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

Show full item record



Permalink

http://hdl.handle.net/10138/161923

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 , vol. 22 , no. 2 , pp. 161-170 . https://doi.org/10.1093/dnares/dsv001

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
Author: Shao, Changwei; Niu, Yongchao; Rastas, Pasi; Liu, Yang; Xie, Zhiyuan; Li, Hengde; Wang, Lei; Jiang, Yong; Tai, Shuaishuai; Tian, Yongsheng; Sakamoto, Takashi; Chen, Songlin
Contributor: University of Helsinki, Biosciences
Date: 2015-04
Language: eng
Number of pages: 10
Belongs to series: DNA Research
ISSN: 1340-2838
URI: http://hdl.handle.net/10138/161923
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.
Subject: Japanese flounder
RAD-seq-based SNP
high-resolution linkage map
QTL mapping
genome synteny
LINKAGE MAP
VERTEBRATE CHROMOSOMES
LYMPHOCYSTIS DISEASE
TELEOST FISHES
OLIVE FLOUNDER
ALPHA GENE
DE-NOVO
DNA
ZEBRAFISH
RECOMBINATION
1184 Genetics, developmental biology, physiology
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
161.full.pdf 673.1Kb PDF View/Open

This item appears in the following Collection(s)

Show full item record