Identification of Pyrus Single Nucleotide Polymorphisms (SNPs) and Evaluation for Genetic Mapping in European Pear and Interspecific Pyrus Hybrids

Publication Overview
TitleIdentification of Pyrus Single Nucleotide Polymorphisms (SNPs) and Evaluation for Genetic Mapping in European Pear and Interspecific Pyrus Hybrids
AuthorsMontanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D
TypeJournal Article
Journal NamePloS one
Volume8
Issue10
Year2013
Page(s)e77022
CitationMontanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D. Identification of Pyrus Single Nucleotide Polymorphisms (SNPs) and Evaluation for Genetic Mapping in European Pear and Interspecific Pyrus Hybrids. PloS one. 2013; 8(10):e77022.

Abstract

We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.

Features
This publication contains information about 1,096 features:
Feature NameUniquenameType
Pear_Bartlett_SNP_AC_160_5092959Pear_Bartlett_SNP_AC_160_5092959genetic_marker
Pear_Bartlett_SNP_AC_231_5149441Pear_Bartlett_SNP_AC_231_5149441genetic_marker
Pear_Bartlett_SNP_AC_232_5144842Pear_Bartlett_SNP_AC_232_5144842genetic_marker
Pear_Bartlett_SNP_AC_241_5068554Pear_Bartlett_SNP_AC_241_5068554genetic_marker
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Pear_Bartlett_SNP_AC_395_5079577Pear_Bartlett_SNP_AC_395_5079577genetic_marker
Pear_Bartlett_SNP_AC_437_5148128Pear_Bartlett_SNP_AC_437_5148128genetic_marker
Pear_Bartlett_SNP_AC_802_5110736Pear_Bartlett_SNP_AC_802_5110736genetic_marker
Pear_Bartlett_SNP_AG_1196_5075267Pear_Bartlett_SNP_AG_1196_5075267genetic_marker
Pear_Bartlett_SNP_AG_160_5060021Pear_Bartlett_SNP_AG_160_5060021genetic_marker
Pear_Bartlett_SNP_AG_162_5088916Pear_Bartlett_SNP_AG_162_5088916genetic_marker
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Pear_Bartlett_SNP_AG_196_5105553Pear_Bartlett_SNP_AG_196_5105553genetic_marker
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Pear_Bartlett_SNP_AG_222_5060101Pear_Bartlett_SNP_AG_222_5060101genetic_marker
Pear_Bartlett_SNP_AG_229_5070075Pear_Bartlett_SNP_AG_229_5070075genetic_marker

Pages

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
IRSC 1K SNP array for pearIRSC 1K SNP array for pearPyrus communis
Featuremaps
This publication contains information about 2 maps:
Map Name
Pear-PM-F1-PEAR3
Pear-PM-F1-Moonglow
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:24155917