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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
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
- Source :
- DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
- Publication Year :
- 2014
-
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.
- Subjects :
- Male
QTL mapping
Genotyping Techniques
TELEOST FISHES
Genetic Linkage
Quantitative Trait Loci
Oryzias
Sequence assembly
RECOMBINATION
Single-nucleotide polymorphism
DE-NOVO
Flounder
high-resolution linkage map
Quantitative trait locus
Genome
Polymorphism, Single Nucleotide
Synteny
LINKAGE MAP
Fish Diseases
OLIVE FLOUNDER
Genetics
Animals
Molecular Biology
Gene
Zebrafish
Disease Resistance
ALPHA GENE
biology
1184 Genetics, developmental biology, physiology
General Medicine
Genome project
DNA
Genomics
Full Papers
biology.organism_classification
Physical Chromosome Mapping
Olive flounder
genome synteny
VERTEBRATE CHROMOSOMES
Japanese flounder
Vibrio Infections
RAD-seq-based SNP
LYMPHOCYSTIS DISEASE
Female
Subjects
Details
- ISSN :
- 17561663
- Volume :
- 22
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- DNA research : an international journal for rapid publication of reports on genes and genomes
- Accession number :
- edsair.doi.dedup.....2bb47a6f03c46f160221bb664fe8b16c