Domestication affected stress and immune response markers in Perca fluviatilis in the early larval stage

Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

BACKGROUND

Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations.

RESULTS

Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3).

CONCLUSIONS

Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.

The Reproductive Biology of Puye (Galaxias maculatus) under Experimental Culture

This study determines the reproductive patterns of puye (Galaxias maculatus) under culture conditions. A population of 567 wild fish was caught in the Cautín River, Chile, and held in captivity for four years. Mortality, sex ratio, gonadosomatic index (GSI), sexual maturity stages, spawning period, type and frequency of spawning, and fecundity were measured. The fish grew throughout the experimental period, with the fastest rate during the first half of the first year of life. The highest mortality occurred during the first three months of the experiment and during the spawning season. The sex ratio was almost 1:1 (female:male). First sexual maturity was reached at one year of age, with an average weight of 0.85 ± 0.01 g, total length of 4.85 ± 0.16 cm, and condition factor 0.0074. The highest GSI in both females (12.14 ± 0.74) and males (17.7 ± 2.70) was recorded in August. Nevertheless, the females spawned 3 to 10 times between September and February, with the highest reproductive peak between September and October. The number of embryos per female per day varied from 1 to 429, while the total number of embryos per female during the entire season evaluated varied from 163 to 1044. There was a high correlation (r = 0.82) between absolute fecundity and body weight. Although further studies are needed in this field, these results are basic for establishing future reproductive programs in captivity as a strategy for sustainable fisheries and aquaculture management.

Long-term stress induced cortisol downregulation, growth reduction and cardiac remodeling in Atlantic salmon

Stress and elevated plasma cortisol in salmonids have been linked with pathological remodeling of the heart and deterioration of fitness and welfare. However, these associations were based on biomarkers that fail to provide a retrospective view of stress. This study is the first whereby the association of long-term stress, using scale cortisol as a chronic stress biomarker, with cardiac morphology and growth performance of wild Atlantic salmon (Salmo salar) is made. Growth, heart morphology, plasma and scale cortisol levels, and expression of genes involved in cortisol regulation of the hypothalamic-pituitary-interrenal axis of undisturbed fish (control) were compared with those of fish exposed daily to stress for 8 weeks. Though scale cortisol levels showed a time-dependent accumulation in both groups, plasma and scale cortisol levels of stress group fish were 29.1% and 25.0% lower than those of control fish, respectively. These results correlated with the overall upregulation of stress-axis genes involved in the systemic negative feedback of cortisol, and local feedback via 11β-hydroxysteroid dehydrogenases, glucocorticoid and mineralocorticoid receptors in the stress treatment at the hypothalamus and pituitary level. These lower cortisol levels were, however, counterintuitive in terms of the growth performance as stress group fish grew 33.7% slower than control fish, which probably influenced the 8.4% increase in relative ventricle mass in the stress group. Though compact myocardium area between the treatments was comparable, these parameters showed significant linear correlations with scale cortisol levels, indicating the involvement of chronic stress in cardiac remodeling. These findings underscore the importance of scale cortisol as biomarker when associating chronic stress with long-term processes including cardiac remodeling.

Changes in the liver of Tinca tinca under successive domestication using an integrated multi-omics approach

Domestication is the process of modifying the phenotype of a population through anthropic selection from human perspectives. Successive generations of domestication have influenced the physiological characteristics of tench Tinca tinca. In current study, we investigated gene and protein expression alterations in the liver of fifth-generation (F5). A total of 420 genes were found to be upregulated and 351 genes were downregulated, while 410 proteins were upregulated and 279 proteins were downregulated in domesticated T. tinca (DT). The integrated analysis of omics data revealed a total of 55 genes/proteins exhibiting consistent upregulation and 12 genes/proteins displaying consistent downregulation in DT. The upregulated genes/proteins in DT, such as SSR1, DERLIN2, OS9, DNAJB11, and HYOU1, exhibit enrichment in the protein processing in the endoplasmic reticulum pathway. Additionally, upregulated genes/proteins such as IL2RB, F13B, and IRF3 are associated with immune response. Conversely, downregulated genes/proteins in DT, including HSD11B1, CYP24A1, and COMT, play roles in hormone metabolism. These findings indicate that domestication can have a substantial impact on the physiological modifications related to protein processing, immune response, and hormone metabolism in DT. These adaptations potentially enhance their ability to thrive in artificial aquaculture environments, leading to improved growth and development. The exploration of genetic changes in DT will not only improve aquaculture practices but also provide significant insights into the broader process of domestication and its effects on physiological functions.

Functional Additives in a Selected European Sea Bass (Dicentrarchus labrax) Genotype: Effects on the Stress Response and Gill Antioxidant Response to Hydrogen Peroxide (H2O2) Treatment

Functional ingredients have profiled as suitable candidates for reinforcing the fish antioxidant response and stress tolerance. In addition, selective breeding strategies have also demonstrated a correlation between fish growth performance and susceptibility to stressful culture conditions as a key component in species domestication processes. The aim of the present study is to evaluate the ability of a selected high-growth genotype of 300 days post-hatch European sea bass (Dicentrarchus labrax) juveniles to use different functional additives as endogenous antioxidant capacity and stress resistance boosters when supplemented in low fish meal (FM) and fish oil (FO) diets. Three isoenergetic and isonitrogenous diets (10% FM/6% FO) were supplemented with 200 ppm of a blend of garlic and Labiatae plant oils (PHYTO0.02), 1000 ppm of a mixture of citrus flavonoids and Asteraceae and Labiatae plant essential oils (PHYTO0.1) or 5000 ppm of galactomannan-oligosaccharides (GMOS0.5). A reference diet was void of supplementation. The fish were fed the experimental diets for 72 days and subjected to a H₂O₂ exposure oxidative stress challenge. The fish stress response was evaluated through measuring the circulating plasma cortisol levels and the fish gill antioxidant response by the relative gene expression analysis of nfΚβ2, il-1b, hif-1a, nd5, cyb, cox, sod, cat, gpx, tnf-1α and caspase 9. After the oxidative stress challenge, the genotype origin determined the capacity of the recovery of basal cortisol levels after an acute stress response, presenting GS fish with a better pattern of recovery. All functional diets induced a significant upregulation of cat gill gene expression levels compared to fish fed the control diet, regardless of the fish genotype. Altogether, suggesting an increased capacity of the growth selected European sea bass genotype to cope with the potential negative side-effects associated to an H₂O₂ bath exposure.