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
PMSSR06643PMSSR06643genetic_marker
PMSSR06644PMSSR06644genetic_marker
PMSSR06645PMSSR06645genetic_marker
PMSSR06646PMSSR06646genetic_marker
PMSSR06647PMSSR06647genetic_marker
PMSSR06648PMSSR06648genetic_marker
PMSSR06649PMSSR06649genetic_marker
PMSSR06650PMSSR06650genetic_marker
PMSSR06651PMSSR06651genetic_marker
PMSSR06652PMSSR06652genetic_marker
PMSSR06653PMSSR06653genetic_marker
PMSSR06654PMSSR06654genetic_marker
PMSSR06655PMSSR06655genetic_marker
PMSSR06656PMSSR06656genetic_marker
PMSSR06657PMSSR06657genetic_marker
PMSSR06658PMSSR06658genetic_marker
PMSSR06659PMSSR06659genetic_marker
PMSSR06660PMSSR06660genetic_marker
PMSSR06661PMSSR06661genetic_marker
PMSSR06662PMSSR06662genetic_marker
PMSSR06663PMSSR06663genetic_marker
PMSSR06664PMSSR06664genetic_marker
PMSSR06665PMSSR06665genetic_marker
PMSSR06666PMSSR06666genetic_marker
PMSSR06667PMSSR06667genetic_marker

Pages