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
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GDsnp01257GDsnp01257genetic_marker
GDsnp01267GDsnp01267genetic_marker
GDsnp01322GDsnp01322genetic_marker
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GDsnp01405GDsnp01405genetic_marker
GDsnp01433GDsnp01433genetic_marker
GDsnp01454GDsnp01454genetic_marker
GDsnp01470GDsnp01470genetic_marker
GDsnp01487GDsnp01487genetic_marker
GDsnp01488GDsnp01488genetic_marker
GDsnp01493GDsnp01493genetic_marker
GDsnp01502GDsnp01502genetic_marker
GDsnp01505GDsnp01505genetic_marker
GDsnp01556GDsnp01556genetic_marker
GDsnp01600GDsnp01600genetic_marker
GDsnp01604GDsnp01604genetic_marker
GDsnp01634GDsnp01634genetic_marker
GDsnp01656GDsnp01656genetic_marker
GDsnp01665GDsnp01665genetic_marker
GDsnp01667GDsnp01667genetic_marker
GDsnp01681GDsnp01681genetic_marker
GDsnp01682GDsnp01682genetic_marker

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