Jose Manuel Yanez

Infectious pancreatic necrosis (IPN) is one of the most economically important viral diseases affecting salmonid aquaculture worldwide. Resistance to infectious pancreatic necrosis virus (IPNV) has been widely studied in rainbow trout (Oncorhynchus mykiss) by using SNP-based approaches. For instance, genome-wide association studies have led to the identification of moderate- to major-effect quantitative trait loci (QTL) controlling the trait. However, causative mutations underlying IPNV resistance in rainbow trout remains poorly understood. The potential contribution of structural variants (SVs) to the genetic architecture of resistance has received little attention despite their recognized role in shaping phenotypic variation and complex traits. In this study, we used whole-genome sequencing combined with a multi-tool SV detection approach to identify structural variants associated with IPNV-resistant and susceptible rainbow trout. A total of 2,564 SVs (2,358 deletions, 206 insertions) were identified as highly associated between resistant and susceptible individuals. Functional annotation showed that twelve of these variants overlapped genes with known immune-related functions, suggesting that they may contribute to variation in host antiviral responses. These findings provide further evidence that structural variation may contribute to resistance-related phenotypes in rainbow trout. Further incorporation of SVs into genomic analyses may improve the resolution of association studies and support the development of more comprehensive genomic selection strategies for disease resistance in aquaculture breeding programs.

Background: The microbiota‒gut‒brain axis modulates pigs’ stress response, behavior, and overall welfare. Stressful management practices can disrupt gut microbiota (GM), negatively impacting pigs' health and welfare. This study evaluated how the quality of human handling influences stress-related physiological responses, productive performance, and gut microbiota (GM) composition in pigs during the nursery phase. Results: Female pigs (n= 36, 21 days old) were randomly assigned to three experimental groups (12 pigs/group, four pens per treatment): positive human handling (PHH), negative human handling (NHH), and a control group (CG). The PHH group experienced gentle tactile interactions, whereas the NHH group was subjected to chronic intermittent stress through acute stressors, and the CG group received minimal handling for routine practices. Hair cortisol concentrations were measured as an indicator of chronic stress (days 15 and 64). Productive performance was assessed through body weight (BW), average daily gain (ADG), average daily feed intake (ADFI), and feed conversion (FC). Fecal samples were collected at baseline (T0, day 16), mid-study (T1, day 37), and end of the study (T2, day 65) and analyzed using 16S rRNA gene amplicon sequencing to assess GM changes over time. Pigs in the PHH group showed a significant reduction in cortisol levels from baseline to post-treatment (P < 0.0001), while no significant changes were observed in the NHH group (P = 0.26). A smaller but significant decrease was also detected in the CG group (P = 0.001). PHH pigs had higher BW (P = 0.0009) and ADG (P = 0.03) during the later growth phase compared to NHH pigs. At T2, PHH pigs exhibited greater diversity and richness compared to NHH pigs, indicating a restorative effect on GM composition. Differential abundance analyses identified four bacterial genera that distinguished treatment groups: Blautia , Megasphaera , and Subdoligranulum were enriched in PHH pigs, while Terrisporobacter was enriched in NHH pigs. Additionally, bacterial interaction networks exhibited the least complex network in the NHH group, with ecological associations primarily involving Clostridium and Terrisporobacter . Conclusions: The quality of human handling influenced stress physiology, performance, and gut microbiota in pigs. Positive handling reduced cortisol levels, improved growth, and promoted microbial diversity, while negative handling was linked to decreased performance and reduced microbial network complexity. These results highlight the potential of positive interactions to enhance welfare and productivity, and identify specific bacterial genera as potential biomarkers differentiating negative and positive handling conditions.

Understanding the genetic architecture of economically important traits is essential for the design and implementation of efficient breeding programs. Here, we analysed 3,653 Eastern oysters (Crassostrea virginica) from 62 crossing groups and 307 full-sib families, all genotyped with a 200 K SNP array, to (i) estimate heritability and genetic correlations for six growth-related traits, (ii) detect quantitative trait loci (QTL) and candidate genes, and (iii) compare the accuracy of pedigree- (PBLUP) versus genomic-based (GBLUP) predictions across marker densities, selection strategies (physical distance (PD) versus linkage disequilibrium (LD) and phenotype-based genotyping strategies. SNP-based Heritabilities ranged from 0.33 to 0.56, and genetic correlations among traits exceeded 0.61, indicating strong pleiotropy. GWAS revealed a polygenic architecture with a shared QTL on chromosome 2; the top SNP explained ≤ 1.1% of phenotypic variance. Except for the 0.5 K LD panel—where PBLUP was more accurate—and the 1 K LD panel—where both methods performed similarly—GBLUP outperformed PBLUP in all scenarios, with the greatest advantage observed for physically spaced (PD) panels. The highest accuracy (0.80) was achieved with the full 100 K SNP set. GBLUP models required panels containing ≥ 0.5 K PD (accuracy ≥ 0.55) or ≥ 2 K LD (accuracy ≥ 0.56) to significatively surpass PBLUP predictions. Training sets built from extreme phenotypes boosted accuracy in small to intermediate sample sizes (e.g., 0.74 at n = 1,500 with 5 K PD SNPs versus 0.53 under random sampling). These results provide novel insights into not only the genomic regions controlling growth in this species but also about the utility of PD-based SNP panels and balanced sampling designs for enhancing GS accuracy in C. virginica.

