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.
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DOI：
10.1093/dnares/dsv001
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发表时间：
2015-04
期刊：
影响因子：
--
通讯作者：
Chen S
中科院分区：
文献类型：
--
作者：
Shao C;Niu Y;Rastas P;Liu Y;Xie Z;Li H;Wang L;Jiang Y;Tai S;Tian Y;Sakamoto T;Chen S
高分辨率遗传图谱对于复杂性状的精细定位、基因组组装和比较基因组分析至关重要。单核苷酸多态性（SNP）是用于遗传图谱构建的主要分子标记。在这项研究中，我们确定了13，362个均匀分布在日本比目鱼（Paralichthys olivaceus）基因组中的SNP。在这些SNP中，对12，712个高置信度SNP进行高通量基因分型，并分配到24个共有连锁群（LGs）。该遗传连锁图的总长度为3497.29cM，平均位点间距离为0.47cM，代表了目前报道的牙鲆遗传连锁图。共检测到9个与鳗弧菌抗病性相关的数量性状基因座（QTL），形成2个主要的QTL簇。所有QTL可解释总表型变异的5.1 - 8.38%。对基因组拼接图上的QTL区域进行同线性分析，共发现12个免疫相关基因，其中4个与鳗弧菌抗病性强相关。此外，246个平均大小为21.79 Mb的基因组组装支架被锚定到LG上;这些支架包含522.99 Mb，代表了组装的基因组序列的95.78%。利用构建的装配支架对斑马鱼和青鳉进行了基因组同线性分析。比目鱼和青鳉几乎具有一对一的同线性，而比目鱼和斑马鱼表现出多同线性对应。新开发的高分辨率遗传图谱将有助于日本比目鱼的QTL定位，支架组装和基因组同线性分析，标志着该物种正在进行的基因组计划的里程碑。
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.
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影响因子：
9.8
作者：
Hillier LW;Miller RD;Baird SE;Chinwalla A;Fulton LA;Koboldt DC;Waterston RH
通讯作者：
Waterston RH
影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
4.4
作者：
Chutimanitsakun Y;Nipper RW;Cuesta-Marcos A;Cistué L;Corey A;Filichkina T;Johnson EA;Hayes PM
通讯作者：
Hayes PM
影响因子：
10.7
作者：
Brunet, Frederic G.;Roest Crollius, Hugues;Robinson-Rechavi, Marc
通讯作者：
Robinson-Rechavi, Marc
影响因子：
2.9
作者：
Berthier-Schaad, Yvette;Kao, Wen Hong Linda;Smith, Michael W.
通讯作者：
Smith, Michael W.