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
JPsnpHou00617JPsnpHou00617genetic_marker
JPsnpHou00120JPsnpHou00120genetic_marker
JPsnpHou00628JPsnpHou00628genetic_marker
JPsnpHou00458JPsnpHou00458genetic_marker
JPsnpHou00583JPsnpHou00583genetic_marker
JPsnpHou00426JPsnpHou00426genetic_marker
JPsnpHou00234JPsnpHou00234genetic_marker
JPsnpHou00397JPsnpHou00397genetic_marker
JPsnpHou00332JPsnpHou00332genetic_marker
JPsnpHou00414JPsnpHou00414genetic_marker
JPsnpHou00287JPsnpHou00287genetic_marker
JPsnpHou00541JPsnpHou00541genetic_marker
JPsnpHou00163JPsnpHou00163genetic_marker
JPsnpHou00598JPsnpHou00598genetic_marker
JPsnpHou00599JPsnpHou00599genetic_marker
JPsnpHou00398JPsnpHou00398genetic_marker
JPsnpHou00364JPsnpHou00364genetic_marker
JPsnpHou00258JPsnpHou00258genetic_marker
JPsnpHou00166JPsnpHou00166genetic_marker
JPsnpHou00440JPsnpHou00440genetic_marker
JPsnpHou00503JPsnpHou00503genetic_marker
JPsnpHou00344JPsnpHou00344genetic_marker
JPsnpHou00353JPsnpHou00353genetic_marker
JPsnpHou00600JPsnpHou00600genetic_marker
JPsnpHou00381JPsnpHou00381genetic_marker

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