic_marker

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