Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.)

Publication Overview
TitleGenome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.)
AuthorsSun L, Zhang Q, Xu Z, Yang W, Guo Y, Lu J, Pan H, Cheng T, Cai M
TypeJournal Article
Journal NameBMC genetics
Volume14
Issue1
Year2013
Page(s)98
CitationSun L, Zhang Q, Xu Z, Yang W, Guo Y, Lu J, Pan H, Cheng T, Cai M. Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.). BMC genetics. 2013 Oct 6; 14(1):98.

Abstract

BACKGROUND
Mei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume 'Fenban' and Prunus mume 'Kouzi Yudie' to identify high-quality polymorphic markers between the two cultivars on a large scale.

RESULTS
A total of 1464.1 Mb and 1422.1 Mb of 'Fenban' and 'Kouzi Yudie' sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent's SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny.

CONCLUSIONS
A large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between 'Fenban' and 'Kouzi Yudie' using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.

Features
This publication contains information about 12,666 features:
Feature NameUniquenameType
PMSNP01036PMSNP01036genetic_marker
PMSNP01033PMSNP01033genetic_marker
PMSNP00162PMSNP00162genetic_marker
PMSNP00095PMSNP00095genetic_marker
PMSNP00545PMSNP00545genetic_marker
PMSNP00082PMSNP00082genetic_marker
PMSNP00071PMSNP00071genetic_marker
PMSNP00068PMSNP00068genetic_marker
PMSNP00021PMSNP00021genetic_marker
PMSNP01203PMSNP01203genetic_marker
PMSNP00307PMSNP00307genetic_marker
PMSNP00457PMSNP00457genetic_marker
PMSNP01407PMSNP01407genetic_marker
PMSNP00349PMSNP00349genetic_marker
PMSNP00453PMSNP00453genetic_marker
PMSNP00470PMSNP00470genetic_marker
PMSNP00815PMSNP00815genetic_marker
PMSNP00818PMSNP00818genetic_marker
PMSNP00821PMSNP00821genetic_marker
PMSNP01299PMSNP01299genetic_marker
PMSNP01309PMSNP01309genetic_marker
PMSNP00463PMSNP00463genetic_marker
PMSNP00448PMSNP00448genetic_marker
PMSNP01379PMSNP01379genetic_marker
PMSNP01140PMSNP01140genetic_marker

Pages

Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:24093913