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
JPsnpHou00207JPsnpHou00207genetic_marker
JPsnpHou00474JPsnpHou00474genetic_marker
JPsnpHou00493JPsnpHou00493genetic_marker
JPsnpHou00489JPsnpHou00489genetic_marker
JPsnpHou00247JPsnpHou00247genetic_marker
JPsnpHou00453JPsnpHou00453genetic_marker
JPsnpHou00596JPsnpHou00596genetic_marker
JPsnpHou00589JPsnpHou00589genetic_marker
JPsnpHou00615JPsnpHou00615genetic_marker
JPsnpHou00196JPsnpHou00196genetic_marker
JPsnpHou00195JPsnpHou00195genetic_marker
JPsnpHou00192JPsnpHou00192genetic_marker
JPsnpHou00355JPsnpHou00355genetic_marker
JPsnpHou00582JPsnpHou00582genetic_marker
JPsnpHou00240JPsnpHou00240genetic_marker
JPsnpHou00462JPsnpHou00462genetic_marker
JPsnpHou00140JPsnpHou00140genetic_marker
JPsnpHou00178JPsnpHou00178genetic_marker
JPsnpHou00227JPsnpHou00227genetic_marker
JPsnpHou00648JPsnpHou00648genetic_marker
JPsnpHou00268JPsnpHou00268genetic_marker
JPsnpHou00554JPsnpHou00554genetic_marker
JPsnpHou00504JPsnpHou00504genetic_marker
JPsnpHou00250JPsnpHou00250genetic_marker
JPsnpHou00643JPsnpHou00643genetic_marker

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