Aquainnovo

Puerto Montt, Chile

Aquainnovo

Puerto Montt, Chile
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Correa K.,University of Chile | Bangera R.,Aquainnovo | Figueroa R.,Aquainnovo | Lhorente J.P.,Aquainnovo | Yanez J.M.,University of Chile
Genetics Selection Evolution | Year: 2017

Sea lice infestations caused by Caligus rogercresseyi are a main concern to the salmon farming industry due to associated economic losses. Resistance to this parasite was shown to have low to moderate genetic variation and its genetic architecture was suggested to be polygenic. The aim of this study was to compare accuracies of breeding value predictions obtained with pedigree-based best linear unbiased prediction (P-BLUP) methodology against different genomic prediction approaches: genomic BLUP (G-BLUP), Bayesian Lasso, and Bayes C. To achieve this, 2404 individuals from 118 families were measured for C. rogercresseyi count after a challenge and genotyped using 37 K single nucleotide polymorphisms. Accuracies were assessed using fivefold cross-validation and SNP densities of 0.5, 1, 5, 10, 25 and 37 K. Accuracy of genomic predictions increased with increasing SNP density and was higher than pedigree-based BLUP predictions by up to 22%. Both Bayesian and G-BLUP methods can predict breeding values with higher accuracies than pedigree-based BLUP, however, G-BLUP may be the preferred method because of reduced computation time and ease of implementation. A relatively low marker density (i.e. 10 K) is sufficient for maximal increase in accuracy when using G-BLUP or Bayesian methods for genomic prediction of C. rogercresseyi resistance in Atlantic salmon. © 2017 The Author(s).


PubMed | Aquainnovo, Genus plc, University of Chile, Data2Bio LLC and 4 more.
Type: Journal Article | Journal: Molecular ecology resources | Year: 2016

A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9736473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200K SNPs were selected to develop an Affymetrix Axiom() myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information.


Brokordt K.,Católica del Norte University | Farias W.,Católica del Norte University | Lhorente J.P.,Aquainnovo | Winkler F.,Católica del Norte University
Animal Behaviour | Year: 2012

Escape behaviours are generally considered adaptive because of their obvious effects on fitness. However, little is known about the genetic basis of escape responses. The estimation of the magnitude of hereditary factors affecting variation in escape responses indicates their potential to evolve by natural selection. Scallops are exceptional among bivalve molluscs because they possess an excellent swimming capacity, which helps them to escape predators. In this study we estimated the narrow-sense heritability (h 2), phenotypic variance components and phenotypic and genetic correlations of several escape response traits (i.e. reaction time, number of claps (rapid valve closures and openings), and the duration and intensity of the clapping response) in juvenile Argopecten purpuratus scallops. We stimulated scallop escape responses using their natural predator, the sea star Meyenaster gelatinosus. Genetic estimates for escape response traits were determined by the animal model. Most studied traits showed substantial amounts of additive genetic variance controlling their phenotypic variation (CV A=18.43-100.2), were repeatable (at least over a short period, R=0.36-0.42), and had significant heritabilities (h 2=0.36-0.57). Indeed, it can be inferred that most of the analysed escape response traits of A. purpuratus could evolve through natural selection. Moreover, significant genetic correlations between some escape response traits were observed, suggesting that selection acting on one escape trait will affect that of another, facilitating their coevolution. © 2012 The Association for the Study of Animal Behaviour.


Valenzuela-Miranda D.,University of Concepción | Boltana S.,University of Concepción | Cabrejos M.E.,University of Chile | Yanez J.M.,Aquainnovo | And 2 more authors.
Fish and Shellfish Immunology | Year: 2015

Infectious salmon anaemia virus (ISAV) is an orthomyxovirus causing high mortality in farmed Atlantic salmon (Salmo salar). The collective data from the Atlantic salmon-ISAV interactions, performed "invitro" using various salmon cell lines and ". invivo" fish infected with different ISAV isolates, have shown astrong regulation of immune related transcripts during the infection. Despite this strong defence response, the majority of fish succumb to infections with ISAV. The deficient protection of the host against ISAV is in part due to virulence factors of the virus, which allow evade the host-defence machinery. As such, the viral replication is uninhibited and viral loads quickly spread to several tissues causing massive cellular damage before the host can develop an effective cell-mediated and humoral outcome. To interrogate the correlation of the viral replication with the host defence response, we used fish that have been infected by cohabitation with ISAV-injected salmons. Whole gene expression patterns were measured with RNA-seq using RNA extracted from Head-kidney, Liver and Gills. The results show divergent mRNA abundance of functional modules related to interferon pathway, adaptive/innate immune response and cellular proliferation/differentiation. Furthermore, gene regulation in distinct tissues during the infection process was independently controlled within the each tissue and the observed mRNA expression suggests high modulation of the ISAV-segment transcription. Importantly this is the first time that strong correlations between functional modules containing significant immune process with protein-protein affinities and viral-segment transcription have been made between different tissues of ISAV-infected fish. © 2015 Elsevier Ltd.


