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
Changwei ShaoSonglin Chen

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 ...Continue Reading

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Citations

Sep 16, 2015·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Qiong ZhangHongwen Huang
May 6, 2016·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yankun WangRongzhan Guan
Nov 6, 2015·International Journal of Molecular Sciences·Jingqun AoXinhua Chen
Apr 5, 2018·International Journal of Molecular Sciences·Hetron Mweemba Munang'anduLior David
May 13, 2020·GigaScience·Graham J EtheringtonFederica Di Palma
Sep 18, 2018·Reviews in Aquaculture·Diego RobledoRoss Houston
Jan 11, 2017·BMC Genomics·Le WangGen Hua Yue
Mar 15, 2018·Frontiers in Plant Science·Zhaoyun TanZhengsheng Zhang
Oct 23, 2018·Evolutionary Applications·Jennifer A Hoey, Malin L Pinsky

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Methods Mentioned

BETA
genotyping
Genome Sequencing
PCR

Software Mentioned

JoinMap
BLASTP
MAP
Ensembl
BLASTN
Lep
WinQTLCart2
custom

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