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
PMID01243PMID01243genetic_marker
PMID01244PMID01244genetic_marker
PMID01245PMID01245genetic_marker
PMID01246PMID01246genetic_marker
PMID01247PMID01247genetic_marker
PMID01248PMID01248genetic_marker
PMID01249PMID01249genetic_marker
PMID01250PMID01250genetic_marker
PMID01251PMID01251genetic_marker
PMID01252PMID01252genetic_marker
PMID01253PMID01253genetic_marker
PMID01254PMID01254genetic_marker
PMID01255PMID01255genetic_marker
PMID01256PMID01256genetic_marker
PMID01257PMID01257genetic_marker
PMID01258PMID01258genetic_marker
PMID01259PMID01259genetic_marker
PMID01260PMID01260genetic_marker
PMID01261PMID01261genetic_marker
PMID01262PMID01262genetic_marker
PMID01263PMID01263genetic_marker
PMID01264PMID01264genetic_marker
PMID01265PMID01265genetic_marker
PMID01266PMID01266genetic_marker
PMID01267PMID01267genetic_marker

Pages