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One of the main pathogens affecting rainbow trout (Oncorhynchus mykiss) farming is the facultative intracellular bacteria Piscirickettsia salmonis. 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. The objectives of this study were to i) identify the genomic regions associated with resistance to P. salmonis; and ii) identify candidate genes associated with the trait in rainbow trout. We experimentally challenged 2,130 rainbow trout with P. salmonis and genotyped them with a 57 K single nucleotide polymorphism (SNP) array. Resistance to P. salmonis was defined as time to death (TD) and as binary survival (BS). Significant heritabilities were estimated for TD and BS (0.48 ± 0.04 and 0.34 ± 0.04, respectively). A total of 2,047 fish and 26,068 SNPs passed quality control for samples and genotypes. Using a single-step genome wide association analysis (ssGWAS) we identified four genomic regions explaining over 1% of the genetic variance for TD and three for BS. Interestingly, the same genomic region located on Omy27 was found to explain the highest proportion of genetic variance for both traits (2.4 and 1.5% for TD and BS, respectively). The identified SNP in this region is located within an exon of a gene related with actin cytoskeletal organization, a protein exploited by P. salmonis during infection. Other important candidate genes identified are related with innate immune response and oxidative stress. The moderate heritability values estimated in the present study show it is possible to improve resistance to P. salmonis through artificial selection in the rainbow trout population studied here. Furthermore, our results suggest a polygenic genetic architecture for the trait and provide novel insights into the candidate genes underpinning resistance to P. salmonis in O. mykiss.

Piscirickettsiosis caused by the intracellular bacterium Piscirickettsia salmonis and caligidosis produced by the ectoparasite Caligus rogercresseyi, are important diseases which generate great economic losses in salmonid farming in Chile. Selective breeding for pathogen resistance has been proposed as an alternative tool for the control of diseases. The objective of the present study is to determine the levels of genetic variation for resistance to P. salmonis and susceptibility to C. rogercresseyi, in addition to investigating the levels of genetic co-variation between these traits and harvest weight in rainbow trout. Resistance to P. salmonis was defined as individual day of death (SRS_DD) and as binary survival (SRS_BS) after an experimental challenge carried out by intraperitoneal injection of an inoculum based on LF89 strain. Susceptibility to C. rogercresseyi (CAL) was measured as the sum of the parasitic load on the pectoral and caudal fins per fish after an experimental challenge. Harvest weight (HW) was recorded in individuals genetically related to challenged fish and analyzed to determine the genetic correlations between this trait and the previous ones. A linear multi-trait animal model was used to estimate (co)variance components for SRS_DD, CAL and HW. A single-trait probit threshold animal model was used to estimate variance components for SRS_BS on the underlying scale. Bivariate linear animal models were used to estimate genetic correlations between SRS_BS on the observed scale and all other traits. The heritabilities for SRS_DD, CAL and HW were 0.45 ± 0.06, 0.08 ± 0.02 and 0.35 ± 0.06, respectively. The heritabilities for SRS_BS were 0.28 ± 0.03 and 0.38 ± 0.05 on the underlying and observed scale, respectively. The genetic correlation between SRS_DD and CAL and between SRS_BS and CAL were 0.39 ± 0.14 and −0.34 ± 0.15, respectively. All other genetic correlations assessed were not significant. We concluded that there is significant additive genetic variation for P. salmonis resistance and C. rogercresseyi susceptibility, which indicates that it is possible to genetically improve these traits in rainbow trout. In addition, there is an unfavorable genetic correlation between P. salmonis resistance and C. rogercresseyi susceptibility and a null genetic correlation between growth and these traits. These results suggest that resistance to P. salmonis or C. rogercresseyi can be simultaneously improved with harvest weight. However, simultaneous selection for P. salmonis and C. rogercresseyi resistance must account for the unfavorable genetic relationship between both traits in this rainbow trout breeding population.

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. The objectives of this study were: (i) to perform genome-wide association studies (GWAS) to dissect the genetic architecture of FY and HW, (ii) to evaluate the accuracy of genotype imputation and (iii) to assess the accuracy of genomic selection using true and imputed low-density (LD) single nucleotide polymorphism (SNP) panels to determine a cost-effective strategy for practical implementation of genomic information in tilapia breeding programs. The data set consisted of 5,866 phenotyped animals and 1,238 genotyped animals (108 parents and 1,130 offspring) using a 50K SNP panel. The GWAS were performed using all genotyped and phenotyped animals. The genotyped imputation was performed from LD panels (LD0.5K, LD1K and LD3K) to high-density panel (HD), using information from parents and 20% of offspring in the reference set and the remaining 80% in the validation set. In addition, we tested the accuracy of genomic selection using true and imputed genotypes comparing the accuracy obtained from pedigree-based best linear unbiased prediction (PBLUP) and genomic predictions. The results from GWAS supports evidence of the polygenic nature of FY and HW. The accuracy of imputation ranged from 0.90 to 0.98 for LD0.5K and LD3K, respectively. The accuracy of genomic prediction outperformed the estimated breeding value from PBLUP. The use of imputation for genomic selection resulted in an increased relative accuracy independent of the trait and LD panel analyzed. The present results suggest that genotype imputation could be a cost-effective strategy for genomic selection in Nile tilapia breeding programs.

Made available in DSpace on 2018-12-11T17:23:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 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. The heritabilities were higher for PBLUP compared to ssGBLUP. The ssGBLUP accuracies outperformed PBLUP in 7 and 11% for days to death and binary survival, respectively. The ssGBLUP could be an alternative approach to improve the accuracy of breeding values for resistance against infectious pancreatic necrosis virus in rainbow trout, using information from genotyped and non-genotyped animals. Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago 8820808, Chile Animal Science Department, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Faculdade de Ciências Agrárias e Veterinárias (FCAV), Campus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, 14884-900 Jaboticabal, Brazil Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Av. Floral 1153, Puno, Perú Aquainnovo, Cardonal S/N, Puerto Montt, Chile Núcleo Milenio INVASAL, Concepción, Chile

