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_AG_32467148_Lg12_00362_MAF30_MDP0000200335_exon11RosBREEDSNP_SNP_AG_32467148_Lg12_00362_MAF30_MDP0000200335_exon11genetic_marker
RosBREEDSNP_SNP_AG_32730568_Lg10_RosCOS3231_MAF50_492103_exon1RosBREEDSNP_SNP_AG_32730568_Lg10_RosCOS3231_MAF50_492103_exon1genetic_marker
RosBREEDSNP_SNP_AG_33312296_Lg3_01667_MAF10_MDP0000473430_exon1RosBREEDSNP_SNP_AG_33312296_Lg3_01667_MAF10_MDP0000473430_exon1genetic_marker
RosBREEDSNP_SNP_AG_3458220_Lg15_218648_MAF20_218648_exon1RosBREEDSNP_SNP_AG_3458220_Lg15_218648_MAF20_218648_exon1genetic_marker
RosBREEDSNP_SNP_AG_35438925_Lg1_02092_MAF10_493004_exon1RosBREEDSNP_SNP_AG_35438925_Lg1_02092_MAF10_493004_exon1genetic_marker
RosBREEDSNP_SNP_AG_39497984_Lg2_00167_MAF50_1631668_exon6RosBREEDSNP_SNP_AG_39497984_Lg2_00167_MAF50_1631668_exon6genetic_marker
RosBREEDSNP_SNP_AG_4025888_Lg2_01476_MAF10_203524_exon1RosBREEDSNP_SNP_AG_4025888_Lg2_01476_MAF10_203524_exon1genetic_marker
RosBREEDSNP_SNP_AG_4035016_Lg15_snpEB134400_MAF30_1675442_exon1RosBREEDSNP_SNP_AG_4035016_Lg15_snpEB134400_MAF30_1675442_exon1genetic_marker
RosBREEDSNP_SNP_AG_4175763_Lg7_RosCOS3240_MAF10_202061_exon1RosBREEDSNP_SNP_AG_4175763_Lg7_RosCOS3240_MAF10_202061_exon1genetic_marker
RosBREEDSNP_SNP_AG_42989883_Lg15_RosCOS1842_MAF10_1681181_exon6RosBREEDSNP_SNP_AG_42989883_Lg15_RosCOS1842_MAF10_1681181_exon6genetic_marker
RosBREEDSNP_SNP_AG_4983233_Lg17_145834_MAF50_145834_exon1RosBREEDSNP_SNP_AG_4983233_Lg17_145834_MAF50_145834_exon1genetic_marker
RosBREEDSNP_SNP_AG_6797491_Lg2_01549_MAF10_MDP0000249190_exon5RosBREEDSNP_SNP_AG_6797491_Lg2_01549_MAF10_MDP0000249190_exon5genetic_marker
RosBREEDSNP_SNP_AG_68160_Lg5_252545_MAF50_252545_exon1RosBREEDSNP_SNP_AG_68160_Lg5_252545_MAF50_252545_exon1genetic_marker
RosBREEDSNP_SNP_AG_68277_Lg5_252545_MAF40_252545_exon1RosBREEDSNP_SNP_AG_68277_Lg5_252545_MAF40_252545_exon1genetic_marker
RosBREEDSNP_SNP_AG_861832_Lg10_00106_MAF10_MDP0000277990_exon2RosBREEDSNP_SNP_AG_861832_Lg10_00106_MAF10_MDP0000277990_exon2genetic_marker
RosBREEDSNP_SNP_AG_9121744_Lg3_RosCOS449_MAF10_491206_exon2RosBREEDSNP_SNP_AG_9121744_Lg3_RosCOS449_MAF10_491206_exon2genetic_marker
RosBREEDSNP_SNP_CA_14009069_Lg14_CXE5_MAF40_192841_exon1RosBREEDSNP_SNP_CA_14009069_Lg14_CXE5_MAF40_192841_exon1genetic_marker
RosBREEDSNP_SNP_CA_1493110_Lg9_01339_MAF10_786476_exon1RosBREEDSNP_SNP_CA_1493110_Lg9_01339_MAF10_786476_exon1genetic_marker
RosBREEDSNP_SNP_CA_2050220_Lg9_01573_MAF10_MDP0000197725_exon1RosBREEDSNP_SNP_CA_2050220_Lg9_01573_MAF10_MDP0000197725_exon1genetic_marker
RosBREEDSNP_SNP_CA_2372354_Lg10_MDP0000199601_MAF20_MDP0000199601_exon2RosBREEDSNP_SNP_CA_2372354_Lg10_MDP0000199601_MAF20_MDP0000199601_exon2genetic_marker
RosBREEDSNP_SNP_CA_26366233_Lg15_01850_MAF20_MDP0000264232_exon5RosBREEDSNP_SNP_CA_26366233_Lg15_01850_MAF20_MDP0000264232_exon5genetic_marker
RosBREEDSNP_SNP_CA_26875026_Lg14_02079_MAF40_1663800_exon5RosBREEDSNP_SNP_CA_26875026_Lg14_02079_MAF40_1663800_exon5genetic_marker
RosBREEDSNP_SNP_CA_27738188_Lg3_00607_MAF10_112030_exon1RosBREEDSNP_SNP_CA_27738188_Lg3_00607_MAF10_112030_exon1genetic_marker
RosBREEDSNP_SNP_CA_27837163_Lg5_01859_MAF20_MDP0000259320_exon1RosBREEDSNP_SNP_CA_27837163_Lg5_01859_MAF20_MDP0000259320_exon1genetic_marker
RosBREEDSNP_SNP_CA_2851448_Lg7_00802_MAF30_MDP0000224757_exon1RosBREEDSNP_SNP_CA_2851448_Lg7_00802_MAF30_MDP0000224757_exon1genetic_marker

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