title: Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus.
abstract: BACKGROUND
  Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns.
  
  
  RESULTS
  We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400-500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595.
  
  
  CONCLUSIONS
  A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits.
authors.affiliation: Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China. zning496@163.com.|Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. zning496@163.com.|College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. zning496@163.com.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China. zhanglinan1206@163.com.
authors.forename: Linan
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China. ye.tao@majorbio.com.
authors.forename: Ye
authors.initials: Y
authors.lastname: Tao
authors.affiliation: Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China. qdguoli@139.com.|Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. qdguoli@139.com.|College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. qdguoli@139.com.
authors.forename: Li
authors.initials: L
authors.lastname: Guo
authors.affiliation: National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China. dfhysunjuan@163.com.
authors.forename: Juan
authors.initials: J
authors.lastname: Sun
authors.affiliation: National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China. lixiamantianxing@163.com.
authors.forename: Xia
authors.initials: X
authors.lastname: Li
authors.affiliation: National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China. zzzznnnnzzzz@hotmail.com.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhao
authors.affiliation: National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China. pengjie333@163.com.
authors.forename: Jie
authors.initials: J
authors.lastname: Peng
authors.affiliation: National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China. yeslxj@sina.com.
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Li
authors.affiliation: Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China. liang.zeng@majorbio.com.
authors.forename: Liang
authors.initials: L
authors.lastname: Zeng
authors.affiliation: Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China. jinsa.chen@majorbio.com.
authors.forename: Jinsa
authors.initials: J
authors.lastname: Chen
authors.affiliation: Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China. yguanpin@mail.ouc.edu.cn.|Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China. yguanpin@mail.ouc.edu.cn.|College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. yguanpin@mail.ouc.edu.cn.
authors.forename: Guanpin
authors.initials: G
authors.lastname: Yang
mesh_terms: D001665:Binding Sites; D002874:Chromosome Mapping; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D008040:Genetic Linkage; D060005:Genotyping Techniques; D055993:Germ Cells, Plant; D044423:Kelp / Q000235:genetics*; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D019849:Sex Determination Processes / Q000235:genetics*
chemical_list: D015252:Deoxyribonucleases, Type II Site-Specific; C027046:TCGA-specific type II deoxyribonucleases