Yanez J.M.,Aquainnovo | Bangera R.,Nofima | Lhorente J.P.,Aquainnovo | Oyarzun M.,Aquainnovo | And 2 more authors.
Aquaculture | Year: 2013

Piscirickettsiosis (Piscirickettsia salmonis) is one of the diseases that cause large economic losses in Chilean salmon industry. Genetic improvement of disease resistance represents one strategy for controlling infectious diseases in farmed fish. However, knowledge of whether genetic variation exists for piscirickettsiosis resistance is needed in order to determine the feasibility of including this trait into the breeding goal. Using data from a challenge test performed on 2601 Atlantic salmon (Salmo salar) from 118 full-sib groups (40 half-sib groups) we found significant genetic variation for resistance to piscirickettsiosis. We used a cross-sectional linear model (CSL) and a binary threshold (probit) model (THR) to analyze the test-period survival, a linear model (LIN), Cox (COX) and Weibull (WB) frailty proportional hazard models to analyse the day at death, and a survival score (SS) model with a logit link to analyze the test-day survival. The estimated heritabilities for the different models ranged from 0.11 (SS) to 0.41 (COX). The Pearson and Spearman correlation coefficients between full-sib families estimated breeding values (EBVs) from the six statistical models were above 0.96 and 0.97, respectively. We used different data subsets, splitting the entire dataset both at random and by tank, in order to predict the accuracy of selection for each model. In both cases COX (0.8 and 0.79) and CSL (0.76 and 0.71) models showed the highest and the lowest accuracy of selection, respectively. These results indicate that resistance against P. salmonis in Atlantic salmon might be genetically improved more efficiently by means of using models which take both time to death and data censoring into account in the genetic evaluations. © 2013 Elsevier B.V.


Valenzuela-Miranda D.,University of Concepción | Cabrejos M.E.,University of Chile | Yanez J.M.,Aquainnovo | Yanez J.M.,University of Chile | Gallardo-Escarate C.,University of Concepción
Marine Genomics | Year: 2015

The infectious salmon anemia virus (ISAV) is a severe disease that mainly affects the Atlantic salmon (Salmo salar) aquaculture industry. Although several transcriptional studies have aimed to understand Salmon-ISAV interaction through the evaluation of host-gene transcription, none of them has focused their attention upon the viral transcriptional dynamics. For this purpose, RNA-Seq and RT-qPCR analyses were conducted in gills, liver and head-kidney of S. salar challenged by cohabitation with ISAV. Results evidence the time and tissue transcript patterns involved in the viral expression and how the transcription levels of ISAV segments are directly linked with the protein abundance found in other virus of the Orthomyxoviridae family. In addition, RT-qPCR result evidenced that quantification of ISAV through amplification of segment 3 would result in a more sensitive approach for detection and quantification of ISAV. This study offers a more comprehensive approach regarding the ISAV infective process and gives novel knowledge for its molecular detection. © 2014 Elsevier B.V.


Correa K.,University of Chile | Lhorente J.P.,Aquainnovo | Lopez M.E.,University of Chile | Bassini L.,University of Chile | And 6 more authors.
BMC Genomics | Year: 2015