Background Body traits are generally controlled by several genes in vertebrates (i.e. polygenes), which in turn make them difficult to identify through association mapping. Increasing the power of association studies by combining approaches such as genotype imputation and multi-trait analysis improves the ability to detect quantitative trait loci associated with polygenic traits, such as body traits. Results A multi-trait genome-wide association study (mtGWAS) was performed to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia (Oreochromis niloticus) using genotypes imputed to whole-genome sequences (WGS). To increase the statistical power of mtGWAS for the detection of genetic associations, summary statistics from single-trait genome-wide association studies (stGWAS) for eight different body traits recorded in 1309 animals were used. The mtGWAS increased the statistical power from the original sample size from 13 to 44%, depending on the trait analyzed. The better resolution of the WGS data, combined with the increased power of the mtGWAS approach, allowed the detection of significant markers which were not previously found in the stGWAS. Some of the lead single nucleotide polymorphisms (SNPs) were found within important functional candidate genes previously associated with growth-related traits in other terrestrial species. For instance, we identified SNP within the α1,6-fucosyltransferase (FUT8), solute carrier family 4 member 2 (SLC4A2), A disintegrin and metalloproteinase with thrombospondin motifs 9 (ADAMTS9) and heart development protein with EGF like domains 1 (HEG1) genes, which have been associated with average daily gain in sheep, osteopetrosis in cattle, chest size in goats, and growth and meat quality in sheep, respectively. Conclusions The high-resolution mtGWAS presented here allowed the identification of significant SNPs, linked to strong functional candidate genes, associated with body traits in Nile tilapia. These results provide further insights about the genetic variants and genes underlying body trait variation in cichlid fish with high accuracy and strong statistical support.

Animal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection known as selection signatures or selective sweeps have been traced in the genomes of many animal livestock species by exploiting variations in linkage disequilibrium patterns and/or reduction of genetic diversity.Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subject to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn that have been previously associated with body weight in Atlantic salmon or sec24d and robo1 that have been associated with disease resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.

Background Salmon Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is one of the primary causes of morbidity and mortality in Atlantic salmon aquaculture, particularly in Chile. Host resistance is a heritable trait, and functional genomic studies have highlighted genes and pathways important in the response of salmon to the bacteria. However, the functional mechanisms underpinning genetic resistance are not yet well understood. In the current study, a large population of salmon pre-smolts were challenged with P. salmonis, with mortality levels recorded and samples taken for genotyping. In parallel, head kidney and liver samples were taken from animals of the same population with high and low genomic breeding values for resistance, and used for RNA-Sequencing to compare their transcriptome profile both pre and post infection. Results A significant and moderate heritability (h2 = 0.43) was shown for the trait of binary survival. Genome-wide association analyses using 38 K imputed SNP genotypes across 2265 animals highlighted that resistance is a polygenic trait. Several thousand genes were identified as differentially expressed between controls and infected samples, and enriched pathways related to the host immune response were highlighted. In addition, several networks with significant correlation with SRS resistance breeding values were identified, suggesting their involvement in mediating genetic resistance. These included apoptosis, cytoskeletal organisation, and the inflammasome. Conclusions While resistance to SRS is a polygenic trait, this study has highlighted several relevant networks and genes that are likely to play a role in mediating genetic resistance. These genes may be future targets for functional studies, including genome editing, to further elucidate their role underpinning genetic variation in host resistance.

Salmonid Rickettsial Septicaemia (SRS), caused by Piscirickettsia salmonis, is a severe bacterial disease in the Chilean salmon farming industry. Vaccines and antibiotics are the current strategies to fight SRS; however, the high frequency of new epizootic events confirms the need to develop new strategies to combat this disease. An innovative opportunity is perturbing the host pathways used by the microorganisms to replicate inside host cells through host-directed antimicrobial drugs (HDAD). Iron is a critical nutrient for P. salmonis infection; hence, the use of iron-chelators becomes an excellent alternative to be used as HDAD. The aim of this work was to use the iron chelator Deferiprone (DFP) as HDAD to treat SRS. Here, we describe the protective effect of the iron chelator DFP over P. salmonis infections at non-antibiotic concentrations, in bacterial challenges both in vitro and in vivo. At the cellular level, our results indicate that DFP reduced the intracellular iron content by 33.1% and P. salmonis relative load during bacterial infections by 78%. These findings were recapitulated in fish, where DFP reduced the mortality of rainbow trout challenged with P. salmonis in 34.9% compared to the non-treated group. This is the first report of the protective capacity of an iron chelator against infection in fish, becoming a potential effective host-directed therapy for SRS and other animals against ferrophilic pathogens.

Made available in DSpace on 2021-06-25T10:35:30Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-29 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Background: Pacu (Piaractus mesopotamicus) is one of the most important Neotropical aquaculture species from South America. Disease outbreaks caused by Aeromonas hydrophila infection have been considered significant contributors to the declining levels of pacu production. The current implementation of genomic selection for disease resistance has been adopted as a powerful strategy for improvement in fish species. This study aimed to investigate the genetic architecture of resistance to A. hydrophila in pacu via Genome-Wide Association Study (GWAS), the identification of suggestive Quantitative Trait Loci (QTLs) and putative genes associated with this trait. The genetic data were obtained from 381 juvenile individuals belonging to 14 full-sibling families. An experimental challenge was performed to gain access to the levels of genetic variation for resistance against the bacteria using the following trait definitions: Binary test survival (TS) and time of death (TD). Results: The analyses of genetic parameters estimated moderate heritability (h 2 ) for both resistance traits: 0.20 (± 0.09) for TS and 0.35 (± 0.15) for TD. A linkage map for pacu was developed to enable the GWAS, resulting in 27 linkage groups (LGs) with 17,453 mapped Single Nucleotide Polymorphisms (SNPs). The length of the LGs varied from 79.95 (LG14) to 137.01 (LG1) cM, with a total map length of 2755.60 cM. GWAS identified 22 putative QTLs associated to A. hydrophila resistance. They were distributed into 17 LGs, and were considered suggestive genomic regions explaining > 1% of the additive genetic variance (AGV) for the trait. Several candidate genes related to immune response were located close to the suggestive QTLs, such as tbk1, trim16, Il12rb2 and lyz2. Conclusion: This study describes the development of the first medium density linkage map for pacu, which will be used as a framework to study relevant traits to the production of this species. In addition, the resistance to A. hydrophila was found to be moderately heritable but with a polygenic architecture suggesting that genomic selection, instead of marker assisted selection, might be useful for efficiently improving resistance to one of the most problematic diseases that affects the South American aquaculture. Saõ Paulo State University (Unesp) Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n Universidade Federal Rural Do Rio de Janeiro Saõ Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences National Council for Scientific and Technological Development (CNPq) Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile Saõ Paulo State University (Unesp) Aquaculture Center of Unesp, Via de Acesso Prof. Paulo Donato Castellane, s/n Saõ Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences

Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, by two haplotype-based (iHS and Rsb) and one FST based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and FST based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed Nile tilapia.

