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
JPsnpHou00272JPsnpHou00272genetic_marker
JPsnpHou00291JPsnpHou00291genetic_marker
JPsnpHou00276JPsnpHou00276genetic_marker
JPsnpHou00606JPsnpHou00606genetic_marker
JPsnpHou00625JPsnpHou00625genetic_marker
JPsnpHou00654JPsnpHou00654genetic_marker
JPsnpHou00354JPsnpHou00354genetic_marker
JPsnpHou00285JPsnpHou00285genetic_marker
JPsnpHou00467JPsnpHou00467genetic_marker
JPsnpHou00147JPsnpHou00147genetic_marker
JPsnpHou00073JPsnpHou00073genetic_marker
JPsnpHou00459JPsnpHou00459genetic_marker
JPsnpHou00610JPsnpHou00610genetic_marker
JPsnpHou00376JPsnpHou00376genetic_marker
JPsnpHou00321JPsnpHou00321genetic_marker
JPsnpHou00570JPsnpHou00570genetic_marker
JPsnpHou00619JPsnpHou00619genetic_marker
JPsnpHou00092JPsnpHou00092genetic_marker
JPsnpHou00112JPsnpHou00112genetic_marker
JPsnpHou00357JPsnpHou00357genetic_marker
JPsnpHou00165JPsnpHou00165genetic_marker
JPsnpHou00616JPsnpHou00616genetic_marker
JPsnpHou00090JPsnpHou00090genetic_marker
JPsnpHou00366JPsnpHou00366genetic_marker
JPsnpHou00601JPsnpHou00601genetic_marker

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