Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout.

Sea lice (Caligus rogercresseyi) is an ectoparasite which causes major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The objectives of this study were to: (1) identify genomic regions associated with resistance to Caligus rogercresseyi in Atlantic salmon and rainbow trout by performing single-step Genome-Wide Association studies (ssGWAS), and (2) identify candidate genes related to trait variation based on exploring orthologous genes within the associated regions across species.

High-Throughput Single Nucleotide Polymorphism (SNP) Discovery and Validation Through Whole-Genome Resequencing in Nile Tilapia (Oreochromis niloticus).

Nile tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world. Currently, the estimation of genetic merit of breeders is typically based on genealogical and phenotypic information.

Single-Step Genome-Wide Association Study for Resistance to in Rainbow Trout ().

One of the main pathogens affecting rainbow trout () farming is the facultative intracellular bacteria Current treatments, such as antibiotics and vaccines, have not had the expected effectiveness in field conditions. Genetic improvement by means of selection for resistance is proposed as a viable alternative for control. Genomic information can be used to identify the genomic regions associated with resistance and enhance the genetic evaluation methods to speed up the genetic improvement for the trait.

Multiple Selection Signatures in Farmed Atlantic Salmon Adapted to Different Environments Across Hemispheres.

Domestication of Atlantic salmon started approximately 40 years ago, using artificial selection through genetic improvement programs. Selection is likely to have imposed distinctive signatures on the salmon genome, which are often characterized by high genetic differentiation across population and/or reduction in genetic diversity in regions associated to traits under selection. The identification of such selection signatures may give insights into the candidate genomic regions of biological and commercial interest.

Genome-Wide Patterns of Population Structure and Linkage Disequilibrium in Farmed Nile Tilapia ().

Nile tilapia () is one of the most produced farmed fish in the world and represents an important source of protein for human consumption. Farmed Nile tilapia populations are increasingly based on genetically improved stocks, which have been established from admixed populations. To date, there is scarce information about the population genomics of farmed Nile tilapia, assessed by dense single nucleotide polymorphism (SNP) panels.

Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium .

is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; ), Atlantic salmon (AS; ), and rainbow trout (RT; ) in several countries, including Norway, Canada, Scotland, Ireland, and Chile. We used Bayesian genome-wide association study analyses to investigate the genetic architecture of resistance to in farmed populations of these species.

Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia ( L.).

Nile tilapia () is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases.

Genome-Wide Association Analysis for Resistance to Infectious Pancreatic Necrosis Virus Identifies Candidate Genes Involved in Viral Replication and Immune Response in Rainbow Trout ().

Infectious pancreatic necrosis (IPN) is a viral disease with considerable negative impact on the rainbow trout () aquaculture industry. The aim of the present work was to detect genomic regions that explain resistance to infectious pancreatic necrosis virus (IPNV) in rainbow trout. A total of 2,278 fish from 58 full-sib families were challenged with IPNV and 768 individuals were genotyped (488 resistant and 280 susceptible), using a 57K SNP panel Axiom, Affymetrix.

Whole Genome Linkage Disequilibrium and Effective Population Size in a Coho Salmon () Breeding Population Using a High-Density SNP Array.

The estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection, and inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using a high-density SNP array. Linkage disequilibrium was estimated between a total of 93,502 SNPs found in 64 individuals (33 dams and 31 sires) from the breeding population.

Genome-Wide Association Study and Cost-Efficient Genomic Predictions for Growth and Fillet Yield in Nile Tilapia ().

Fillet yield (FY) and harvest weight (HW) are economically important traits in Nile tilapia production. Genetic improvement of these traits, especially for FY, are lacking, due to the absence of efficient methods to measure the traits without sacrificing fish and the use of information from relatives to selection. However, genomic information could be used by genomic selection to improve traits that are difficult to measure directly in selection candidates, as in the case of FY.

Discovery and Functional Annotation of Quantitative Trait Loci Affecting Resistance to Sea Lice in Atlantic Salmon.

Sea lice () are ectoparasitic copepods which have a large negative economic and welfare impact in Atlantic salmon () aquaculture, particularly in Chile. A multi-faceted prevention and control strategy is required to tackle lice, and selective breeding contributes via cumulative improvement of host resistance to the parasite. While host resistance has been shown to be heritable, little is yet known about the individual loci that contribute to this resistance, the potential underlying genes, and their mechanisms of action.

Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss).

Growth is one of the most important traits from both a physiological and economic perspective in aquaculture species. Thus, identifying the genomic regions and genes underpinning genetic variation for this trait is of particular interest in several fish species, including rainbow trout. In this work, we perform a genome-wide association study (GWAS) to identify the genomic regions associated with body weight at tagging (BWT) and at 18 months (BW18M) using a dense SNP panel (57 k) and 4596 genotyped rainbow trout from 105 full-sib families belonging to a Chilean breeding population.

Population Genomic Structure and Genome-Wide Linkage Disequilibrium in Farmed Atlantic Salmon ( L.) Using Dense SNP Genotypes.

Chilean Farmed Atlantic salmon () populations were established with individuals of both European and North American origins. These populations are expected to be highly genetically differentiated due to evolutionary history and poor gene flow between ancestral populations from different continents. The extent and decay of linkage disequilibrium (LD) among single nucleotide polymorphism (SNP) impacts the implementation of genome-wide association studies and genomic selection and provides relevant information about demographic processes of fish populations.

Genomic Predictions and Genome-Wide Association Study of Resistance Against in Coho Salmon () Using ddRAD Sequencing.

is one of the main infectious diseases affecting coho salmon () farming, and current treatments have been ineffective for the control of this disease. Genetic improvement for 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.

Single-step genomic evaluation improves accuracy of breeding value predictions for resistance to infectious pancreatic necrosis virus in rainbow trout.

The aim of this study was to compare the accuracy of breeding values (EBVs) predicted using the traditional pedigree based Best Linear Unbiased Prediction (PBLUP) and the single-step genomic Best Linear Unbiased Prediction (ssGBLUP) for resistance against infectious pancreatic necrosis virus (IPNV) in rainbow trout. A total of 2278 animals were challenged against IPNV and 768 individuals were genotyped using a 57 K single nucleotide polymorphism array for rainbow trout. Accuracies for both methods were assessed using five-fold cross-validation.

Genomic Prediction Accuracy for Resistance Against in Farmed Rainbow Trout.

Salmonid rickettsial syndrome (SRS), caused by the intracellular bacterium , is one of the main diseases affecting rainbow trout () farming. To accelerate genetic progress, genomic selection methods can be used as an effective approach to control the disease. The aims of this study were: (i) to compare the accuracy of estimated breeding values using pedigree-based best linear unbiased prediction (PBLUP) with genomic BLUP (GBLUP), single-step GBLUP (ssGBLUP), Bayes C, and Bayesian Lasso (LASSO); and (ii) to test the accuracy of genomic prediction and PBLUP using different marker densities (0.

The use of genomic information increases the accuracy of breeding value predictions for sea louse (Caligus rogercresseyi) resistance in Atlantic salmon (Salmo salar).

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.

Genomic predictions can accelerate selection for resistance against Piscirickettsia salmonis in Atlantic salmon (Salmo salar).

Background: Salmon Rickettsial Syndrome (SRS) caused by Piscirickettsia salmonis is a major disease affecting the Chilean salmon industry. Genomic selection (GS) is a method wherein genome-wide markers and phenotype information of full-sibs are used to predict genomic EBV (GEBV) of selection candidates and is expected to have increased accuracy and response to selection over traditional pedigree based Best Linear Unbiased Prediction (PBLUP). Widely used GS methods such as genomic BLUP (GBLUP), SNPBLUP, Bayes C and Bayesian Lasso may perform differently with respect to accuracy of GEBV prediction.

Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes.

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.

Disease resistance in Atlantic salmon (Salmo salar): coinfection of the intracellular bacterial pathogen Piscirickettsia salmonis and the sea louse Caligus rogercresseyi.

Background: Naturally occurring coinfections of pathogens have been reported in salmonids, but their consequences on disease resistance are unclear. We hypothesized that 1) coinfection of Caligus rogercresseyi reduces the resistance of Atlantic salmon to Piscirickettsia salmonis; and 2) coinfection resistance is a heritable trait that does not correlate with resistance to a single infection.

Methodology: In total, 1,634 pedigreed Atlantic salmon were exposed to a single infection (SI) of P.

The consequences of including non-additive effects on the genetic evaluation of harvest body weight in Coho salmon (Oncorhynchus kisutch).

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.