Made available in DSpace on 2020-12-12T01:59:33Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-06-30 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Tambaqui (Colossoma macropomum) is the main native fish farmed in South American continental aquaculture. One of the major pathogens affecting world fresh water aquaculture is the bacterium Aeromonas hydrophila, which generates several disease outbreaks and production losses in farmed tambaqui stocks. Up to date, there are no studies focusing on understanding the quantitative basis for the genetic improvement for disease resistance in tambaqui. Thus, the objective of this study was to determine the genetic parameters for resistance to A. hydrophila and the genetic correlation with average daily gain in juveniles of tambaqui, to determine whether these traits can be included in selective breeding programs. Estimation of genetic parameters was performed using data from an experimental challenge performed in 18 full-sib families, using a total of 576 individuals. Before bacterial challenge, all animals were evaluated for average daily gain (ADG) in the juvenile phase during 30 days. The challenge spanned 120 h (5 days) and disease resistance traits were defined as: i) binary survival (BS) and, ii) time of death (TD) of fish presenting clinical signs of A. hydrophila infection. The mean ADG was 0.49 g/day (SD = 0.21) in the population and heritability for this trait was moderate (h2 = 0.37 ± 0.13). BS and TD varied considerably among families (26% to 89% and 10.7 h to 69.2 h, respectively), which indicated a significant genetic variation related to resistance to A. hydrophila infection. Low to moderate values for heritability were found for BS and TD (0.17 ± 0.06 and 0.23 ± 0.09, respectively). The genetic correlations between resistance to A. hydrophila and ADG in juveniles of tambaqui were not significantly different from zero. The significant genetic variation found for A. hydrophila resistance in tambaqui indicates that selecting superior genotypes is a viable approach to reducing the impact of diseases outbreaks in aquaculture. São Paulo State University (Unesp) Aquaculture Center of Unesp Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile São Paulo State University (Unesp) Aquaculture Center of Unesp CAPES: 001 FAPESP: 2017/19717–3 FAPESP: 2018/08416–5 FAPESP: 2019/10662–7 CNPq: 311559/2018–2 CNPq: 422670/2018–9

Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth-, quality- and robustness-related traits. Novel phenotyping technologies (i.e. phenomics), lower-cost whole-genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.

The introduction of wild Atlantic salmon into captivity, and their subsequent artificial selection for production traits, has caused phenotypic differences between domesticated fish and their wild counterparts. Identification of regions of the genome underling these changes offers the promise of characterizing the early biological consequences of domestication. In the current study, we sequenced a population of farmed European Atlantic salmon and compared the observed patterns of SNP variation to those found in conspecific wild populations. This identified 139 genomic regions that contained significantly elevated SNP homozygosity in farmed fish when compared to their wild counterparts. The most extreme was adjacent to versican, a gene involved in control of neural crest cell migration. To control for false positive signals, a second and independent dataset of farmed and wild European Atlantic salmon was assessed using the same methodology. A total of 81 outlier regions detected in the first dataset showed significantly reduced homozygosity within the second one, strongly suggesting the genomic regions identified are enriched for true selection sweeps. Examination of the associated genes identified a number previously characterized as targets of selection in other domestic species and that have roles in development, behavior and olfactory system. These include arcvf, sema6, errb4, id2-like, and 6n1-like genes. Finally, we searched for evidence of parallel sweeps using a farmed population of North American origin. This failed to detect a convincing overlap to the putative sweeps present in European populations, suggesting the factors that drive patterns of variation under domestication and early artificial selection were largely independent. This is the first analysis on domestication of aquaculture species exploiting whole-genome sequence data and resulted in the identification of sweeps common to multiple independent populations of farmed European Atlantic salmon.

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&reg, myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two &ldquo, pure&rdquo, 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 (&lt, 4 Mb), and for POP C no segment &gt, 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.

Ajuts: this study was supported by INNOVA-CORFO (No. 09MCSS-6691 and 09MCSS-6698), FONDECYT (No. 1161015; 11150807; 11180705; 11181133), DICYT- USACH, VRIDEI-USACH (USA1899 VRIDEI 021943IB-PAP), and Universidad Mayor startup funds (No. OI101205; SR-C). The authors also thank to the grants from CONICYT-BCH (Chile) Postdoctoral fellowship (No. 74170091; EV-V), International postdoctoral stay 2019 (Universidad de Chile, UCH1566; EV-V) and VRIDEI-USACH (FR-L). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Single-nucleotide polymorphisms (SNPs) are single genetic code variations considered one of the most common forms of nucleotide modifications. Such SNPs can be located in genes associated to immune response and, therefore, they may have direct implications over the phenotype of susceptibility to infections affecting the productive sector. In this study, a set of immune-related genes (cc motif chemokine 19 precursor [ ccl19 ], integrin β2 (itβ2, also named cd18), glutathione transferase omega-1 [ gsto-1 ], heat shock 70 KDa protein [ hsp70 ], major histocompatibility complex class I [ mhc-I ]) were analyzed to identify SNPs by data mining. These genes were chosen based on their previously reported expression on infectious pancreatic necrosis virus (IPNV)-infected Atlantic salmon phenotype. The available EST sequences for these genes were obtained from the Unigene database. Twenty-eight SNPs were found in the genes evaluated and identified most of them as transition base changes. The effect of the SNPs located on the 5'-untranslated region (UTR) or 3'-UTR upon transcription factor binding sites and alternative splicing regulatory motifs was assessed and ranked with a low-medium predicted FASTSNP score risk. Synonymous SNPs were found on itβ2 (c.2275G > A), gsto-1 (c.558G > A), and hsp70 (c.1950C > T) with low FASTSNP predicted score risk. The difference in the relative synonymous codon usage (RSCU) value between the variant codons and the wild-type codon (ΔRSCU) showed one negative (hsp70 c.1950C > T) and two positive ΔRSCU values (itβ2 c.2275G > A; gsto-1 c.558G > A), suggesting that these synonymous SNPs (sSNPs) may be associated to differences in the local rate of elongation. Nonsynonymous SNPs (nsSNPs) in the gsto-1 translatable gene region were ranked, using SIFT and POLYPHEN web-tools, with the second highest (c.205A > G; c484T > C) and the highest (c.499T > C; c.769A > C) predicted score risk possible. Using homology modeling to predict the effect of these nonsynonymous SNPs, the most relevant nucleotide changes for gsto-1 were observed for the nsSNPs c.205A > G, c484T > C, and c.769A > C. Molecular dynamics was assessed to analyze if these GSTO-1 variants have significant differences in their conformational dynamics, suggesting these SNPs could have allosteric effects modulating its catalysis. Altogether, these results suggest that candidate SNPs identified may play a crucial potential role in the immune response of Atlantic salmon.