Background: Pisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses. Selective breeding for disease resistance represents one approach for controlling SRS in farmed Atlantic salmon. Knowledge concerning the architecture of the resistance trait is needed before deciding on the most appropriate approach to enhance artificial selection for P. salmonis resistance in Atlantic salmon. The purpose of the study was to dissect the genetic variation in the resistance to this pathogen in Atlantic salmon. Methods: 2,601 Atlantic salmon smolts were experimentally challenged against P. salmonis by means of intra-peritoneal injection. These smolts were the progeny of 40 sires and 118 dams from a Chilean breeding population. Mortalities were recorded daily and the experiment ended at day 40 post-inoculation. Fish were genotyped using a 50K Affymetrix® Axiom® myDesignTM Single Nucleotide Polymorphism (SNP) Genotyping Array. A Genome Wide Association Analysis was performed on data from the challenged fish. Linear regression and logistic regression models were tested. Results: Genome Wide Association Analysis indicated that resistance to P. salmonis is a moderately polygenic trait. There were five SNPs in chromosomes Ssa01 and Ssa17 significantly associated with the traits analysed. The proportion of the phenotypic variance explained by each marker is small, ranging from 0.007 to 0.045. Candidate genes including interleukin receptors and fucosyltransferase have been found to be physically linked with these genetic markers and may play an important role in the differential immune response against this pathogen. Conclusions: Due to the small amount of variance explained by each significant marker we conclude that genetic resistance to this pathogen can be more efficiently improved with the implementation of genetic evaluations incorporating genotype information from a dense SNP array. © 2015 Correa et al.


Yanez J.M.,Aquainnovo | Bassini L.N.,Aquainnovo | Filp M.,Aquainnovo | Lhorente J.P.,Aquainnovo | And 3 more authors.
Aquaculture | Year: 2014

A commercial breeding nucleus of coho salmon (Oncorhynchus kisutch) was established in Chile in 1997. This nucleus consists of two independent populations corresponding to different year-classes (even and odd, depending on the spawning year), which have been successfully selected for harvest weight (approximate genetic gain per generation of 10%). In order to constrain the buildup of inbreeding a strategy based on avoiding full-sib mating in each generation was used. In this study we assess the inbreeding levels and effective population size of the two year-classes to evaluate the outcome of the mating strategy within the nucleus. The average rate of inbreeding in the two year classes was around 1% per generation. However, rapid increase of inbreeding coefficients in the latest generations suggests that the simple mating strategy used should be improved in order to constrain maximum inbreeding values in further generations. The effective population size calculated based on the regression of the average rate of co-ancestry across generations was 34 and 39 for the odd and even populations, respectively. The effective population number is 50 for both, odd and even populations, based on the regression of the average rate of inbreeding over generations. The results indicate that the mate allocation strategy has contained the rate of inbreeding within acceptable values to date, but that current effective population size must be increased in order to be adequate for the viability of the breeding program in the medium to long term. However, the effective population size of these populations is far below 500, the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. Further strategies to constrain maximum inbreeding levels across all the individuals belonging to the nucleus and to maintain a satisfactory effective population size for ensuring the sustainability of this breeding scheme are proposed. © 2013 Elsevier B.V.


PubMed | Genus plc, University of Chile, Simon Fraser University and Aquainnovo
Type: | Journal: BMC genomics | Year: 2015

Pisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses. Selective breeding for disease resistance represents one approach for controlling SRS in farmed Atlantic salmon. Knowledge concerning the architecture of the resistance trait is needed before deciding on the most appropriate approach to enhance artificial selection for P. salmonis resistance in Atlantic salmon. The purpose of the study was to dissect the genetic variation in the resistance to this pathogen in Atlantic salmon.2,601 Atlantic salmon smolts were experimentally challenged against P. salmonis by means of intra-peritoneal injection. These smolts were the progeny of 40 sires and 118 dams from a Chilean breeding population. Mortalities were recorded daily and the experiment ended at day 40 post-inoculation. Fish were genotyped using a 50K Affymetrix Axiom myDesignTM Single Nucleotide Polymorphism (SNP) Genotyping Array. A Genome Wide Association Analysis was performed on data from the challenged fish. Linear regression and logistic regression models were tested.Genome Wide Association Analysis indicated that resistance to P. salmonis is a moderately polygenic trait. There were five SNPs in chromosomes Ssa01 and Ssa17 significantly associated with the traits analysed. The proportion of the phenotypic variance explained by each marker is small, ranging from 0.007 to 0.045. Candidate genes including interleukin receptors and fucosyltransferase have been found to be physically linked with these genetic markers and may play an important role in the differential immune response against this pathogen.Due to the small amount of variance explained by each significant marker we conclude that genetic resistance to this pathogen can be more efficiently improved with the implementation of genetic evaluations incorporating genotype information from a dense SNP array.

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