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
JPsnpHou00115JPsnpHou00115genetic_marker
JPsnpHou00460JPsnpHou00460genetic_marker
JPsnpHou00574JPsnpHou00574genetic_marker
JPsnpHou00047JPsnpHou00047genetic_marker
JPsnpHou00612JPsnpHou00612genetic_marker
JPsnpHou00436JPsnpHou00436genetic_marker
JPsnpHou00251JPsnpHou00251genetic_marker
JPsnpHou00537JPsnpHou00537genetic_marker
JPsnpHou00634JPsnpHou00634genetic_marker
JPsnpHou00254JPsnpHou00254genetic_marker
JPsnpHou00404JPsnpHou00404genetic_marker
JPsnpHou00079JPsnpHou00079genetic_marker
JPsnpHou00180JPsnpHou00180genetic_marker
JPsnpHou00262JPsnpHou00262genetic_marker
JPsnpHou00101JPsnpHou00101genetic_marker
JPsnpHou00324JPsnpHou00324genetic_marker
JPsnpHou00527JPsnpHou00527genetic_marker
JPsnpHou00063JPsnpHou00063genetic_marker
JPsnpHou00614JPsnpHou00614genetic_marker
JPsnpHou00488JPsnpHou00488genetic_marker
JPsnpHou00464JPsnpHou00464genetic_marker
JPsnpHou00413JPsnpHou00413genetic_marker
JPsnpHou00136JPsnpHou00136genetic_marker
JPsnpHou00319JPsnpHou00319genetic_marker
JPsnpHou00273JPsnpHou00273genetic_marker

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