International audience; Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.

We performed a genome-wide association study to detect markers associated with growth traits in Atlantic salmon. The analyzed traits included body weight at tagging (BWT) and body weight at 25 months (BW25M). Genotypes of 4662 animals were imputed from the 50K SNP chip to the 200K SNP chip using fimpute software. The markers were simultaneously modeled using Bayes C to identify genomic regions associated with the traits. We identified windows explaining a maximum of 3.71% and 3.61% of the genetic variance for BWT and BW25M respectively. We found potential candidate genes located within the top ten 1-Mb windows for BWT and BW25M. For instance, the vitronectin (VTN) gene, which has been previously reported to be associated with cell growth, was found within one of the top ten 1-Mb windows for BWT. In addition, the WNT1-inducible-signaling pathway protein 3, melanocortin 2 receptor accessory protein 2, myosin light chain kinase, transforming growth factor beta receptor type 3 and myosin light chain 1 genes, which have been reported to be associated with skeletal growth in humans, growth stimulation during the larval stage in zebrafish, body weight in pigs, feed conversion in chickens and growth rate of sheep skeletal muscle respectively, were found within some of the top ten 1-Mb windows for BW25M. These results indicate that growth traits are most likely controlled by many variants with relatively small effects in Atlantic salmon. The genomic regions associated with the traits studied here may provide further insight into the functional regions underlying growth traits in this species.

Infectious pancreatic necrosis (IPN) is one of the most prevalent and economically important diseases in rainbow trout aquaculture ( Oncorhynchus mykiss ). Vaccines as a conventional control measure have shown variable results under production conditions. Genetic improvement for resistance to IPN represents an alternative for the prevention of disease outbreaks. The objective of the present work was to estimate the heritability and genetic correlation for IPN resistance and harvest weight (HW) in rainbow trout. To determine the genetic resistance to the IPN virus, a total of 2278 fingerlings from 58 full-sib families were used, which were challenged with IPN virus to induce the disease. Resistance refers to survival to the disease and was defined as the day of death of each fish. HW was also recorded in 13,241 genetically related individuals from the same population. For the genetic analysis we fitted a bivariate mixed linear model including HW and resistance to IPN as dependent variables; tank:year:sex as a fixed contemporary group and age at harvest as a covariate for HW; and final weight as a covariate for resistance to IPN. The animal effect was included as a random effect for both traits. A random effect associated with common environment was also included for HW. The estimated heritability for IPN resistance was 0.39 ± 0.08 and 0.35 ± 0.06 for HW. Genetic correlation between IPN and HW resistance was not significant (0.05 ± 0.25). The results indicate that the heritability for both traits is moderately high in this population, and that there is no significant genetic correlation between them. The presence of significant genetic variation for both IPN and HW resistance and the absence of genetic correlation between both traits indicate the feasibility of improving them simultaneously by means of artificial selection.

The sea louse (Caligus rogercresseyi) is an external parasite and considered one of the most important health problems in the salmon farming industry. Resistance to conventional chemical treatments has been demonstrated. Sufficient additive genetic variation has been determined to include selection for resistance to this parasite in Atlantic salmon breeding programs. The aim of this study was to perform a Genome Wide Association Study in order to dissect the genetic factors involved in the resistance to C. rogercresseyi, one of the most important species of sea lice in the Chilean salmon farming. 2628 Atlantic salmon smolts, which had been experimentally infested with C. rogercresseyi, were genotyped using a 50K SNP array. Genome Wide Association Analysis was conducted using a polygenic model. A heritability of 0.12 for resistance to this louse species was estimated using genomic information. This result was consistent with estimates from previous studies which used pedigree records in the same population. Only one SNP, located on chromosome 21, was significant at a local level, explaining 0.5% of the phenotypic variance and 4% of the genomic heritability for sea lice resistance. This SNP is located in an intronic region of a predicted gene which codes for Collagen alpha-1. Our results suggest that resistance to C. rogercresseyi can be considered a polygenic trait, controlled by many variants of relatively small effect. Thus the incorporation of genomic information through genomic selection could be the most appropriate approach for breeding purposes. Statement of relevance Caligus resistance has a polygenic genetic architecture.

Chilean coho salmon (Oncorhynchus kisutch) represents about 90% of the worldwide production. From a commercial perspective rapid growth to market weights and product quality are important aspects of profitability. The objective of this study was to determine genetic parameters, genetic trends and correlated response of flesh color (FC) after eight generations of selection for harvest weight (HW) in two coho salmon populations spawning independently in even and odd years. A total of 41,597 and 37,319 records for HW and 4946 and 6731 for FC were included in the analysis for the even and odd populations, respectively. A linear bivariate animal model was used to estimate genetic parameters and compute breeding values for both traits. Estimated heritabilities for HW and FC were 0.41 ± 0.03 and 0.08 ± 0.02 in the even population and 0.22 ± 0.03 and 0.04 ± 0.01 the in odd population, respectively. Genetic and phenotypic correlations between HW and FC were 0.15 ± 0.11 and 0.07 ± 0.02 in the even population and 0.25 ± 0.14 and 0.12 ± 0.02 in odd population, respectively. Response to selection was measured as the slope of the linear regression fitted on the mean breeding values per generation per trait. We found a positive genetic trend for both traits after eight generations of selection for HW. The increase in HW per generation was 0.31 ± 0.01 and 0.26 ± 0.02 kg for the even and odd populations, respectively. The correlated increase in FC was 0.04 ± 0.01 and 0.04 ± 0.00 fan units per generation in the even and odd population, respectively, showing that selection for HW can increase FC. Statement of relevance. Correlated response in color to selection for growth in coho

