title: Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.
abstract: High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.
authors.affiliation: Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan.
authors.forename: Changwei
authors.initials: C
authors.lastname: Shao
authors.affiliation: BGI-Shenzhen, Shenzhen 518000, China.
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Niu
authors.affiliation: Department of Biosciences, Metapopulation Research Group, University of Helsinki, Helsinki FI-00014, Finland.
authors.forename: Pasi
authors.initials: P
authors.lastname: Rastas
authors.affiliation: Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen 518000, China.
authors.forename: Zhiyuan
authors.initials: Z
authors.lastname: Xie
authors.affiliation: Chinese Academy of Fisheries Science, Beijing 100039, China.
authors.forename: Hengde
authors.initials: H
authors.lastname: Li
authors.affiliation: Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: National Oceanographic Center, Qingdao 266071, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: BGI-Shenzhen, Shenzhen 518000, China.
authors.forename: Shuaishuai
authors.initials: S
authors.lastname: Tai
authors.affiliation: Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China.
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Tian
authors.affiliation: Faculty of Marine Science, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan chensl@ysfri.ac.cn takashis@kaiyodai.ac.jp.
authors.forename: Takashi
authors.initials: T
authors.lastname: Sakamoto
authors.affiliation: Ministry of Agriculture, Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Qingdao 266071, China Function Laboratory for Marine Fisheries Science and Food Production Processes, National Lab for Ocean Science and Technology, Qingdao 266071, China chensl@ysfri.ac.cn takashis@kaiyodai.ac.jp.
authors.forename: Songlin
authors.initials: S
authors.lastname: Chen
mesh_terms: D000818:Animals; D060467:Disease Resistance / Q000235:genetics; D005260:Female; D005393:Fish Diseases / Q000235:genetics* / Q000382:microbiology; D005432:Flounder / Q000235:genetics* / Q000382:microbiology; D008040:Genetic Linkage; D016678:Genome; D023281:Genomics; D060005:Genotyping Techniques; D008297:Male; D009990:Oryzias / Q000235:genetics; D020161:Physical Chromosome Mapping; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D026801:Synteny; D014735:Vibrio Infections / Q000235:genetics / Q000382:microbiology / Q000662:veterinary*; D015027:Zebrafish / Q000235:genetics
keywords: Japanese flounder; QTL mapping; RAD-seq-based SNP; genome synteny; high-resolution linkage map