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

文献类型： 外文期刊

第一作者： Shao, Changwei

作者： Shao, Changwei;Liu, Yang;Wang, Lei;Tian, Yongsheng;Chen, Songlin;Shao, Changwei;Liu, Yang;Wang, Lei;Tian, Yongsheng;Chen, Songlin;Shao, Changwei;Sakamoto, Takashi;Niu, Yongchao;Xie, Zhiyuan;Tai, Shuaishuai;Rastas, Pasi;Li, Hengde;Jiang, Yong

作者机构：

关键词： Japanese flounder;RAD-seq-based SNP;high-resolution linkage map;QTL mapping;genome synteny

期刊名称：DNA RESEARCH （ 影响因子：4.458； 五年影响因子：5.371 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： 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.

分类号： Q75

  • 相关文献

[1]Genetic diversity in three Japanese flounder (Paralichthys olivaceus) populations revealed by ISSR markers. Liu, YG,Chen, SL,Li, J,Li, BF. 2006

[2]Molecular identification and expression analysis of natural resistance associated macrophage protein (Nramp) cDNA from Japanese flounder (Paralichthys olivaceus). Chen, SL,Wang, ZJ,Xu, MY,Gui, JF. 2006

[3]Screening and analysis of PoAkirin1 and two related genes in response to immunological stimulants in the Japanese flounder (Paralichthys olivaceus). Yang, Chang-Geng,Sun, Bing,Liu, Shan-Shan,Chen, Song-Lin,Yang, Chang-Geng,Wang, Xian-Li,Zhang, Bo. 2013

[4]Effects of dietary supplementation of A3 alpha-peptidoglycan on innate immune responses and defense activity of Japanese flounder (Paralichthys olivaceus). Zhou, J,Song, XL,Huang, J,Wang, XH. 2006

[5]Production and confirmation of clones using gynogenesis in Japanese flounder. Liu, Haijin,Liu, Yongxin,Wang, Guixing,Wang, Yufen,Si, Fei,Sun, Zhaohui,Zhang, Xiaoyan,Liu, Yi,Hou, Jilun. 2011

[6]Assessing the genetic structure of three Japanese flounder (Paralichthys olivaceus) stocks by microsatellite markers. Liu, YG,Chen, SL,Li, BF. 2005

[7]Major histocompatibility complex class IIB allele polymorphism and its association with resistance/susceptibility to Vibrio anguillarum in Japanese flounder (Paralichthys olivaceus). Zhang, Y. X.,Chen, S. L.,Liu, Y. G.,Sha, Z. X.,Liu, Z. J.. 2006

[8]Production and verification of heterozygous clones in Japanese flounder, Paralichthys olivaceus by microsatellite marker. Liu, Haijin,Liu, Yongxin,Wang, Guixing,Wang, Yufen,Si, Fei,Sun, Zhaohui,Zhang, Xiaoyan,Liu, Yi,Hou, Jilun. 2011

[9]Tissue-specific accumulation of cadmium and its effects on antioxidative responses in Japanese flounder juveniles. Cao, Liang,Huang, Wei,Shan, Xiujuan,Dou, Shuozeng,Huang, Wei,Shan, Xiujuan,Ye, Zhenjiang.

[10]Genetic verification of doubled haploid Japanese flounder, Paralichthys olivaceus by genotyping telomeric microsatellite loci. Liu, Yongxin,Liu, Haijin,Wang, Guixing,Wang, Yufen,Si, Fei,Sun, Zhaohui,Zhang, Xiaoyan,Liu, Yi,Hou, Jilun. 2012

[11]Efficacy of Vibrio anguillarum antigen administered by intraperitoneal injection route in Japanese flounder, Paralichthys olivaceus (Temminck et Schlegel). Li, J,Gao, DM,Wang, Q,Wang, JY,Wang, QY. 2005

[12]Estimation of genetic parameters for growth traits of Japanese flounder Paralichthys olivaceus using an animal model. Liu, Yong-Xin,Liu, Hai-Jin,Wang, Gui-Xing,Wang, Yu-Fen,Si, Fei,Sun, Zhao-Hui,Zhang, Xiao-Yan,Wang, Jia-Di. 2011

[13]Influence of epistatic segregation distortion loci on genetic marker linkages in Japanese flounder. Zhao, Jingli,Gao, Jin,Yang, Runqing,Han, Dandan,Shi, Kuntao,Wang, Li. 2018

[14]Molecular cloning, structure and expressional profiles of two novel single-exon genes (PoCCR6A and PoCCR6B) in the Japanese flounder (Paralichthys olivaceus). Wang, Lei,Zhang, Yong-zhen,Xu, Wen-teng,Jia, Xiao-dong,Chen, Song-lin.

[15]Constructing a genetic linkage map and mapping quantitative trait loci for skeletal traits in Japanese flounder. Liu, Yi,Zhang, Xiaoyan,Si, Fei,Sun, Zhaohui,Wang, Guixing,Wang, Yufen,Liu, Yi,Liu, Yongxin,Liu, Yingjie,Yang, Runqing,Liu, Haijin.

[16]Proteome profiling reveals immune responses in Japanese flounder (Paralichthys olivaceus) infected with Edwardsiella tarda by iTRAQ analysis. Wang, Lei,Shao, Changwei,Xu, Wenteng,Zhou, Qian,Wang, Na,Chen, Songlin,Wang, Lei,Shao, Changwei,Xu, Wenteng,Zhou, Qian,Wang, Na,Chen, Songlin.

[17]A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice. Hu, Zejun,Sun, Fan,Xin, Xiaoyun,Qian, Xi,Yang, Jingshui,Luo, Xiaojin,Hu, Zejun,He, Haohua,Wang, Wenxiang,Zhang, Shiyong. 2012

[18]High-Density Linkage Map Construction and Mapping of Salt-Tolerant QTLs at Seedling Stage in Upland Cotton Using Genotyping by Sequencing (GBS). Latyr Diouf,Du, Xiongming,Zhaoe Pan,Shou-Pu He,Wen-Fang Gong,Yin Hua Jia,Richard Odongo Magwanga,Kimbembe Romesh Eric Romy,Harun or Rashid,Joy Nyangasi Kirungu,Xiongming Du. 2017

[19]Dynamic QTL mapping for plant height in Upland cotton (Gossypium hirsutum). Shang, Lianguang,Abduweli, Abdugheni,Cai, Shihu,Liu, Fang,Wang, Kunbo,Wang, Yumei.

[20]High-Density Genetic Mapping Identifies New Major Loci for Tolerance to Low-Phosphorus Stress in Soybean. Zhang, Dan,Li, Hongyan,Chu, Shanshan,Lv, Haiyan,Wang, Jinshe,Zhang, Hengyou,Hu, Zhenbin,Yu, Deyue. 2016

作者其他论文 更多>>

微信小程序