DNA markers developed from genome sequencing analysis in Japanese pear (Pyrus pyrifolia)

Publication Overview
TitleDNA markers developed from genome sequencing analysis in Japanese pear (Pyrus pyrifolia)
AuthorsYamamoto T, Terakami S, Moriya S, Hosaka F, Kurita K, Kanamori H, Katayose Y, Saito T, Nishitani C
TypeJournal Article
Journal NameActa horticulturae
Issue976
Year2013
Page(s)477-483
CitationYamamoto T, Terakami S, Moriya S, Hosaka F, Kurita K, Kanamori H, Katayose Y, Saito T, Nishitani C. DNA markers developed from genome sequencing analysis in Japanese pear (Pyrus pyrifolia). Acta horticulturae. 2013; (976)477-483.

Abstract

We performed random shotgun sequencing to obtain genome sequences from Japanese pear 'Housui' (Pyrus pyrifolia) for use in developing molecular markers. Nearly 2.7 million single-read sequences were obtained, with an average read length of 374 bases. More than 990 Mb of nucleotide sequence were recovered, which is equivalent to twice the size of the Japanese pear genome. We designed 237 simple sequence repeat (SSR) markers with motifs of 4, 5, or 10-14 nucleotides based on more than 50,000 SSR sequences. Out of these 237 markers, 128 loci could be added to at least one of three genetic linkage maps: European pears (P. communis) ‘Bartlett’ and 'La France', and Japanese pear ‘Housui’. 86 of the 144 tested expressed sequence tag (EST)-SSR markers from apple (Malus × domestica) were mapped in one or more of the pear cultivars. The new genetic linkage map of 'Bartlett' consisted of 485 loci from SSR and single-nucleotide polymorphism markers, covering 17 linkage groups with a total length of 965 cM. The linkage map of 'La France' contained 370 loci in 17 linkage groups, with a total length of 1160 cM, and that of ‘Housui’ contained 415 loci in 20 linkage groups, with a total length of 1177 cM. The information obtained from this study will help us develop genome-wide markers and perform marker-assisted selection in pear breeding programs.
Features
This publication contains information about 117 features:
Feature NameUniquenameType
TsuGNH235TsuGNH235genetic_marker
TsuGNH239TsuGNH239genetic_marker
TsuGNH240TsuGNH240genetic_marker
TsuGNH241TsuGNH241genetic_marker
TsuSNP001TsuSNP001genetic_marker
TsuSNP002TsuSNP002genetic_marker
TsuSNP003TsuSNP003genetic_marker
TsuSNP004TsuSNP004genetic_marker
TsuSNP005TsuSNP005genetic_marker
TsuSNP006TsuSNP006genetic_marker
TsuSNP007TsuSNP007genetic_marker
TsuSNP011TsuSNP011genetic_marker
TsuSNP015TsuSNP015genetic_marker
TsuSNP016TsuSNP016genetic_marker
TsuSNP019TsuSNP019genetic_marker
TsuSNP020TsuSNP020genetic_marker
NB116bNB116bgenetic_marker
NB119bNB119bgenetic_marker
NB120aNB120agenetic_marker
NB123aNB123agenetic_marker
NH046aNH046agenetic_marker
NZmsEB106592NZmsEB106592genetic_marker
NZmsEB132582NZmsEB132582genetic_marker
RLG1-1RLG1-1genetic_marker
TsuGNH006TsuGNH006genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Pear-Ba-F1-2013
Stocks
This publication contains information about 1 stocks:
Stock NameUniquenameType
BartlettBartlettaccession