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
JPsnpHou00375JPsnpHou00375genetic_marker
JPsnpHou00042JPsnpHou00042genetic_marker
JPsnpHou00256JPsnpHou00256genetic_marker
JPsnpHou00096JPsnpHou00096genetic_marker
JPsnpHou00421JPsnpHou00421genetic_marker
JPsnpHou00581JPsnpHou00581genetic_marker
JPsnpHou00209JPsnpHou00209genetic_marker
JPsnpHou00549JPsnpHou00549genetic_marker
JPsnpHou00494JPsnpHou00494genetic_marker
JPsnpHou00260JPsnpHou00260genetic_marker
JPsnpHou00214JPsnpHou00214genetic_marker
JPsnpHou00532JPsnpHou00532genetic_marker
JPsnpHou00077JPsnpHou00077genetic_marker
JPsnpHou00230JPsnpHou00230genetic_marker
JPsnpHou00497JPsnpHou00497genetic_marker
JPsnpHou00345JPsnpHou00345genetic_marker
JPsnpHou00302JPsnpHou00302genetic_marker
JPsnpHou00064JPsnpHou00064genetic_marker
JPsnpHou00385JPsnpHou00385genetic_marker
JPsnpHou00204JPsnpHou00204genetic_marker
JPsnpHou00391JPsnpHou00391genetic_marker
JPsnpHou00051JPsnpHou00051genetic_marker
JPsnpHou00106JPsnpHou00106genetic_marker
JPsnpHou00323JPsnpHou00323genetic_marker
JPsnpHou00568JPsnpHou00568genetic_marker

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