Nile tilapia (Oreochromis niloticus) 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. The patterns of linkage disequilibrium (LD) may affect the success of genome-wide association studies (GWAS) and genomic selection and can also provide key information about demographic history of farmed Nile tilapia populations. The objectives of this study were to provide further knowledge about the population structure and LD patterns, as well as, estimate the effective population size (Ne) for three farmed Nile tilapia populations, one from Brazil (POP A) and two from Costa Rica (POP B and POP C). A total of 55, 56 and 57 individuals from POP A, POP B and POP C, respectively, were genotyped using a 50K SNP panel selected from a whole-genome sequencing (WGS) experiment. Two principal components explained about 20% of the total variation and clearly discriminated between the three populations. Population genetic structure analysis showed evidence of admixture, especially for POP C. The contemporary Ne values calculated based to LD values, ranged from 71 to 141. No differences were observed in the LD decay among populations, with a rapid decrease of r2 when increasing inter-marker distance. Average r2 between adjacent SNP pairs ranged from 0.03 to 0.18, 0.03 to 0.17 and 0.03 to 0.16 for POP A, POP B and POP C, respectively. Based on the number of independent chromosome segments in the Nile tilapia genome, at least 4.2 K SNP are required for the implementation of GWAS and genomic selection in farmed Nile tilapia populations.

Piscirickettsia salmonis 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; Oncorhynchus kisutch), Atlantic salmon (AS; Salmo salar), and rainbow trout (RT; Oncorhynchus mykiss) 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 P. salmonis in farmed populations of these species. Resistance to SRS was defined as the number of days to death and as binary survival (BS). A total of 828 CS, 2130 RT, and 2601 AS individuals were phenotyped and then genotyped using double-digest restriction site-associated DNA sequencing and 57K and 50K Affymetrix® Axiom® single nucleotide polymorphism (SNP) panels, respectively. Both traits of SRS resistance in CS and RT appeared to be under oligogenic control. In AS, there was evidence of polygenic control of SRS resistance. To identify candidate genes associated with resistance, we applied a comparative genomics approach in which we systematically explored the complete set of genes adjacent to SNPs, which explained more than 1% of the genetic variance of resistance in each salmonid species (533 genes in total). Thus, genes were classified based on the following criteria: i) shared function of their protein domains among species, ii) shared orthology among species, iii) proximity to the SNP explaining the highest proportion of the genetic variance, and iv) presence in more than one genomic region explaining more than 1% of the genetic variance within species. Our results allowed us to identify 120 candidate genes belonging to at least one of the four criteria described above. Of these, 21 of them were part of at least two of the criteria defined above and are suggested to be strong functional candidates influencing P. salmonis resistance. These genes are related to diverse biological processes, such as kinase activity, GTP hydrolysis, helicase activity, lipid metabolism, cytoskeletal dynamics, inflammation, and innate immune response, which seem essential in the host response against P. salmonis infection. These results provide fundamental knowledge on the potential functional genes underpinning resistance against P. salmonis in three salmonid species.

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. The markers encompass all 30 coho salmon chromosomes and comprise 1,684.62 Mb of the genome. The average density of markers per chromosome ranged from 48.31 to 66 per 1 Mb. The minor allele frequency averaged 0.26 (with a range from 0.22 to 0.27). The overall average linkage disequilibrium among SNPs pairs measured as r 2 was 0.10. The Average r 2 value decreased with increasing physical distance, with values ranging from 0.21 to 0.07 at a distance lower than 1 kb and up to 10 Mb, respectively. An r 2 threshold of 0.2 was reached at distance of approximately 40 Kb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (>0.20 at distances lower than 1 Mb). Average r 2 values were lower than 0.15 for all chromosomes at distances greater than 4 Mb. An effective population size of 43 was estimated for the population 10 generations ago, and 325, for 139 generations ago. Based on the effective number of chromosome segments, we suggest that at least 74,000 SNPs would be necessary for an association mapping study and genomic predictions. Therefore, the SNP panel used allowed us to capture high-resolution information in the farmed coho salmon population. Furthermore, based on the contemporary N e, a new mate allocation strategy is suggested to increase the effective population size.

Made available in DSpace on 2022-04-28T19:40:53Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Universidad de Santiago de Chile 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. A total of 2626 Atlantic salmon and 2643 rainbow trout were challenged and genotyped with 50 K and 57 K SNP panels, respectively. We ran two independent ssGWAS for sea lice resistance on each species and identified 7 and 13 regions explaining more than 1% of the genetic variance for the trait, with the most important regions explaining 3% and 2.7% for Atlantic salmon and rainbow trout, respectively. We identified genes associated with immune response, cytoskeleton function, and cell migration when focusing on important genomic regions for each species. Moreover, we found 15 common orthogroups which were present in more than one associated genomic region, within- or between-species; however, only one orthogroup showed a clear potential biological relevance in the response against sea lice. For instance, dual-specificity protein phosphatase 10-like (dusp10) and dual-specificity protein phosphatase 8 (dusp8) were found in genomic regions associated with lice density in Atlantic salmon and rainbow trout, respectively. Dusp10 and dusp8 are modulators of the MAPK pathway and might be involved in the differences of the inflammation response between lice resistant and susceptible fish from both species. Our results provide further knowledge on candidate genes related to sea lice resistance and may help establish better control for sea lice in fish populations. Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile, Av. Santa Rosa 11735, La Pintana The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh Easter Bush Fisheries and Oceans Canada, 4160 Marine Drive Escuela de Medicina Veterinaria Facultad de Ciencias de la Vida Universidad Andres Bello School of Agricultural and Veterinary Sciences UNESP-Sao Paulo State University Aquainnovo, Cardonal S/N Núcleo Milenio INVASAL Center for Research and Innovation in Aquaculture (CRIA) Universidad de Chile School of Agricultural and Veterinary Sciences UNESP-Sao Paulo State University Universidad de Santiago de Chile: MR/N026144/1

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. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to measure into the breeding goal. Thus, single nucleotide polymorphisms (SNPs) are required to investigate phenotype–genotype associations and determine the genomic basis of economically important traits. We performed de novo SNP discovery in three different populations of farmed Nile tilapia. A total of 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After applying several filtering steps, including removing SNP based on genotype and site quality, presence of Mendelian errors, and non-unique position in the genome, a total of 50,000 high-quality SNPs were selected for the development of a custom Illumina BeadChip SNP panel. These SNPs were highly informative in the three populations analyzed showing between 43,869 (94%) and 46,139 (99%) SNPs in Hardy-Weinberg Equilibrium; 37,843 (76%) and 45,171(90%) SNPs with a minor allele frequency (MAF) higher than 0.05; and 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The 50K SNP panel developed in the current work will be useful for the dissection of economically relevant traits, enhancing breeding programs through genomic selection, as well as supporting genetic studies in farmed populations of Nile tilapia using dense genome-wide information.

Nile tilapia (Oreochromis niloticus) 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. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.

Made available in DSpace on 2021-06-25T10:28:03Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-07-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The inclusion of genomic information became a reality in shrimp breeding and it is expected to accelerate the genetic gain over time. The decay of linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs) is an important measure to evaluate the feasibility of implementing genomic selection. The aim of this study was to evaluate the use of a novel 50 K SNP array tool to characterize the genomic diversity, LD and effective population size (Ne) in a farmed shrimp population. A total of 96 animals (40 sires and 56 dams) were genotyped using the novel Illumina AquaArray HD (50 K) vannamei®. Quality control (QC) of genomic data was performed and three different minor allele frequency (MAF) exclusion thresholds were applied: < 0.10 (QC1), < 0.05 (QC2) and < 0.01 (QC3). After QC, 34,425, 39,091 and 42,789 SNPs were retained for QC1, QC2 and QC3, respectively, validating the high informativeness of this SNP array to this particular shrimp breeding population. The population showed a considerable high overall heterozygosity in comparison to other aquaculture species meaning that genetic diversity is stable despite selection. The principal component analysis revealed three genetically distant groups with the first two principal components explaining 27.7 % of total variation. LD decayed rapidly in the first 30Kb of distance between markers from 0.20 to 0.07 and then decreased to 0.02 in the long-range distance. These results suggest a relatively recent incorporation of animals from different populations in the broodstock. Ne size reduced from 7,871 to 301 animals in 827 generations for QC1, 8,253 to 305 animals for QC2 and 8,957 to 315 animals for QC3, both in 899 generations. Contemporary Ne was close to 86 for all QCs. The level of LD estimated suggests that genomic selection and genome-wide association studies are feasible in shrimp by using this SNP array. School of Agricultural and Veterinary Sciences UNESP - São Paulo State University Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile OPUMARSA National Council for Scientific and Technological Development (CNPq) School of Agricultural and Veterinary Sciences UNESP - São Paulo State University

The aim of this research was to statistically analyze the association between antimicrobial susceptibility/resistance to erythromycine, gentamicin, ciprofloxacin, and tetracycline and 11 virulence genes associated with adherence, invasion, and cytotoxicity in 528 isolates of Campylobacter coli and Campylobacter jejuni obtained from retail meat and fecal samples from food-producing animals and human patients. A high percentage of Campylobacter strains were resistant to antimicrobials, specifically ciprofloxacin and tetracycline. Moreover, we observed a wide distribution of virulence genes within the analyzed strains. C. jejuni strains were more susceptible to antimicrobials, and showed greater number of virulence genes than C. coli strains. Genes related to invasion capability, such as racR, ciaB, and pldA, were associated with antimicrobial-susceptible strains in both species. The genes cdtA and dnaJ, a citotoxin unit and an adherence-related gene, respectively, were associated with antimicrobial-resistant strains in both species. In conclusion, Campylobacter strains show a statistically significant association between antimicrobial susceptibility and the presence of virulence genes.

One of the major infectious diseases affecting coho salmon (Oncorhynchus kisutch) aquaculture is the Salmon Rickettsial Syndrome caused by Piscirickettsia salmonis. Conventional control measures such as antibiotics and vaccines have shown inconsistent results in production conditions. Thus, genetic improvement for P. salmonis resistance represents an alternative for the prevention of outbreaks. In the present study we aimed to determine both the levels of genetic variation for P. salmonis resistance (PSR) and genetic co-variation between PSR and harvest weight (HW) in coho salmon. A total of 2606 siblings from 108 maternal full-sib families (60 paternal half-sib families) were challenged against P. salmonis. The cumulative mortality rates among families ranged from 5% to 82%, with an average of 39%, indicating considerable phenotypic variation. For the genetic analyses PSR was defined as the day of death for each fish. We also recorded HW in 41,597 genetically related individuals of the challenged fish from the same breeding population. A linear bivariate animal model was used to estimate (co)variance components and to calculate genetic parameters. Estimated heritabilities for PSR and HW were 0.16 ± 0.04 and 0.41 ± 0.03, respectively. The genetic correlation between PSR and HW was − 0.50 ± 0.13. The levels of genetic variation detected in the present study indicate that selective breeding for these traits is feasible. However, the magnitude and direction of the genetic correlation between PSR and HW must be taken into account when selecting both traits simultaneously. Statement of relevance Negative relationship between resistance and growth in coho.

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 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K 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 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 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.

