PUBLICATION
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
- Authors
- Shao, C., Niu, Y., Rastas, P., Liu, Y., Xie, Z., Li, H., Wang, L., Jiang, Y., Tai, S., Tian, Y., Sakamoto, T., Chen, S.
- ID
- ZDB-PUB-150313-4
- Date
- 2015
- Source
- DNA research : an international journal for rapid publication of reports on genes and genomes 22(2): 161-70 (Journal)
- Registered Authors
- Keywords
- Japanese flounder, QTL mapping, RAD-seq-based SNP, genome synteny, high-resolution linkage map
- MeSH Terms
-
- Animals
- Disease Resistance/genetics
- Female
- Fish Diseases/genetics*
- Fish Diseases/microbiology
- Flounder/genetics*
- Flounder/microbiology
- Genetic Linkage
- Genome*
- Genomics
- Genotyping Techniques
- Male
- Oryzias/genetics
- Physical Chromosome Mapping*
- Polymorphism, Single Nucleotide
- Quantitative Trait Loci*
- Synteny
- Vibrio Infections/genetics
- Vibrio Infections/microbiology
- Vibrio Infections/veterinary*
- Zebrafish/genetics
- PubMed
- 25762582 Full text @ DNA Res.
Citation
Shao, C., Niu, Y., Rastas, P., Liu, Y., Xie, Z., Li, H., Wang, L., Jiang, Y., Tai, S., Tian, Y., Sakamoto, T., Chen, S. (2015) 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. DNA research : an international journal for rapid publication of reports on genes and genomes. 22(2):161-70.
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 522.995 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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping