An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14,620 SNP loci including 2,336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11,728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to co-localize with several candidate genes including HSP70, a gene known to be involved in thermal respo...

鲑科鱼类（Salmonids）是兼具重要文化与生态价值的类群，其原生分布与引种范围几乎覆盖全球。既往研究已为多个鲑科物种构建了连锁图谱与基因组学资源，并为其中两个物种完成了基因组组装。本研究首先依托图谱构建与基因分型技术的改进成果，通过整合多来源的家系数据，为大鳞大麻哈鱼（Chinook salmon，Oncorhynchus tshawytscha）构建了高密度连锁图谱。本研究成功将14620个单核苷酸多态性（SNP）位点定位至该图谱，其中包括位于亚端粒区域的2336个旁系同源基因位点。随后，该优化后的高密度连锁图谱被用作基础框架，整合了用于基因注释与群体基因组学分析的各类基因组学资源。我们将大西洋鲑（Atlantic salmon）基因组中共计286个支架序列（scaffold）锚定至该连锁图谱，为11728个大鳞大麻哈鱼表达序列标签（EST）的定位提供了参照框架。此前已被鉴定的耐热性数量性状位点（QTL）被发现与多个候选基因共定位，其中包括已知参与热应激响应的HSP70基因……