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_GA_39231189_Lg2_01938_MAF20_MDP0000277119_exon2RosBREEDSNP_SNP_GA_39231189_Lg2_01938_MAF20_MDP0000277119_exon2genetic_marker
RosBREEDSNP_SNP_GA_4160553_Lg17_RosCOS742_MAF10_MDP0000120520_exon2RosBREEDSNP_SNP_GA_4160553_Lg17_RosCOS742_MAF10_MDP0000120520_exon2genetic_marker
RosBREEDSNP_SNP_GA_5246231_Lg6_00082_MAF20_1647361_exon4RosBREEDSNP_SNP_GA_5246231_Lg6_00082_MAF20_1647361_exon4genetic_marker
RosBREEDSNP_SNP_GA_5726495_Lg17_00606_MAF10_MDP0000240646_exon7RosBREEDSNP_SNP_GA_5726495_Lg17_00606_MAF10_MDP0000240646_exon7genetic_marker
RosBREEDSNP_SNP_GA_5748318_Lg15_01185_MAF40_518704_exon1RosBREEDSNP_SNP_GA_5748318_Lg15_01185_MAF40_518704_exon1genetic_marker
RosBREEDSNP_SNP_GA_5884301_Lg4_02263_MAF50_749161_exon1RosBREEDSNP_SNP_GA_5884301_Lg4_02263_MAF50_749161_exon1genetic_marker
RosBREEDSNP_SNP_GA_649841_Lg13_01579_MAF50_415180_exon3RosBREEDSNP_SNP_GA_649841_Lg13_01579_MAF50_415180_exon3genetic_marker
RosBREEDSNP_SNP_GA_6539382_Lg3_01921_MAF30_1666387_exon1RosBREEDSNP_SNP_GA_6539382_Lg3_01921_MAF30_1666387_exon1genetic_marker
RosBREEDSNP_SNP_GA_6632118_Lg2_00333_MAF40_MDP0000229589_exon1RosBREEDSNP_SNP_GA_6632118_Lg2_00333_MAF40_MDP0000229589_exon1genetic_marker
RosBREEDSNP_SNP_GA_8129810_Lg15_00389_MAF40_1641199_exon1RosBREEDSNP_SNP_GA_8129810_Lg15_00389_MAF40_1641199_exon1genetic_marker
RosBREEDSNP_SNP_GA_8526607_Lg7_01780_MAF40_517647_exon1RosBREEDSNP_SNP_GA_8526607_Lg7_01780_MAF40_517647_exon1genetic_marker
RosBREEDSNP_SNP_GA_9344917_Lg6_02258_MAF30_MDP0000143112_exon9RosBREEDSNP_SNP_GA_9344917_Lg6_02258_MAF30_MDP0000143112_exon9genetic_marker
RosBREEDSNP_SNP_GA_9346488_Lg7_RosCOS2471_MAF20_MDP0000232592_exon9RosBREEDSNP_SNP_GA_9346488_Lg7_RosCOS2471_MAF20_MDP0000232592_exon9genetic_marker
RosBREEDSNP_SNP_GA_993478_Lg5_01694_MAF50_470798_exon2RosBREEDSNP_SNP_GA_993478_Lg5_01694_MAF50_470798_exon2genetic_marker
RosBREEDSNP_SNP_GT_11012131_Lg7_01882_MAF30_MDP0000138110_exon3RosBREEDSNP_SNP_GT_11012131_Lg7_01882_MAF30_MDP0000138110_exon3genetic_marker
RosBREEDSNP_SNP_GT_11255413_Lg13_325270__325270_exon1RosBREEDSNP_SNP_GT_11255413_Lg13_325270__325270_exon1genetic_marker
RosBREEDSNP_SNP_GT_13708618_Lg10_snpEG631376_MAF30_MDP0000139189_exon4RosBREEDSNP_SNP_GT_13708618_Lg10_snpEG631376_MAF30_MDP0000139189_exon4genetic_marker
RosBREEDSNP_SNP_GT_1707020_Lg11_02626_MAF30_MDP0000285338_exon2RosBREEDSNP_SNP_GT_1707020_Lg11_02626_MAF30_MDP0000285338_exon2genetic_marker
RosBREEDSNP_SNP_GT_1789261_Lg10_RosCOS3613_MAF40_325791_exon1RosBREEDSNP_SNP_GT_1789261_Lg10_RosCOS3613_MAF40_325791_exon1genetic_marker
RosBREEDSNP_SNP_GT_1993476_Lg3_RosCOS1698_MAF10_1627375_exon1RosBREEDSNP_SNP_GT_1993476_Lg3_RosCOS1698_MAF10_1627375_exon1genetic_marker
RosBREEDSNP_SNP_GT_20107856_Lg2_176242_MAF30_176242_exon1RosBREEDSNP_SNP_GT_20107856_Lg2_176242_MAF30_176242_exon1genetic_marker
RosBREEDSNP_SNP_GT_20420907_Lg15_02080_MAF40_388343_exon1RosBREEDSNP_SNP_GT_20420907_Lg15_02080_MAF40_388343_exon1genetic_marker
RosBREEDSNP_SNP_GT_20541681_Lg12_00599_MAF10_348860_exon1RosBREEDSNP_SNP_GT_20541681_Lg12_00599_MAF10_348860_exon1genetic_marker
RosBREEDSNP_SNP_GT_21216802_Lg9RosBREEDSNP_SNP_GT_21216802_Lg9genetic_marker
RosBREEDSNP_SNP_GT_2372329_Lg10_MDP0000199601_MAF10_MDP0000199601_exon2RosBREEDSNP_SNP_GT_2372329_Lg10_MDP0000199601_MAF10_MDP0000199601_exon2genetic_marker

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