This study presents a comprehensive molecular and epidemiological characterisation of infectious pancreatic necrosis virus (IPNV) in Chilean salmon aquaculture. Between 2015 and 2016, 26 sampling events were conducted in freshwater and seawater farms spanning a broad latitudinal gradient (30.3° S to 52.6° S). Three diagnostic methods were used: Quantitative real‐time Polymerase Chain Reaction (PCR) (qRT‐PCR) (targeting VP1 and VP2 protein coding genes), nested PCR and virus isolation in CHSE‐214 cells. In addition, a 523‐bp VP2 gene fragment was sequenced directly from samples. These approaches were employed to assess detection sensitivity and to explore IPNV genogroup distribution and persistence. Nested PCR and viral isolation detected IPNV in 50 of 53 samples, outperforming qRT‐PCR, which detected only 39. Phylogenetic analysis of the 523‐bp VP2 gene fragment classified the isolates into two genogroups—5 ( Salmo salar ) and 1 ( Oncorhynchus spp.), confirming host‐specific associations. Identical or near‐identical sequences were identified in geographically distant farms and temporally spaced samples, suggesting persistent isolates and potential long‐distance spread, likely via egg transfers or fish movement. The most severe mortality event (> 125,000 fish) occurred during a genogroup 1 outbreak (Isla del Rey, GMTS, O. kisutch ), followed by genogroup 5 outbreaks documented in Molco Alto (PMLC, S. salar ) and Chayahue ( S. salar ). Although less frequently detected, genogroup 1 was associated with higher virulence, particularly in coho salmon. These findings highlight the need of integrated diagnostic strategies, genogroup‐specific monitoring and strengthened biosecurity to mitigate the impact of IPNV in Chilean salmon farming.

Thermal variability significantly impacts fish performance, and current breeding objectives may soon be suboptimal due to climate change. Growth is a critical trait for aquaculture profitability. Understanding the genomic differences in growth under varying water temperatures is essential to predict climate change's impact on cold water species production. This study examined a rainbow trout population grown under low (~ 7 °C) and high (~ 22 °C) non-lethal temperatures. The objectives were to: (i) explore the genetic architecture of growth under upper and lower temperature (UT and LT) conditions using multi-trait genome-wide association, and (ii) identify candidate genes and biological processes related to growth in these conditions through a gene-based meta-analysis approach. The results revealed: (i) significant genetic variation for body weight, body length, and average daily gain at both LT and UT conditions, with genomic heritabilities ranging from 0.19 ± 0.06 to 0.32 ± 0.05 and 0.16 ± 0.05 to 0.39 ± 0.08, respectively; (ii) distinct genetic architectures and genes associated with UT and LT growth, with SNP effect correlations from r = 0.06 to 0.22; (iii) shared biological functions for growth at UT and LT, involving cardiovascular function maintenance and cell communication. Cytoskeleton-related functions were predominant in growth at LT, while DNA repair functions were more significant at UT. Notably, sema6ba emerges as a potential candidate gene involved in growth-related traits across contrasting thermal environments in rainbow trout, given its strong association under both low and high temperature conditions.

Background/Objetives: Sea lice (Caligus rogercresseyi) pose a major threat to Atlantic salmon (Salmo salar) aquaculture by compromising fish health and reducing production efficiency. While genetic variation in parasite load has been reported, the molecular mechanisms underlying this variation remain unclear. Methods: two sea lice challenge trials were conducted, achieving high infestation rates (47.5% and 43.5%). A total of 85 fish, selected based on extreme phenotypes for lice burden (42 low, 43 high), were subjected to transcriptomic analysis. Differential gene expression was integrated with allele-specific expression (ASE) analysis to uncover cis-regulatory variation influencing host response. Results: Sixty genes showed significant ASE (p < 0.05), including 33 overexpressed and 27 underexpressed. Overexpressed ASE genes included Keratin 15, Collagen IV/V, TRIM16, and Angiopoietin-1-like, which are associated with epithelial integrity, immune response, and tissue remodeling. Underexpressed ASE genes such as SOCS3, CSF3R, and Neutrophil cytosolic factor suggest individual variation in cytokine signaling and oxidative stress pathways. Conclusions: several ASE genes co-localized with previously identified QTLs for sea lice resistance, indicating that cis-regulatory variants contribute to phenotypic differences in parasite susceptibility. These results highlight ASE analysis as a powerful tool to identify functional regulatory elements and provide valuable candidates for selective breeding and genomic improvement strategies in aquaculture.

