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_CA_35395640_Lg12_01793_MAF40_MDP0000276157_exon2RosBREEDSNP_SNP_CA_35395640_Lg12_01793_MAF40_MDP0000276157_exon2genetic_marker
RosBREEDSNP_SNP_CA_35420388_Lg12_01793_MAF10_1619944_exon6RosBREEDSNP_SNP_CA_35420388_Lg12_01793_MAF10_1619944_exon6genetic_marker
RosBREEDSNP_SNP_CA_40085225_Lg2_02535_MAF40_MDP0000320988_exon20RosBREEDSNP_SNP_CA_40085225_Lg2_02535_MAF40_MDP0000320988_exon20genetic_marker
RosBREEDSNP_SNP_CA_7292798_Lg15_00274_MAF40_183488_exon1RosBREEDSNP_SNP_CA_7292798_Lg15_00274_MAF40_183488_exon1genetic_marker
RosBREEDSNP_SNP_CA_7606033_Lg13_02124_MAF20_1677651_exon1RosBREEDSNP_SNP_CA_7606033_Lg13_02124_MAF20_1677651_exon1genetic_marker
RosBREEDSNP_SNP_CT_10376441_Lg17_01044_MAF20_1628527_exon2RosBREEDSNP_SNP_CT_10376441_Lg17_01044_MAF20_1628527_exon2genetic_marker
RosBREEDSNP_SNP_CT_11367113_Lg14_02214_MAF20_MDP0000222294_exon1RosBREEDSNP_SNP_CT_11367113_Lg14_02214_MAF20_MDP0000222294_exon1genetic_marker
RosBREEDSNP_SNP_CT_11711211_Lg5_RosCOS544_MAF20_378820_exon2RosBREEDSNP_SNP_CT_11711211_Lg5_RosCOS544_MAF20_378820_exon2genetic_marker
RosBREEDSNP_SNP_CT_12512364_Lg2_00174_MAF30_141353_exon1RosBREEDSNP_SNP_CT_12512364_Lg2_00174_MAF30_141353_exon1genetic_marker
RosBREEDSNP_SNP_CT_1323911_Lg8_00487_MAF40_1687140_exon1RosBREEDSNP_SNP_CT_1323911_Lg8_00487_MAF40_1687140_exon1genetic_marker
RosBREEDSNP_SNP_CT_13600964_Lg7_01305_MAF30_MDP0000269737_exon1RosBREEDSNP_SNP_CT_13600964_Lg7_01305_MAF30_MDP0000269737_exon1genetic_marker
RosBREEDSNP_SNP_CT_13752663_Lg5_01505_MAF20_1624285_exon5RosBREEDSNP_SNP_CT_13752663_Lg5_01505_MAF20_1624285_exon5genetic_marker
RosBREEDSNP_SNP_CT_13756374_Lg5_01505_MAF10_MDP0000321161_exon3RosBREEDSNP_SNP_CT_13756374_Lg5_01505_MAF10_MDP0000321161_exon3genetic_marker
RosBREEDSNP_SNP_CT_14012847_Lg14_CXE5_MAF40_1659491_exon4RosBREEDSNP_SNP_CT_14012847_Lg14_CXE5_MAF40_1659491_exon4genetic_marker
RosBREEDSNP_SNP_CT_14112918_Lg4_01929_MAF40_MDP0000243428_exon3RosBREEDSNP_SNP_CT_14112918_Lg4_01929_MAF40_MDP0000243428_exon3genetic_marker
RosBREEDSNP_SNP_CT_1459011_Lg9_01339_MAF50_1643399_exon1RosBREEDSNP_SNP_CT_1459011_Lg9_01339_MAF50_1643399_exon1genetic_marker
RosBREEDSNP_SNP_CT_1606574_Lg2_snpCO903605_MAF10_99551_exon1RosBREEDSNP_SNP_CT_1606574_Lg2_snpCO903605_MAF10_99551_exon1genetic_marker
RosBREEDSNP_SNP_CT_16729529_Lg10_01710_MAF40_703557_exon1RosBREEDSNP_SNP_CT_16729529_Lg10_01710_MAF40_703557_exon1genetic_marker
RosBREEDSNP_SNP_CT_18416836_Lg14_02426_MAF30_1671446_exon2RosBREEDSNP_SNP_CT_18416836_Lg14_02426_MAF30_1671446_exon2genetic_marker
RosBREEDSNP_SNP_CT_19384185_Lg11_01878_MAF20_MDP0000829038_exon1RosBREEDSNP_SNP_CT_19384185_Lg11_01878_MAF20_MDP0000829038_exon1genetic_marker
RosBREEDSNP_SNP_CT_21201745_Lg17_00423_MAF30_623380_exon1RosBREEDSNP_SNP_CT_21201745_Lg17_00423_MAF30_623380_exon1genetic_marker
RosBREEDSNP_SNP_CT_21618606_Lg9_02230_MAF50_MDP0000320823_exon3RosBREEDSNP_SNP_CT_21618606_Lg9_02230_MAF50_MDP0000320823_exon3genetic_marker
RosBREEDSNP_SNP_CT_23903552_Lg1_RosCOS1602_MAF20_MDP0000235263_exon4RosBREEDSNP_SNP_CT_23903552_Lg1_RosCOS1602_MAF20_MDP0000235263_exon4genetic_marker
RosBREEDSNP_SNP_CT_24064868_Lg14_01531_MAF20_MDP0000199415_exon1RosBREEDSNP_SNP_CT_24064868_Lg14_01531_MAF20_MDP0000199415_exon1genetic_marker
RosBREEDSNP_SNP_CT_24104888_Lg2_MDP0000136940_MAF50_MDP0000136940_exon1RosBREEDSNP_SNP_CT_24104888_Lg2_MDP0000136940_MAF50_MDP0000136940_exon1genetic_marker

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