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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GDsnp00321GDsnp00321genetic_marker
GDsnp00324GDsnp00324genetic_marker
GDsnp00329GDsnp00329genetic_marker
GDsnp00330GDsnp00330genetic_marker
GDsnp00331GDsnp00331genetic_marker
GDsnp00334GDsnp00334genetic_marker
GDsnp00347GDsnp00347genetic_marker
GDsnp00349GDsnp00349genetic_marker
GDsnp00357GDsnp00357genetic_marker
GDsnp00358GDsnp00358genetic_marker
GDsnp00360GDsnp00360genetic_marker
GDsnp00361GDsnp00361genetic_marker
GDsnp00366GDsnp00366genetic_marker
GDsnp00419GDsnp00419genetic_marker
GDsnp00425GDsnp00425genetic_marker
GDsnp00438GDsnp00438genetic_marker
GDsnp00444GDsnp00444genetic_marker
GDsnp00471GDsnp00471genetic_marker
GDsnp00503GDsnp00503genetic_marker
GDsnp00514GDsnp00514genetic_marker
GDsnp00522GDsnp00522genetic_marker
GDsnp00527GDsnp00527genetic_marker
GDsnp00532GDsnp00532genetic_marker
GDsnp00539GDsnp00539genetic_marker

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