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
JPsnpHou00479JPsnpHou00479genetic_marker
JPsnpHou00484JPsnpHou00484genetic_marker
JPsnpHou00595JPsnpHou00595genetic_marker
JPsnpHou00386JPsnpHou00386genetic_marker
JPsnpHou00057JPsnpHou00057genetic_marker
JPsnpHou00416JPsnpHou00416genetic_marker
JPsnpHou00347JPsnpHou00347genetic_marker
JPsnpHou00558JPsnpHou00558genetic_marker
JPsnpHou00396JPsnpHou00396genetic_marker
JPsnpHou00531JPsnpHou00531genetic_marker
JPsnpHou00072JPsnpHou00072genetic_marker
JPsnpHou00545JPsnpHou00545genetic_marker
JPsnpHou00181JPsnpHou00181genetic_marker
JPsnpHou00631JPsnpHou00631genetic_marker
JPsnpHou00587JPsnpHou00587genetic_marker
JPsnpHou00233JPsnpHou00233genetic_marker
JPsnpHou00257JPsnpHou00257genetic_marker
JPsnpHou00231JPsnpHou00231genetic_marker
JPsnpHou00119JPsnpHou00119genetic_marker
JPsnpHou00103JPsnpHou00103genetic_marker
JPsnpHou00308JPsnpHou00308genetic_marker
JPsnpHou00433JPsnpHou00433genetic_marker
JPsnpHou00410JPsnpHou00410genetic_marker
JPsnpHou00496JPsnpHou00496genetic_marker
JPsnpHou00446JPsnpHou00446genetic_marker

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