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
GDsnp00189GDsnp00189genetic_marker
GDsnp00193GDsnp00193genetic_marker
GDsnp00195GDsnp00195genetic_marker
GDsnp00196GDsnp00196genetic_marker
GDsnp00203GDsnp00203genetic_marker
GDsnp00213GDsnp00213genetic_marker
GDsnp00225GDsnp00225genetic_marker
GDsnp00231GDsnp00231genetic_marker
GDsnp00238GDsnp00238genetic_marker
GDsnp00241GDsnp00241genetic_marker
GDsnp00243GDsnp00243genetic_marker
GDsnp00248GDsnp00248genetic_marker
GDsnp00250GDsnp00250genetic_marker
GDsnp00252GDsnp00252genetic_marker
GDsnp00265GDsnp00265genetic_marker
GDsnp00269GDsnp00269genetic_marker
GDsnp00272GDsnp00272genetic_marker
GDsnp00273GDsnp00273genetic_marker
GDsnp00277GDsnp00277genetic_marker
GDsnp00287GDsnp00287genetic_marker
GDsnp00290GDsnp00290genetic_marker
GDsnp00308GDsnp00308genetic_marker
GDsnp00309GDsnp00309genetic_marker
GDsnp00312GDsnp00312genetic_marker
GDsnp00319GDsnp00319genetic_marker

Pages