Background Flavobacterium oreochromis has been associated with elevated mortality rates during the early stages of tambaqui (Colossoma macropomum) aquaculture. This study investigated genetic responses to bacterial infection in juvenile fish by comparing gene expression profiles between symptomatic (IS) and asymptomatic (IA) individuals. Methods and results Skin samples from both IA and IS individuals were collected for transcriptome sequencing. Approximately 21 million reads per library were aligned to the tambaqui genome. Differential expression analysis revealed 2,176 upregulated and 1,219 downregulated genes in IS individuals, whereas 1,358 genes were upregulated and 488 downregulated in IA individuals. Notably, genes upregulated in both groups were associated with autophagy (e.g., atg4b and ulk2) and oxidative stress responses (e.g., klf9 and txnip). In contrast, genes related to tissue integrity, such as unc45b and akap6, were consistently downregulated during infection. These results suggest a dual host response to F. oreochromis infection, characterized by activation of cellular stress pathways and the suppression of genes involved in maintaining structural integrity. The upregulation of autophagy-related (atg4b, ulk2) and oxidative stress-regulating (klf9 and txnip) genes likely reflects an attempt by the host to counteract bacterial invasion through enhanced intracellular degradation and redox homeostasis. Conversely, the downregulation of unc45b and akap6 may indicate a compromise in structural defense mechanisms. Conclusion These findings offer valuable insights into the immunogenetics of tambaqui and have direct implications for enhancing disease resistance in aquaculture. Moreover, they contribute to a better understanding of the complex interplay between molecular pathways involved in F. oreochromis infection.

Sea lice (Caligus rogercresseyi), represents a major constraint to Atlantic salmon (Salmo salar) aquaculture, affecting both fish health and production efficiency. Genetic variation for sea lice load has been previously documented in Atlantic salmon. To investigate the basis of the variation in sea lice burden at a transcriptomic level, two consecutive challenge trials were conducted. Infestation success rates of 47.5% and 43.5% were achieved, indicating high parasite attachment efficiency. For transcriptomic analysis, a total of 85 fish were selected based on their phenotypic values of parasite load, comprising 42 individuals with low lice burden and 43 with high lice burden. To elucidate the regulatory mechanisms underlying sea lice load variation, allele-specific expression (ASE) analysis was integrated with differential gene expression profiling. A total of 60 genes (33 overexpressed, 27 underexpressed) exhibited significant ASE (p < 0.05), indicating the presence of cis-regulatory variants influencing key host response pathways. Notably, overexpressed ASE genes included structural and immune-related components such as Keratin 15, Collagen types IV and V, TRIM16, and Angiopoietin-1-like, which are associated with epithelial integrity, inflammation, and tissue remodeling. In contrast, underexpressed ASE genes such as SOCS3, CSF3R, and Neutrophil cytosolic factor suggest genotype-dependent modulation of cytokine signaling and oxidative stress responses. Several ASE genes co-localized with previously reported QTLs for sea lice burden variation, supporting a model in which cis-regulatory variation contributes to phenotypic variation in host response against the parasite. These findings underscore the utility of ASE analysis for the identification of functionally relevant genomic regions and provide promising candidates for genetic improvement and precision breeding.

Salmonids play vital ecological and economic roles and have been introduced to many regions worldwide. When not held captive in farms, they can be classified as free‐living salmonids, a group that includes native, feral, and naturalized populations, as well as fish that have escaped from aquaculture facilities. Compared to farmed salmonids, knowledge of viral infections affecting free‐living populations remains limited, creating a significant gap in understanding the ecological impacts of interactions between aquaculture and natural ecosystems. To address this knowledge gap, we reviewed global reports and summarized the information on viruses infecting free‐living salmonids. Most viral detections reported in the reviewed studies were found in native wild salmonids, with escaped salmon ranking second in detection frequency. Atlantic salmon (Salmo salar), sockeye salmon (Oncorhynchus nerka), and brown trout (Salmo trutta) were the most commonly reported host species. The most frequently reported viruses included infectious hematopoietic necrosis virus (IHNV), piscine orthoreovirus (PRV), infectious pancreatic necrosis virus (IPNV), and infectious salmon anemia virus (ISAV). Evidence from some studies suggests a bidirectional transmission of viruses between farmed and free‐living salmonids, highlighting the complex interplay between these groups. Beyond their potential role as reservoirs for aquaculture pathogens, free‐living salmonids may also be negatively impacted by viruses from farmed fish, contributing to the decline of native populations. By enhancing our understanding of the prevalence and impacts of viral infections in free‐living salmonids, we can inform future research and management strategies to protect the health of both farmed and wild fish populations.