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

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• 作者：Masafumi Yagi ; Kenta Shirasawa ; Takamitsu Waki…
• 关键词：Carnation ; Restriction site ; associated DNA (RAD) ; Simple sequence repeat (SSR) ; Linkage map
• 刊名：Plant Molecular Biology Reporter
• 出版年：2017
• 出版时间：February 2017
• 年：2017
• 卷：35
• 期：1
• 页码：110-117
• 全文大小：
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Plant Sciences; Plant Breeding/Biotechnology; Proteomics; Metabolomics; Bioinformatics;
• 出版者：Springer US
• ISSN：1572-9818
• 卷排序：35

文摘

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.