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_TC_22757315_Lg11_00743_MAF50_1632808_exon1RosBREEDSNP_SNP_TC_22757315_Lg11_00743_MAF50_1632808_exon1genetic_marker
RosBREEDSNP_SNP_TC_23899418_Lg1_RosCOS1602_MAF20_MDP0000283296_exon1RosBREEDSNP_SNP_TC_23899418_Lg1_RosCOS1602_MAF20_MDP0000283296_exon1genetic_marker
RosBREEDSNP_SNP_TC_24722012_Lg15_02859_MAF50_29205_exon3RosBREEDSNP_SNP_TC_24722012_Lg15_02859_MAF50_29205_exon3genetic_marker
RosBREEDSNP_SNP_TC_25194345_Lg8_01598_MAF20_521738_exon1RosBREEDSNP_SNP_TC_25194345_Lg8_01598_MAF20_521738_exon1genetic_marker
RosBREEDSNP_SNP_TC_26371625_Lg15_01850_MAF50_1639406_exon1RosBREEDSNP_SNP_TC_26371625_Lg15_01850_MAF50_1639406_exon1genetic_marker
RosBREEDSNP_SNP_TC_2694414_Lg17_00508_MAF10_888417_exon1RosBREEDSNP_SNP_TC_2694414_Lg17_00508_MAF10_888417_exon1genetic_marker
RosBREEDSNP_SNP_TC_27018809_Lg13_MDP0000163961_MAF10_MDP0000163961_exon1RosBREEDSNP_SNP_TC_27018809_Lg13_MDP0000163961_MAF10_MDP0000163961_exon1genetic_marker
RosBREEDSNP_SNP_TC_27687938_Lg3_00607_MAF30_605396_exon1RosBREEDSNP_SNP_TC_27687938_Lg3_00607_MAF30_605396_exon1genetic_marker
RosBREEDSNP_SNP_TC_31070932_Lg12_00915_MAF40_514144_exon1RosBREEDSNP_SNP_TC_31070932_Lg12_00915_MAF40_514144_exon1genetic_marker
RosBREEDSNP_SNP_TC_33063540_Lg9_01200_MAF30_MDP0000183373_exon2RosBREEDSNP_SNP_TC_33063540_Lg9_01200_MAF30_MDP0000183373_exon2genetic_marker
RosBREEDSNP_SNP_TC_33199372_Lg13_02487_MAF20_678754_exon1RosBREEDSNP_SNP_TC_33199372_Lg13_02487_MAF20_678754_exon1genetic_marker
RosBREEDSNP_SNP_TC_35445616_Lg12_01793_MAF50_1622722_exon9RosBREEDSNP_SNP_TC_35445616_Lg12_01793_MAF50_1622722_exon9genetic_marker
RosBREEDSNP_SNP_TC_35605655_Lg12_01855_MAF10_MDP0000216404_exon5RosBREEDSNP_SNP_TC_35605655_Lg12_01855_MAF10_MDP0000216404_exon5genetic_marker
RosBREEDSNP_SNP_TC_3601288_Lg7_01717_MAF10_MDP0000120040_exon1RosBREEDSNP_SNP_TC_3601288_Lg7_01717_MAF10_MDP0000120040_exon1genetic_marker
RosBREEDSNP_SNP_TC_3879648_Lg17_MDP0000196554_MAF20_MDP0000196554_exon2RosBREEDSNP_SNP_TC_3879648_Lg17_MDP0000196554_MAF20_MDP0000196554_exon2genetic_marker
RosBREEDSNP_SNP_TC_5365087_Lg16_00030_MAF40_1630198_exon1RosBREEDSNP_SNP_TC_5365087_Lg16_00030_MAF40_1630198_exon1genetic_marker
RosBREEDSNP_SNP_TC_5936130_Lg3_01263_MAF20_1677543_exon1RosBREEDSNP_SNP_TC_5936130_Lg3_01263_MAF20_1677543_exon1genetic_marker
RosBREEDSNP_SNP_TC_6589830_Lg15_00076_MAF50_1635697_exon1RosBREEDSNP_SNP_TC_6589830_Lg15_00076_MAF50_1635697_exon1genetic_marker
RosBREEDSNP_SNP_TC_7741659_Lg12_01703_MAF20_MDP0000736860_exon1RosBREEDSNP_SNP_TC_7741659_Lg12_01703_MAF20_MDP0000736860_exon1genetic_marker
RosBREEDSNP_SNP_TC_8352379_Lg13_84982_MAF20_84982_exon1RosBREEDSNP_SNP_TC_8352379_Lg13_84982_MAF20_84982_exon1genetic_marker
RosBREEDSNP_SNP_TC_9308967_Lg1_00703_MAF20_MDP0000292549_exon1RosBREEDSNP_SNP_TC_9308967_Lg1_00703_MAF20_MDP0000292549_exon1genetic_marker
RosBREEDSNP_SNP_TC_9330075_Lg12_02053_MAF40_MDP0000321559_exon8RosBREEDSNP_SNP_TC_9330075_Lg12_02053_MAF40_MDP0000321559_exon8genetic_marker
RosBREEDSNP_SNP_TC_9418092_Lg10_00875_MAF20_1667779_exon1RosBREEDSNP_SNP_TC_9418092_Lg10_00875_MAF20_1667779_exon1genetic_marker
RosBREEDSNP_SNP_TG_12055755_Lg10_RosCOS2353_MAF50_1665006_exon5RosBREEDSNP_SNP_TG_12055755_Lg10_RosCOS2353_MAF50_1665006_exon5genetic_marker
RosBREEDSNP_SNP_TG_13348417_Lg8_RosCOS689_MAF20_1684268_exon1RosBREEDSNP_SNP_TG_13348417_Lg8_RosCOS689_MAF20_1684268_exon1genetic_marker

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