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整合连锁图谱揭示了奇努克鲑鱼(Oncorhynchus tshawytscha)适应变异的候选基因。

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

机构信息

School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, USA.

出版信息

Mol Ecol Resour. 2016 May;16(3):769-83. doi: 10.1111/1755-0998.12479. Epub 2015 Nov 25.

Abstract

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 2336 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 colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.

摘要

鲑鱼是一种重要的文化和生态资源,在其原生和引入范围之间表现出近乎全球分布。先前的研究已经为几个物种生成了连锁图谱和基因组资源,以及两个物种的基因组组装。我们首先利用映射和基因分型方法的改进,通过组装来自不同来源的家族数据,为奇努克鲑鱼 Oncorhynchus tshawytscha 创建了一个密集的连锁图谱。我们成功地映射了 14620 个 SNP 基因座,包括 2336 个端粒附近区域的旁系同源基因座。然后,这个改进的图谱被用作整合基因组资源进行基因注释和群体基因组分析的基础。我们总共将来自大西洋鲑鱼基因组的 286 个支架锚定到连锁图谱上,为放置 11728 个奇努克鲑鱼 ESTs 提供了一个框架。先前确定的耐热性 QTL 被发现与几个候选基因共定位,包括 HSP70,这是一个已知参与热响应的基因,以及它的抑制剂。还鉴定出了基因组中多个种群之间分化程度较高的区域,这些区域的 EST 注释鉴定出了与适应相关性状(如应激反应、生长和行为)的候选基因。总的来说,这些结果表明,将基因组资源与连锁图谱相结合来增强进化推断是有用的。

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