Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai)

Publication Overview
TitleTranscriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai)
AuthorsTerakami S, Nishitani C, Kunihisa M, Shirasawa K, Sato S, Tabata S, Kurita K, Kanamori H, Katayose Y, Takada N, Saito T, Yamamoto T
TypeJournal Article
Journal NameTree genetics & genomes
Volume10
Issue4
Year2014
Page(s)853-863
CitationTerakami S, Nishitani C, Kunihisa M, Shirasawa K, Sato S, Tabata S, Kurita K, Kanamori H, Katayose Y, Takada N, Saito T, Yamamoto T. Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai). Tree genetics & genomes. 2014; 10(4):853-863.

Abstract

The development of single nucleotide polymorphism (SNP) markers in Japanese pear (Pyrus pyrifolia Nakai) offers the opportunity to use DNA markers for marker-assisted selection in breeding programs because of their high abundance, codominant inheritance, and potential for automated high-throughput analysis. We developed a 1,536-SNP bead array without a reference genome sequence from more than 44,000 base changes on the basis of a large-scale expressed sequence tag (EST) analysis combined with 454 genome sequencing data of Japanese pear ‘Housui’. Among the 1,536 SNPs on the array, 756 SNPs were genotyped, and 609 SNP loci were mapped to linkage groups on a genetic linkage map of ‘Housui’, based on progeny of an interspecific cross between European pear (Pyrus communis L.) ‘Bartlett’ and ‘Housui’. The newly constructed genetic linkage map consists of 951 loci, comprising 609 new SNPs, 110 pear genomic simple sequence repeats (SSRs), 25 pear EST–SSRs, 127 apple SSRs, 61 pear SNPs identified by the “potential intron polymorphism” method, and 19 other loci. The map covers 22 linkage groups spanning 1341.9 cM with an average distance of 1.41 cM between markers and is anchored to reference genetic linkage maps of European pears and apples. A total of 514 contigs containing mapped SNP loci showed significant similarity to known proteins by functional annotation analysis.
Features
This publication contains information about 609 features:
Feature NameUniquenameType
JPsnpHou00352JPsnpHou00352genetic_marker
JPsnpHou00184JPsnpHou00184genetic_marker
JPsnpHou00630JPsnpHou00630genetic_marker
JPsnpHou00098JPsnpHou00098genetic_marker
JPsnpHou00447JPsnpHou00447genetic_marker
JPsnpHou00128JPsnpHou00128genetic_marker
JPsnpHou00379JPsnpHou00379genetic_marker
JPsnpHou00445JPsnpHou00445genetic_marker
JPsnpHou00362JPsnpHou00362genetic_marker
JPsnpHou00652JPsnpHou00652genetic_marker
JPsnpHou00099JPsnpHou00099genetic_marker
JPsnpHou00502JPsnpHou00502genetic_marker
JPsnpHou00566JPsnpHou00566genetic_marker
JPsnpHou00501JPsnpHou00501genetic_marker
JPsnpHou00168JPsnpHou00168genetic_marker
JPsnpHou00415JPsnpHou00415genetic_marker
JPsnpHou00368JPsnpHou00368genetic_marker
JPsnpHou00044JPsnpHou00044genetic_marker
JPsnpHou00627JPsnpHou00627genetic_marker
JPsnpHou00349JPsnpHou00349genetic_marker
JPsnpHou00114JPsnpHou00114genetic_marker
JPsnpHou00528JPsnpHou00528genetic_marker
JPsnpHou00439JPsnpHou00439genetic_marker
JPsnpHou00406JPsnpHou00406genetic_marker
JPsnpHou00293JPsnpHou00293genetic_marker

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Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication Date2014
Published Location|||
Language Abbreng
Publication Model[electronic resource].
URLhttp://dx.doi.org/10.1007/s11295-014-0726-0
KeywordsPyrus communis, Pyrus pyrifolia, apples, chromosome mapping, expressed sequence tags, genetic markers, genome, genomics, introns, linkage groups, loci, marker-assisted selection, microsatellite repeats, pears, progeny, proteins, single nucleotide polymorphism
Cross References
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DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:4846994