RESUMO
Piscirickettsiosis is the most important bacterial disease in the Chilean salmon industry, which has borne major economic losses due to failure to control it. Cells use extracellular vesicles (EVs) as an inter-cellular communicators to deliver several factors (e.g., microRNAs) that may regulate the responses of other cells. However, there is limited knowledge about the identification and characterization of EV-miRNAs in salmonids or the effect of infections on these. In this study, Illumina sequencing technology was used to identify Coho salmon plasma EV-miRNAs upon Piscirickettsia salmonis infection at four different time points. A total of 118 novels and 188 known EV-miRNAs, including key immune teleost miRNAs families (e.g., miR-146, miR-122), were identified. A total of 245 EV-miRNAs were detected as differentially expressed (FDR < 5%) in terms of control, with a clear down-regulation pattern throughout the disease. KEGG enrichment results of EV-miRNAs target genes showed that they were grouped mainly in cellular, stress, inflammation and immune responses. Therefore, it is hypothesized that P. salmonis could potentially benefit from unbalanced modulation response of Coho salmon EV-miRNAs in order to promote a hyper-inflammatory and compromised immune response through the suppression of different key immune host miRNAs during the course of the infection, as indicated by the results of this study.
Assuntos
Doenças dos Peixes/microbiologia , MicroRNAs/metabolismo , Oncorhynchus kisutch/metabolismo , Infecções por Piscirickettsiaceae/imunologia , Animais , Vesículas Extracelulares/metabolismo , Doenças dos Peixes/imunologia , Regulação da Expressão Gênica , Inflamação , Oncorhynchus kisutch/genética , Oncorhynchus kisutch/imunologia , Piscirickettsia/fisiologiaRESUMO
The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon (Oncorhynchus kisutch) breeding nuclei, genotyped using a 200 K Affymetrix Axiom® myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two "pure" lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available.
Assuntos
Genoma/genética , Genômica , Endogamia , Oncorhynchus kisutch/genética , Animais , Cruzamento , Pesqueiros , Genótipo , Homozigoto , Linhagem , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
The increasing capacity of transcriptomic analysis by high throughput sequencing has highlighted the presence of a large proportion of transcripts that do not encode proteins. In particular, long non-coding RNAs (lncRNAs) are sequences with low coding potential and conservation among species. Moreover, cumulative evidence has revealed important roles in post-transcriptional gene modulation in several taxa. In fish, the role of lncRNAs has been scarcely studied and even less so during the immune response against sea lice. In the present study we mined for lncRNAs in Atlantic salmon (Salmo salar) and Coho salmon (Oncorhynkus kisutch), which are affected by the sea louse Caligus rogercresseyi, evaluating the degree of sequence conservation between these two fish species and their putative roles during the infection process. Herein, Atlantic and Coho salmon were infected with 35 lice/fish and evaluated after 7 and 14 days post-infestation (dpi). For RNA sequencing, samples from skin and head kidney were collected. A total of 5658/4140 and 3678/2123 lncRNAs were identified in uninfected/infected Atlantic and Coho salmon transcriptomes, respectively. Species-specific transcription patterns were observed in exclusive lncRNAs according to the tissue analyzed. Furthermore, neighbor gene GO enrichment analysis of the top 100 highly regulated lncRNAs in Atlantic salmon showed that lncRNAs were localized near genes related to the immune response. On the other hand, in Coho salmon the highly regulated lncRNAs were localized near genes involved in tissue repair processes. This study revealed high regulation of lncRNAs closely localized to immune and tissue repair-related genes in Atlantic and Coho salmon, respectively, suggesting putative roles for lncRNAs in salmon against sea lice infestation.
Assuntos
Doenças dos Peixes/genética , Imunidade/genética , Infestações por Piolhos/genética , Oncorhynchus kisutch/genética , RNA Longo não Codificante/genética , Salmo salar/genética , Transcriptoma , Animais , Copépodes/imunologia , Copépodes/fisiologia , Doenças dos Peixes/imunologia , Perfilação da Expressão Gênica , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Interações Hospedeiro-Parasita , Infestações por Piolhos/imunologia , Infestações por Piolhos/parasitologia , Oncorhynchus kisutch/imunologia , Oncorhynchus kisutch/parasitologia , Salmo salar/imunologia , Salmo salar/parasitologia , Especificidade da Espécie , Cicatrização/genéticaRESUMO
Piscirickettsia salmonis is one of the main infectious diseases affecting coho salmon (Oncorhynchus kisutch) farming, and current treatments have been ineffective for the control of this disease. Genetic improvement for P. salmonis resistance has been proposed as a feasible alternative for the control of this infectious disease in farmed fish. Genotyping by sequencing (GBS) strategies allow genotyping of hundreds of individuals with thousands of single nucleotide polymorphisms (SNPs), which can be used to perform genome wide association studies (GWAS) and predict genetic values using genome-wide information. We used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic architecture of resistance against P. salmonis in a farmed coho salmon population and to identify molecular markers associated with the trait. We also evaluated genomic selection (GS) models in order to determine the potential to accelerate the genetic improvement of this trait by means of using genome-wide molecular information. A total of 764 individuals from 33 full-sib families (17 highly resistant and 16 highly susceptible) were experimentally challenged against P. salmonis and their genotypes were assayed using ddRAD sequencing. A total of 9,389 SNPs markers were identified in the population. These markers were used to test genomic selection models and compare different GWAS methodologies for resistance measured as day of death (DD) and binary survival (BIN). Genomic selection models showed higher accuracies than the traditional pedigree-based best linear unbiased prediction (PBLUP) method, for both DD and BIN. The models showed an improvement of up to 95% and 155% respectively over PBLUP. One SNP related with B-cell development was identified as a potential functional candidate associated with resistance to P. salmonis defined as DD.
