Ana Sofia Lindeza

Fitness-related traits are shaped by both additive and nonadditive genetic effects, resulting in a complex and context-dependent genetic architecture. However, the relative contribution of these components remains poorly understood, particularly for major-effect loci underlying life-history traits. In this study, we investigated the additive genetic contributions and potential epistatic interactions between 2 unlinked major-effect loci, vgll3 and six6, that influence age-at-maturity in Atlantic salmon (Salmo salar). By crossing parents heterozygous at both loci to create and rear 6 large full-sib families in a common-garden environment, we assessed male maturation, and additional fitness-related traits, 1-year post fertilization. We found that vgll3 and six6 significantly influenced maturation probability in an additive manner, with the likelihood of early maturation increasing with the number of early-maturing (E) alleles. Double homozygote males with 4 E alleles, vgll3*EE;six6*EE, showed an estimated 60% probability of maturation, compared with only a 20% probability for double late (L) homozygotes, vgll3*LL;six6*LL. Models accounting for the interaction showed no evidence of epistasis between vgll3 and six6, supporting an additive relationship. Additionally, body condition differed by maturation status in a genotype-dependent manner, particularly at vgll3. Studied here in combination for the first time under controlled common-garden settings, we show that vgll3 and six6 contribute additively to the regulation of male maturation age in Atlantic salmon. This work, which complements earlier studies conducted separately on these 2 loci, shows the importance of distinguishing additive from nonadditive genetic effects when dissecting the genetic architecture of fitness-related traits, as this distinction is fundamental for quantifying heritable variation and more accurately predicting evolutionary responses to selection.

Rapid environmental change is exposing organisms to conditions that do not match those under which they evolved, making it increasingly important to understand how genetic variation shapes phenotypic responses to environmental stress. Since most phenotypic traits arise from interactions between genetic variation and the environments experienced throughout an organism’s lifetime, understanding the genetic architecture of these interactions is central to predicting how populations will respond to novel environments. While genotype-by-environment interactions (G×E) are well studied in quantitative genetics, identifying specific loci that contribute to environmentally dependent trait expression remains rare. Salmonids already exhibit a wide portfolio of plastic life-history strategies, reflecting adaptation to highly heterogeneous environments, yet it remains unclear whether known major-effect loci involved in life-history regulation also contribute to variation in plastic responses to environmental change. One such major-effect locus is the transcription factor six6 , which has been repeatedly associated with variation in age at maturity across multiple populations of rainbow trout ( Oncorhynchus mykiss ). Since maturation timing is closely linked to growth trajectories and patterns of energetic allocation during early development, allelic variation at this locus may also influence growth responses to warming conditions. Here, we test this hypothesis using a common-garden experiment in which 6 months old juvenile rainbow trout were reared under current and warming (+2°C) temperature regimes. By quantifying genotype-specific reaction norms across environments, we show that six6 genotype contributes to environmentally dependent variation in growth and body composition, with individuals heterozygous for the six6 locus showing a distinct and steeper response to warming relative to homozygotes. These findings provide evidence that a major life-history gene shapes plastic responses to thermal stress in juvenile rainbow trout, with novel implications for how standing genetic variation at in large-effect loci may influence population-level responses to climate warming.

Atlantic Salmon life-histories are shaped by interactions between environmental and genetic factors. The mitochondrial NADP-dependent malic enzyme ( me3 or mMEP-2), historically described as a polymorphic allozyme varying across populations, has been associated with age at maturity in wild populations. However, more recently, other loci ( vgll3 and six6) have also been shown to influence age at maturity, and studies disentangling their relative effects are lacking. This is especially important given that me3 and vgll3 are located on the same chromosome. Here, we used a common-garden experiment to investigate the impact of the me3 locus on male parr maturation probability in a Finnish population while accounting for variation at the vgll3 and six6 loci. Although we found linkage disequilibrium between the me3 and vgll3 loci, me3 remained moderately associated with maturation probability even when vgll3 genotype was accounted for. Together, these results support observations from wild populations of a genetic effect of me3 on maturation probability, but they also highlight the importance of considering both me3 and vgll3 when investigating the mechanism linking these loci to maturation.

The Näätämö River, in the far north of Europe, hosts a large Atlantic salmon (Salmo salar) stock with high socio-economic value. The catchment has near-pristine environmental conditions, although there are recent signs of stock declines. It nevertheless offers a good opportunity to monitor the status of a near pristine wild salmon system. This study aimed to characterize the fine-scale genetic structure of Atlantic salmon in the Näätämö River and evaluated the possibility to assign individuals to their population of origin. We genotyped juveniles sampled from eight locations using a 60 K single nucleotide polymorphism (SNP) panel to characterize within-river genetic diversity and structure. We also tested the performance of a previously designed 180 SNP panel to assign individuals to their population of origin. The genetic structure of the Näätämö River salmon population appears weak (F_ST ranging from 0.001–0.035), possibly due to natural straying. The performance of the predesigned panel in assigning individuals to their population of origin was moderate to high (82–85%), but customization could further enhance its accuracy. Additionally, we described the life-history diversity of salmon within the river using a long-term scale archive of c. 22,000 individuals collected over 48 years, identifying 59 unique life-history strategies. We suggest that to protect the self-sustaining salmon population in the Näätämö River, it would be important to manage the salmon fishery and conserve the population by incorporating up-to-date knowledge of stock status, considering their genetic structure, substantial gene flow and diverse life history.

Understanding the molecular basis of plasticity and physiological tolerance to environmental changes is crucially important in the era of global change. Salmonids, a diverse family of fishes that includes salmon, trout, and charr, are emerging as powerful models for studying molecular responses to such changes. These species inhabit a wide range of aquatic environments, including freshwater and marine ecosystems, and are known for their remarkable adaptability to varying environmental conditions and for their variety of life history strategies. This review synthesizes current research on some of the major molecular mechanisms underlying transcriptional responses to important environmental changes. We discuss key studies that have applied state-of-the-art genomic tools in salmonids to uncover some of the gene expression changes underpinning plastic or acclimatory responses due to changes in temperature, salinity, oxygen levels or pH. By presenting examples of genes involved in these processes in salmonids, this review aims to provide insights into the broader implications of these findings, namely for conservation strategies and management. We also consider the potential of salmonids as emerging model species for monitoring the impacts of climate change on aquatic ecosystems, and their capacity to cope with rapid and inevitable environmental change. Finally, we outline future research directions to further elucidate the molecular pathways underlying plastic responses to environmental changes, with potential implications for evolutionary adaptation in these species.