Construction of an SSR and RAD Marker-Based Genetic Linkage Map for Carnation (Dianthus caryophyllus L.)

A high-density genetic map, an essential tool for comparative genomic studies and quantitative trait locus fine mapping, can also facilitate genome sequence assembly. The sequence-based marker technology known as restriction site-associated DNA (RAD) enables synchronous, single nucleotide polymorphi...

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Bibliographic Details
Published in:Plant molecular biology reporter 2017-02, Vol.35 (1), p.110-117
Main Authors: Yagi, Masafumi, Shirasawa, Kenta, Waki, Takamitsu, Kume, Takashi, Isobe, Sachiko, Tanase, Koji, Yamaguchi, Hiroyasu
Format: Article
Language:English
Subjects:
Bioinformatics
Biomedical and Life Sciences
Gene mapping
Life Sciences
Metabolomics
Original Paper
Plant biology
Plant Breeding/Biotechnology
Plant Sciences
Proteomics
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Summary:A high-density genetic map, an essential tool for comparative genomic studies and quantitative trait locus fine mapping, can also facilitate genome sequence assembly. The sequence-based marker technology known as restriction site-associated DNA (RAD) enables synchronous, single nucleotide polymorphism marker discovery, and genotyping using massively parallel sequencing. We constructed a high-density linkage map for carnation ( Dianthus caryophyllus L.) based on simple sequence repeat (SSR) markers in combination with RAD markers developed by double-digest RAD sequencing (ddRAD-seq). A total of 2404 (285 SSR and 2119 RAD) markers could be assigned to 15 linkage groups spanning 971.5 cM, with an average marker interval of 0.4 cM. The total length of scaffolds with identified map positions was 95.6 Mb, which is equivalent to 15.4 % of the estimated genome size. The generated map is the first SSR and RAD marker-based high-density linkage map reported for carnation. The ddRAD-seq pipeline developed in this study should also help accelerate genetic and genomics analyses and molecular breeding of carnation and other non-model crops.
ISSN:0735-9640
1572-9818
DOI:10.1007/s11105-016-1010-2