Aquaculture

The role of linked genomic architecture in shaping population structure and complex phenotypes in farmed Atlantic salmon

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Abstract

There is strong scientific evidence that large structural chromosomal rearrangements in Atlantic salmon (Salmo salar) influence recombination rates and function as "supergenes" affecting complex traits. These rearrangements typically suppress recombination in specific genomic regions, forming large linked haplotype blocks that allow co-adapted alleles at multiple loci to be inherited together. Increasingly, smaller-scale (but still large) haplotype blocks are also being implicated in the genetic architecture of complex traits. In this study, we investigated the presence of such haplotype blocks in Atlantic salmon and their associations with production and adaptation-related traits. We analyzed high-density SNP genotypes (200K) from over 3,400 individuals sampled across Canada, Norway, and Tasmania. Local principal component analyses across the genome identified genomic regions where local population structure diverged significantly from the genome-wide pattern. These regions exhibited patterns of differentiation, minor allele frequency, heterozygosity, and linkage disequilibrium consistent with linked genomic architecture. A total of 38 outlier regions were identified, distributed across 23 chromosomes (out of 29 of the European lineage). These regions included those encompassing well known large structural chromosomal rearrangements, thereby highlighting the adequacy of the method to detect linked genomic architecture. The relatively smaller outlier regions, not associated with large chromosomal rearrangements, ranged from 0.30 Mb to 8.62 Mb, with an average size of 1.48 Mb. Interestingly, some of these regions showed evidence of segregation within and across populations. Using a comprehensive phenotypic dataset from a well-structured selective breeding program in the Tasmanian Atlantic salmon population (TAS), we found significant associations between TAS haplotype clusters and complex traits in several outlier regions. While associations involving relatively smaller haplotype blocks were generally not as strong as those linked to large chromosomal rearrangements, they remained strongly significant according to permutation tests adjusted for multiple comparisons. For instance, the genetic merit difference between haplotype clusters in a region on chromosome Ssa3 (81.07-82.02 Mb) corresponded to 8.3% of the phenotypic mean of summer survival. Similarly, a region on Ssa19 (22.19-23.68 Mb) showed a 9.4% difference in resistance to amoebic gill disease. Furthermore, we identified Mendelian inheritance pattern for some of the linked genomic architecture with significant associations, indicating that selection and mating decisions could be planned to favor the prevalence of specific haplotype blocks and, consequently, accelerate the genetic progress of certain traits. Overall, our findings underscore the role of linked genomic architectures in shaping population structure and provide strong evidence of their contribution to the expression of complex traits in farmed Atlantic salmon, offering new opportunities for selective breeding programs to accelerate genetic progress.

Keywords: 2026

How to Cite:

Carvalheiro, R., Mekkawy, W., Khaw, H., Luke, T., Evans, B., Lind, C. & Kijas, J., (2026) “The role of linked genomic architecture in shaping population structure and complex phenotypes in farmed Atlantic salmon”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283634. doi: https://doi.org/10.31274/wcgalp.23506

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