Artificial selection can be advantageous for breeding fish that are better adapted to temperature changes induced by climate change. Selecting fish with better growth performance and survival under long term thermal stress would require an understanding of the level of additive genetic variation for these traits. Moreover, disentangling the genetic co-variation between growth- and robustness-related traits is key to understand potential antagonisms between selection for an increased performance and survivability. Thus, this study aimed at: i) assessing levels of genetic variation for growth and survival under chronic heat stress, and ii) evaluating the genetic relationship between these two traits and a broad range of growth- and robustness-related traits to identify potential trade-offs in rainbow trout. Phenotypic and pedigree records (n = 65,298 animals) from a rainbow trout breeding population were used. Growth and survival under chronic thermal stress were defined as the final body weight (FWHT) and days to death (TSR), after the experimental chronic exposure to high temperature (between 18 and 22 °C). Other growth-related traits analyzed here were: body weight at smolt stage (SW), harvest weight (HW), weight at processing plant (WPP), fillet weight (FW), weight of the eviscerated fish (GUW) and body weight at low temperature (FWLT). Robustness-related traits evaluated here were: resistance against Piscirickettsia salmonis (PSR) and Flavobacterium psychrophilum (FPR), and susceptibility to Caligus rogercresseyi (CS). The heritabilites estimated were: FWHT = 0.41 ± 0.14; TSR = 0.13 ± 0.05; SW = 0.54 ± 0.01; HW = 0.63 ± 0.01; WPP = 0.19 ± 0.02; FW = 0.03 ± 0.03; GUW = 0.18 ± 0.02; FWLT = 0.59 ± 0.17; FPR = 0.35 ± 0.05; PSR = 0.30 ± 0.05; and CS 0.08 ± 0.02. In general, strong compensations were identified between the robustness- and growth- related traits with genetic correlations that ranged from −0.28 to −0.98, except for resistance to F. psychrophilum and growth-related traits, which showed correlation values from 0.28 to 0.46. Genetic improvement for growth and survival under chronic upper thermal exposure is feasible. Compensations between growth- and robustness- related traits have to be accounted for when simultaneously including performance and disease resistance traits in the breeding objective.

In breeding programs, genetic evaluations can be performed using phenotypic information from the selection candidates per se or from relatives to obtain breeding values (EBV) by the traditional method known as the Best Linear Unbiased Predictor (BLUP). Using phenotypic information from relatives (e.g. sib-testing) is a common practice particularly in aquaculture, because some economically important traits, including disease resistance and carcass quality, would require the slaughtering of animals before they could become breeders. The ability to better predict genetic merit has made the incorporation of genomic information into genetic evaluation a common practice in livestock and aquaculture species. Genomic selection uses genotypic information from single nucleotide polymorphism (SNP) arrays or genotyping-by-sequencing assays to increase the accuracy of selection by means of exploiting realized within and between family trait information. The cost of genotyping dense SNP panels in the training population and selection candidates limits the practical implementation of genomic selection. Imputation from low- to high-density genotypes represents an alternative which decreases the cost of genotyping while maintaining prediction accuracies. The present study compared EBV accuracies obtained with BLUP and genomic selection (GBLUP) methods using simulation. We simulated five generations of a rainbow trout (Oncorhynchus mykiss) breeding program, using 1662 individuals with real genotypic data from 42,822 SNP as a founder population. The scenarios varied using three heritability levels (h2 = 0.1; 0.2 and 0.4) and four imputation error rates (10%, 5%, 1% and 0%), mimicking different densities of low-density SNP panels (0.5 K, 3 K, 7 K and 42 K, respectively). The simulations showed: (1) an increase in accuracy ranging from 3% to 25% when comparing GBLUP against BLUP across all scenarios, (2) a non-linear increase in accuracy for both BLUP and GBLUP across generations and heritability levels, and (3) comparable performance between GBLUP0.5 K, GBLUP3K and GBLUP7K models in terms of accuracy. We conclude that low cost genomic selection can be applied in aquaculture breeding programs using a combined approach of low-density SNP panels (e.g. 500 SNPs) and genotype imputation., This work has been partly funded by projects AGL2013-41834-R and AGL2016-78709-R (Ministry of Economy and Competitiveness, Spain) lead by MP-E, and FONDEF project ITI10100 and FONDECYT REGULAR N° 1171720 directed by JMY. JMY is supported by Núcleo Milenio INVASAL funded by Chile's government program, Iniciativa Cientifica Milenio from Ministerio de Economia, Fomento y Turismo.

Made available in DSpace on 2019-10-04T11:55:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-12-14 CONICYT (Government of Chile) Nucleo Milenio INVASAL from Iniciativa Cientifica Milenio (Ministerio de Economia, Fomento y Turismo, Gobierno de Chile) Chilean Farmed Atlantic salmon (Salmo safer) 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. We assessed the population structure and characterized the extent and decay of LD in three Chilean commercial populations of Atlantic salmon with North American (NAM), Scottish (SCO), and Norwegian (NOR) origin. A total of 123 animals were genotyped using a 159 K SNP Axiom (R) myDesign (TM) Genotyping Array. A total of 32 K SNP markers, representing the common SNPs along the three populations after quality control were used. The principal component analysis explained 78.9% of the genetic diversity between populations, clearly discriminating between populations of North American and European origin, and also between European populations. NAM had the lowest effective population size, followed by SCO and NOR. Large differences in the LD decay were observed between populations of North American and European origin. An r(2) threshold of 0.2 was estimated for marker pairs separated by 7,800, 64, and 50 kb in the NAM, SCO, and NOR populations, respectively. In this study we show that this SNP panel can be used to detect association between markers and traits of interests and also to capture high-resolution information for genome-enabled predictions. Also, we suggest the feasibility to achieve similar prediction accuracies using a smaller SNP data set for the NAM population, compared with samples with European origin which would need a higher density SNP array. Univ Chile, Fac Ciencias Vet & Pecuarias, La Pintana, Chile Univ Estadual Paulista Julio de Mesquite Filho, Fac Ciencias Agr & Vet, Jaboticabal, Brazil Benchmark Genet SA, Puerto Montt, Chile Nucleo Milenio INVASAL, Concepcion, Chile Univ Estadual Paulista Julio de Mesquite Filho, Fac Ciencias Agr & Vet, Jaboticabal, Brazil CONICYT (Government of Chile): IT14I10100

