Kjærner-Semb Erik, Edvardsen Rolf B, Ayllon Fernando, Vogelsang Petra, Furmanek Tomasz, Rubin Carl Johan, Veselov Alexey E, Nilsen Tom Ole, McCormick Stephen D, Primmer Craig R, Wargelius Anna
Institute of Marine Research Bergen Norway.
Uppsala University Uppsala Sweden.
Evol Appl. 2020 Sep 23;14(2):446-461. doi: 10.1111/eva.13129. eCollection 2021 Feb.
Most Atlantic salmon ( L.) populations follow an anadromous life cycle, spending early life in freshwater, migrating to the sea for feeding, and returning to rivers to spawn. At the end of the last ice age ~10,000 years ago, several populations of Atlantic salmon became landlocked. Comparing their genomes to their anadromous counterparts can help identify genetic variation related to either freshwater residency or anadromy. The objective of this study was to identify consistently divergent loci between anadromous and landlocked Atlantic salmon strains throughout their geographical distribution, with the long-term aim of identifying traits relevant for salmon aquaculture, including fresh and seawater growth, omega-3 metabolism, smoltification, and disease resistance. We used a Pool-seq approach ( = 10-40 individuals per population) to sequence the genomes of twelve anadromous and six landlocked Atlantic salmon populations covering a large part of the Northern Hemisphere and conducted a genomewide association study to identify genomic regions having been under different selection pressure in landlocked and anadromous strains. A total of 28 genomic regions were identified and included on Chr 13 and on Chr 18. Seven of the regions additionally displayed consistently reduced heterozygosity in fish obtained from landlocked populations, including the genes , and on Chr 15. We also found 16 regions, including on Chr 17, which consistently display reduced heterozygosity in the anadromous populations compared to the freshwater populations, indicating relaxed selection on traits associated with anadromy in landlocked salmon. In conclusion, we have identified 37 regions which may harbor genetic variation relevant for improving fish welfare and quality in the salmon farming industry and for understanding life-history traits in fish.
大多数大西洋鲑（L.）种群遵循溯河洄游的生命周期，在淡水中度过早期生活，洄游到海洋觅食，然后返回河流产卵。在约1万年前的上一个冰河时代末期，一些大西洋鲑种群变成了陆封型。将它们的基因组与其溯河洄游型对应种群进行比较，有助于识别与淡水栖息或溯河洄游相关的遗传变异。本研究的目的是在整个地理分布范围内，识别溯河洄游型和陆封型大西洋鲑品系之间持续存在差异的基因座，其长期目标是识别与鲑鱼养殖相关的性状，包括淡水和海水生长、ω-3代谢、降海洄游和抗病性。我们采用Pool-seq方法（每个种群10 - 40个个体）对覆盖北半球大部分地区的12个溯河洄游型和6个陆封型大西洋鲑种群的基因组进行测序，并开展全基因组关联研究，以识别在陆封型和溯河洄游型品系中受到不同选择压力的基因组区域。总共识别出28个基因组区域，并包括13号染色体上的 和18号染色体上的 。其中7个区域在来自陆封型种群的鱼类中还表现出杂合性持续降低，包括15号染色体上的 、 和 基因。我们还发现16个区域，包括17号染色体上的 ，与淡水种群相比，这些区域在溯河洄游型种群中杂合性持续降低，这表明陆封型鲑鱼与溯河洄游相关的性状受到的选择有所放松。总之，我们已经识别出37个区域，这些区域可能蕴藏着与改善鲑鱼养殖业中鱼类福利和品质以及理解鱼类生活史性状相关的遗传变异。
