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
JPsnpHou00388JPsnpHou00388genetic_marker
JPsnpHou00500JPsnpHou00500genetic_marker
JPsnpHou00451JPsnpHou00451genetic_marker
JPsnpHou00399JPsnpHou00399genetic_marker
JPsnpHou00641JPsnpHou00641genetic_marker
JPsnpHou00138JPsnpHou00138genetic_marker
JPsnpHou00645JPsnpHou00645genetic_marker
JPsnpHou00135JPsnpHou00135genetic_marker
JPsnpHou00295JPsnpHou00295genetic_marker
JPsnpHou00358JPsnpHou00358genetic_marker
JPsnpHou00425JPsnpHou00425genetic_marker
JPsnpHou00069JPsnpHou00069genetic_marker
JPsnpHou00303JPsnpHou00303genetic_marker
JPsnpHou00475JPsnpHou00475genetic_marker
JPsnpHou00255JPsnpHou00255genetic_marker
JPsnpHou00442JPsnpHou00442genetic_marker
JPsnpHou00174JPsnpHou00174genetic_marker
JPsnpHou00200JPsnpHou00200genetic_marker
JPsnpHou00505JPsnpHou00505genetic_marker
JPsnpHou00122JPsnpHou00122genetic_marker
JPsnpHou00094JPsnpHou00094genetic_marker
JPsnpHou00053JPsnpHou00053genetic_marker
JPsnpHou00564JPsnpHou00564genetic_marker
JPsnpHou00333JPsnpHou00333genetic_marker
JPsnpHou00218JPsnpHou00218genetic_marker

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