Daniel Żarski

Background: Parental contributions to offspring phenotype extend beyond genetic inheritance, encompassing non-genetic factors that influence early development. However, the interplay between maternal and paternal effects remains poorly understood. This study investigates these contributions in Eurasian perch ( Perca fluviatilis ) — a valuable model to study parental effect in finfishes — by analyzing early life traits and transcriptomic profiles of larvae resulting from crosses between wild and domesticated parents. Results: Maternal effects dominated key developmental traits, including hatching success, growth, and swim bladder inflation. Transcriptomic analysis revealed a complex regulatory interplay, with 573 genes under exclusive maternal control, while no genes were solely influenced by paternal input. Maternal-effect genes were primarily associated with metabolic, developmental, and stress-response pathways, shaping early larval physiology. Further analysis identified Eurasian-perch-specific candidate maternal-effect genes, such as crtac1 , slc16a7 , cox5b , kdr , cald1 , and bin2 , highlighting their potential role in early development. Although paternal contributions were limited, a subset of genes exhibited conditional paternal influence, suggesting a nuanced parental interplay in gene expression regulation. Conclusions: These findings challenge the traditional perspective of strictly coordinated parental contributions, instead revealing a dynamic parental interplay over gene expression and offspring traits. The dominance of maternal effects suggests a primary role in shaping early development, while paternal factors may modulate expression patterns in a context-dependent manner. This study enhances our understanding of parental effects in fish, providing valuable insights for aquaculture breeding strategies and evolutionary biology research.

An important element of modern aquaculture is the creation of optimal environmental conditions for economically profitable fish farming, as only such conditions can guarantee a high growth rate and the welfare of the fish. One of the most important factors is the photoperiod, which has a substantial influence on the circadian rhythm, as it is a direct modulator of physiological functions. It has been reported that the photoperiod affects the microbiome of fish, which could potentially serve as an indicator of their welfare. Therefore, the main aim of this study was to determine the possible effects of shortening and lengthening daylight on the gut microbiome of Eurasian perch ( Perca fluviatilis L.) in a recirculating aquaculture system. Our study indicates that rearing the fish in very short daylight for 2 months has no significant effects on their biomass and length; however, long daylight reduced the specific growth rate in comparison to the control group. Furthermore, no significant differences in the structure of the gut microbiome were observed. Importantly, potential differences in the structure of the gut microbiome of fish kept under different light conditions could be masked by the possibility of bacterial transfer between tanks within individual recirculation systems. Nevertheless, discriminant analysis showed that the abundance of Flavobacterium sp. and members of the Microbacteriaceae family was significantly increased in the group of fish reared in the dark for 22 h compared to the control group. Similarly, Pseudopropionibacterium sp. was identified as a significant biomarker between the group of fish reared in the light for 24 h and the control group. These results expand our understanding of the influence of the gut microbiome on the welfare of fish in aquaculture.

Background: The influence of paternity on progeny quality, particularly during early developmental stages, has long been underappreciated. However, altered sperm phenotypes are increasingly recognized as effective tools for identifying paternal-effect-associated genes (PEAGs), whose expression in the progeny is influenced by genetic or non-genetic factors carried by the sperm. This study investigated the impact of post-thaw sperm storage (PTS) as a stressor to verify its effect on larval performance in common garden rearing trial and to reveal PEAGs in Eurasian perch ( Perca fluviatilis ) progeny. In vitro fertilizations were performed using cryopreserved sperm that was either used immediately after thawing (0 min; CON) or after 30 min of post-thaw storage at 4 °C. Results: Despite a marked decline in sperm motility during PTS, fertilization success remained unaffected, allowing the use of PTS to study its effect on progeny phenotype. Notably, larvae from the PTS group exhibited significantly higher mortality starting from 9 days post hatch, indicating strong paternal influences on early larval viability. Transcriptomic profiling of larvae at the mouth-opening stage, selected to minimize rearing-induced variation, identified 41 differentially expressed genes (DEGs), many linked to immune regulatory pathways. This suggests that paternal inputs may shape larval immune function, potentially contributing to observed mortality differences. Among the DEGs, several genes, mfap4 , gimap , hlag , pigr , neo1 , and pde6g , emerged as strong candidate PEAGs. Conclusions: This study shows that even a brief, 30-minute PTS not only reduces sperm motility but also imprints lasting effects on progeny performance and survival. By selectively shaping the pool of functional sperm, PTS acts as an additional layer of selection, enriching for cells with specific traits and offering a powerful, controlled system for studying non-genetic inheritance factors and identifying PEAGs in fish. Transcriptomic analysis uncovered a deeper dimension to this process, revealing that maternal identity can amplify or buffer paternal contributions which serves as evidence of a complex parental interplay that influences early development. In effect, this study provides a robust experimental model based on controlled, paired fertilization design together with transcriptomic profiling of the offspring to identify novel PEAGs and reveal molecular consequences of paternal variation induced by post-thaw storage.

