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
PMID00193PMID00193genetic_marker
PMID00194PMID00194genetic_marker
PMID00195PMID00195genetic_marker
PMID00196PMID00196genetic_marker
PMID00197PMID00197genetic_marker
PMID00198PMID00198genetic_marker
PMID00199PMID00199genetic_marker
PMID00200PMID00200genetic_marker
PMID00201PMID00201genetic_marker
PMID00202PMID00202genetic_marker
PMID00203PMID00203genetic_marker
PMID00204PMID00204genetic_marker
PMID00205PMID00205genetic_marker
PMID00206PMID00206genetic_marker
PMID00207PMID00207genetic_marker
PMID00208PMID00208genetic_marker
PMID00209PMID00209genetic_marker
PMID00210PMID00210genetic_marker
PMID00211PMID00211genetic_marker
PMID00212PMID00212genetic_marker
PMID00213PMID00213genetic_marker
PMID00214PMID00214genetic_marker
PMID00215PMID00215genetic_marker
PMID00216PMID00216genetic_marker
PMID00217PMID00217genetic_marker

Pages