Construction of an SSR and RAD Marker-Based Genetic Linkage Map for Carnation (Dianthus caryophyllus L.)
Construction of an SSR and RAD Marker-Based Genetic Linkage Map for Carnation (Dianthus caryophyllus L.)
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DOI：
10.1007/s11105-016-1010-2
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发表时间：
2017-02
影响因子：
2.1
通讯作者：
M. Yagi;K. Shirasawa;T. Waki;T. Kume;S. Isobe;K. Tanase;H. Yamaguchi
中科院分区：
文献类型：
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作者：
M. Yagi;K. Shirasawa;T. Waki;T. Kume;S. Isobe;K. Tanase;H. Yamaguchi
高密度遗传图谱是比较基因组研究和数量性状基因座精细定位的重要工具，也可以促进基因组序列组装。被称为限制性位点相关DNA（RAD）的基于序列的标记技术使得能够使用大规模平行测序进行同步的单核苷酸多态性标记发现和基因分型。构建了香石竹（Dianthus carvellusL.）基于简单序列重复（SSR）标记与通过双消化RAD测序（ddRAD-seq）开发的RAD标记的组合。共检测到2404个标记（285个SSR标记和2119个RAD标记），分布在15个连锁群中，标记间距为971.5cM，平均标记间距为0.4cM。具有鉴定的图谱位置的支架的总长度为95.6 Mb，其相当于估计的基因组大小的15.4%。该图谱是国内首次报道的基于SSR和RAD标记的康乃馨高密度连锁图谱。这项研究中开发的ddRAD-seq管道还将有助于加速康乃馨和其他非模式作物的遗传和基因组学分析以及分子育种。
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 caryophyllusL.) 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.