The production of European perch (Perca fluviatilis) has become notably refined, with numerous physiological and nutritional studies conducted in recent years. However, it is still an expensive undertaking due to the high amount of animal protein required in the feed. Therefore, we investigated the possibility of using hemp meal (HM) as an alternative source of protein in extruded feed for perch reared in recirculating aquaculture systems (RASs). Perch fry (initial body weight of 68.1 g) was divided into four groups (HM0, HM10, HM20, HM30; 100 fish in each) and fed with diets containing different levels of HM (0, 10, 20 or 30%, respectively) for 10 weeks. Overall, dietary inclusion of HM did not affect body parameters, muscle composition, or blood parameters, nor did it cause any serious histopathological lesions. Nonetheless, basic production indices (SGR, FCR, PER) all peaked in the HM20 group, and predominantly positive changes in intestinal mucosa were found in all three HM-inclusion groups. Furthermore, the expression patterns of several genes in the intestine and liver were different in groups HM20-30 than in HM0-10. Lastly, hepatic activities of alkaline phosphatase (ALP) and glutathione peroxidase (GPX) diminished with increasing dietary HM inclusion levels. In summary, there were no negative effects of HM on the homeostasis of studied fish or, more specifically, the physiology of their digestive organs. When accounting for minor tendencies in the results, the dietary inclusion of hemp meal at 20% turned out to be the most promising fish meal alternative for the European perch.

Aquaculture in rural areas, carried out in accordance with current EU requirements, aims to contribute significantly to the conservation of the biodiversity of aquatic resources, the protection of which is a prerequisite for sustainable economic and social development. The objective of this study was to present the conceptual and technical framework and to analyze the costs and profitability of producing the consumer-attractive Eurasian perch (Perca fluviatilis L.) based on the untapped potential of hatchery infrastructure and dedicated earthen ponds for common carp (Cyprinus carpio L.) production. The experiments were conducted under Polish conditions, but the results/methods can be successfully applied in other countries, mainly in Central and Eastern Europe, where production in earthen ponds is the basis of aquaculture production. The analysis of the profitability of the venture shows that the cost structure was dominated by labor and feed inputs. Despite high variable costs, this type of production can be profitable and contribute to food security and economic development in line with the EU’s Blue Growth Strategy. The article also analyzes the potential opportunities and risks of fish production based on the Recirculating Aquaculture System (RAS) and the Recirculating Aquaculture Multitrophic Pond System (RAMPS).

Background: The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies inPerca fluviatilis,Perca schrenkii, andSander vitreusalong with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems.Results: We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene inP. flavescens. Phylogenetically related and structurally similar amhr2duplicates (amhr2b) were found inP. schrenkiiandSander lucioperca, potentially dating this duplication event to their last common ancestor around 19–27 Mya. InP. fluviatilisandS. vitreus, thisamhr2bduplicate has been likely lost while it was subject to amplification inS. lucioperca. Analyses of theamhr2blocus inP. schrenkiisuggest that this duplication could be also male-specific as it is inP. flavescens. InP. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting thatP. fluviatilishas a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198,hsdl1,tbc1d32) with higher expression in the testis than in the ovary.Conclusions: Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three knownPercaspecies.

Knowledge about paternal-effect-genes (PEGs) (genes whose expression in the progeny is influenced by paternal factors present in the sperm) in fish is very limited. To explore this issue, we used milt cryopreservation as a specific challenge test for sperm cells, thus enabling selection amidst cryo-sensitivity. We created two groups of Eurasian perch (Perca fluviatilis) as a model – eggs fertilized either with fresh (Fresh group) or cryopreserved (Cryo group) milt from the same male followed by phenotypic-transcriptomic examination of consequences of cryopreservation in obtained progeny (at larval stages). Most of the phenotypical observations were similar in both groups, except the final weight which was higher in the Cryo group. Milt cryopreservation appeared to act as a "positive selection" factor, upregulating most PEGs in the Cryo group. Transcriptomic profile of freshly hatched larvae sourced genes involved in the development of visual perception and we identified them as PEGs. Consequently, larvae from the Cryo group exhibited enhanced eyesight, potentially contributing to more efficient foraging and weight gain compared to the Fresh group. This study unveils, for the first time, the significant influence of the paternal genome on the development of the visual system in fish, highlighting pde6g, opn1lw1, and rbp4l as novel PEGs.