Assuntos
DNA/genética , Resistência à Doença/genética , Estudo de Associação Genômica Ampla , Genômica , Oncorhynchus kisutch/genética , Oncorhynchus kisutch/microbiologia , Piscirickettsia/fisiologia , Mapeamento por Restrição/métodos , Animais , Cruzamento , Feminino , Doenças dos Peixes/genética , Doenças dos Peixes/microbiologia , Marcadores Genéticos , Estimativa de Kaplan-Meier , Masculino , LinhagemRESUMO
The genes of the major histocompatibility complex (MHC) are amongst the most variable in vertebrates and represent some of the best candidates to study processes of adaptive evolution. However, despite the number of studies available, most of the information on the structure and function of these genes come from studies in mammals and birds in which the MHC class I and II genes are tightly linked and class II alpha exhibits low variability in many cases. Teleost fishes are among the most primitive vertebrates with MHC and represent good organisms for the study of MHC evolution because their class I and class II loci are not physically linked, allowing for independent evolution of both classes of genes. We have compared the diversity and molecular mechanisms of evolution of classical MH class II alpha and class II beta loci in farm populations of three salmonid species: Oncorhynchus kisutch, Oncorhynchus mykiss and Salmo salar. We found single classical class II loci and high polymorphism at both class II alpha and beta genes in the three species. Mechanisms of evolution were common for both class II genes, with recombination and point mutation involved in generating diversity and positive selection acting on the peptide-binding residues. These results suggest that the maintenance of variability at the class IIalpha gene could be a mechanism to increase diversity in the MHC class II in salmonids in order to compensate for the expression of one single classical locus and to respond to a wider array of parasites.
Assuntos
Evolução Molecular , Genes MHC da Classe II , Salmonidae/genética , Salmonidae/imunologia , Alelos , Sequência de Aminoácidos , Animais , Sequência de Bases , DNA/genética , Primers do DNA/genética , Proteínas de Peixes/genética , Proteínas de Peixes/imunologia , Variação Genética , Antígenos de Histocompatibilidade Classe II/genética , Modelos Genéticos , Dados de Sequência Molecular , Oncorhynchus kisutch/genética , Oncorhynchus kisutch/imunologia , Oncorhynchus mykiss/genética , Oncorhynchus mykiss/imunologia , Recombinação Genética , Salmo salar/genética , Salmo salar/imunologia , Salmonidae/classificação , Seleção Genética , Homologia de Sequência de Aminoácidos , Especificidade da EspécieRESUMO
BACKGROUND: In this study, we used different animal models to estimate genetic and environmental variance components on harvest weight in two populations of Oncorhynchus kisutch, forming two classes i.e. odd- and even-year spawners. METHODS: The models used were: additive, with and without inbreeding as a covariable (A + F and A respectively); additive plus common environmental due to full-sib families and inbreeding (A + C + F); additive plus parental dominance and inbreeding (A + D + F); and a full model (A + C + D + F). Genetic parameters and breeding values obtained by different models were compared to evaluate the consequences of including non-additive effects on genetic evaluation. RESULTS: Including inbreeding as a covariable did not affect the estimation of genetic parameters, but heritability was reduced when dominance or common environmental effects were included. A high heritability for harvest weight was estimated in both populations (even = 0.46 and odd = 0.50) when simple additive models (A + F and A) were used. Heritabilities decreased to 0.21 (even) and 0.37 (odd) when the full model was used (A + C + D + F). In this full model, the magnitude of the dominance variance was 0.19 (even) and 0.06 (odd), while the magnitude of the common environmental effect was lower than 0.01 in both populations. The correlation between breeding values estimated with different models was very high in all cases (i.e. higher than 0.98). However, ranking of the 30 best males and the 100 best females per generation changed when a high dominance variance was estimated, as was the case in one of the two populations (even). CONCLUSIONS: Dominance and common environmental variance may be important components of variance in harvest weight in O. kisutch, thus not including them may produce an overestimation of the predicted response; furthermore, genetic evaluation was seen to be partially affected, since the ranking of selected animals changed with the inclusion of non-additive effects in the animal model.
Assuntos
Cruzamento , Oncorhynchus kisutch/genética , Animais , Peso Corporal/genética , Pesos e Medidas Corporais , Meio Ambiente , Feminino , Endogamia , Masculino , Análise de RegressãoRESUMO
We evaluated the effects of inbreeding on traits related to territorial dominance and tested whether the magnitude of inbreeding depression (ID) was modified by social environment in Coho salmon. Evaluation of behaviour in paired contests between juvenile salmon with different inbreeding (low, LI=9.5%; medium, MI=29.6%), did not show significant differences between their capacities for establishing territorial dominance (mean aggressiveness score, LI=20.0+/-22; MI=16.7+/-23 or for feeding attempts, LI=18.3+/-12; MI=21.1+/-12). However, fish with low inbreeding (LI) showed almost twice the aggressive pursuit of fish with medium inbreeding (MI), and had a higher specific growth rate (SGR) in culture (SGR(MI)=1.83+/-0.58; SGR(LI)=2.20+/-0.67). Additionally, we found evidence that the magnitude of ID was modified by social environment: (1) Masking: In small groups of fish (N=20), large dominant fish of MI, cultivated with small subordinate fish of LI, showed the same SGR as dominant fish of LI cultivated with small subordinate fish of MI. (2) Magnifying: A significant effect of ID on juvenile survival was detected only in high-density competitive environments. Thus, the number of lethal equivalents was 2.70 at high-density, and only 0.24 in a low-density environment. Our results show that differences in size associated with territorial dominance may mask deleterious effects of inbreeding under certain conditions, and support the concept that intraspecific competition usually magnifies the deleterious effects of inbreeding.