BackgroundBreeding for disease resistance has become a highly desirable strategy for mitigating infectious disease problems in aquaculture. However, knowledge of the genetic relationship between resistance and other economically important traits, such as growth, is important to assess prior to including disease resistance into the breeding goal. Our study assessed the genetic correlations between growth and survival traits in a large bacterial infection challenge experiment. A population of 2,606 coho salmon individuals from 107 full-sibling families were challenged with the bacteria Piscirickettsia salmonis. Growth was measured as average daily gain prior (ADG0) and during (ADGi) the experimental infection and as harvest weight (HW). Resistance was measured as Survival time (ST) and binary survival (BS). Furthermore, individual measures of bacterial load (BL) were assessed as new resistance phenotypes and to provide an indication of genetic variation in tolerance in salmonid species.ResultsSignificant moderate heritabilities were estimated for ADG0 (0.30 ± 0.05), HW (0.38 ± 0.03), and for the survival traits ST (0.16 ± 0.03) and BS (0.18 ± 0.03). In contrast, heritabilities for ADGi and log-transformed BL were low (0.07 ± 0.02 (significant) and 0.04 ± 0.03, respectively), although these increased to moderate significant levels (0.20 ± 0.09 and 0.12 ± 0.05, respectively) when traits were assessed in survivors only. Significant and favorable genetic correlations were found between ADG0 and the growth traits ADGi (0.40 ± 0.16) and HW (0.64 ± 0.09), as well as with resistance as ST (0.43 ± 0.18), indicating that fish with higher genetic growth rate early on and prior to infection not only tend to maintain their genetic growth advantage until harvest, but also tend to grow faster and survive longer during infection. Furthermore, no robust unfavorable genetic correlations between ADG0 and any of the other traits considered in this study, in particular BL, was identified. Adding log BL as covariates into the models for growth under infection and survival provided an indication for genetic variation in tolerance.ConclusionsThese results suggest that selective breeding for early growth would be expected to simultaneously increase survival time and growth performance during an infection with Piscirickettsia salmonis after accounting for variation in bacterial load, and harvest weight in this coho salmon population, without negatively impacting on pathogen burden.

Sea lice (Caligus rogercresseyi) are ectoparasitic copepods which have a large negative economic and welfare impact in Atlantic salmon (Salmo salar) 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. In this study we took a multifaceted approach to identify and characterise quantitative trait loci (QTL) affecting hose resistance in a population of 2,688 Caligus-challenged Atlantic salmon post-smolts from a commercial breeding programme. We used low and medium density genotyping to collect genome-wide SNP marker data for all animals. Moderate heritablility estimates of 0.28 and 0.24 were obtained for lice density (as a measure of host resistance) and growth during infestation respectively. Three QTL explaining between 7 and 13 % of the genetic variation in resistance to sea lice (as represented by the traits of lice density) were detected on chromosomes 3, 18 and 21. Characterisation of these QTL regions was undertaken using RNA sequencing and pooled whole genome sequencing data. This resulted in the identification of a shortlist of potential underlying causative genes, and candidate functional mutations for further study. For example, candidates within the chromosome 3 QTL include a putative premature stop mutation in TOB1 (an anti-proliferative transcription factor involved in T cell regulation) and an uncharacterized protein which showed significant differential allelic expression (implying the existence of a cis-acting regulatory mutation). While host resistance to sea lice is polygenic in nature, the results of this study highlight significant QTL regions together explaining a moderate proportion of the heritability of the trait. Future investigation of these QTL may enable improved knowledge of the functional mechanisms of host resistance to sea lice, and incorporation of functional variants to improve genomic selection accuracy.

Made available in DSpace on 2019-10-06T16:13:40Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-06-01 Fondo Nacional de Desarrollo Científico y Tecnológico Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) 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. Analysis was performed by means of single-step GBLUP approach. Genetic variance explained by 20 adjacent SNP windows across the whole genome is reported. To further explore candidate genes, we focused on windows that explained the highest proportion of genetic variance in the top 10 chromosomes for each trait. The main window from the top 10 chromosomes was explored by BLAST using the first and last SNP position of each window to determine the target nucleotide sequence. As expected, the percentage of genetic variance explained by windows was relatively low, due to the polygenic nature of body weight. The most important genomic region for BWT and BW18M were located on chromosomes 15 and 24 and they explained 2.14% and 3.02% of the genetic variance for each trait, respectively. Candidate genes including several growth factors, genes involved in development of skeletal muscle and bone tissue and nutrient metabolism were identified within the associated regions for both traits BWT and BW18M. These results indicate that body weight is polygenic in nature in rainbow trout, with the most important loci explaining as much as 3% of the genetic variance for the trait. The genes identified here represent good candidates for further functional validation to uncover biological mechanisms underlying variation for growth in rainbow trout. Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile, Santa Rosa 11735 Departamento de Engenharia de Pesca Campus Experimental de Registro Universidade Estadual Paulista “Júlio de Mesquita Filho”, Av. Nelso Briho Badur 430 School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp) Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane Benchmark Genetics Chile S.A. Núcleo Milenio INVASAL Departamento de Engenharia de Pesca Campus Experimental de Registro Universidade Estadual Paulista “Júlio de Mesquita Filho”, Av. Nelso Briho Badur 430 School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp) Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane Fondo Nacional de Desarrollo Científico y Tecnológico: 1171720 FAPESP: 2017/00123-6

Made available in DSpace on 2018-12-11T16:52:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-04-01 The objectives of this study were: (i) to assess genotype imputation accuracy in different scenarios using genome-wide single nucleotide polymorphisms (SNP) data from a population comprising two generations of farmed Atlantic salmon and (ii) to assess the accuracy of genomic predictions for a quantitative trait (body weight) using the imputed genotypes. The pedigree consisted of 53 parents and 1069 offspring genotyped using a high-density SNP panel (50 K). Two groups were created: Group A: 90% of the offspring were included into training and 10% into validation sets; Group B: 10% of the offspring were included into training and 90% into validation sets. Different scenarios of available genotypic information from relatives were tested for the two groups previously described. Imputation was performed using three in silico low-density panels (0.5, 3 and 6 K) with all markers except the markers present on the low-density panel masked in the validation sets. The accuracy of genomic selection was tested using the scenarios that resulted in the best and the worst imputation accuracy for the three low density panels and were compared to accuracy obtained from pedigree-based best linear unbiased prediction (PBLUP) and genomic predictions using the 50 K SNP panel. In general, imputation accuracy ranged from 0.74 to 0.98 depending on scenario. For the best scenario with the highest number of animals in reference population (Group A), the accuracy of imputation ranged from 0.95 to 0.98 depending on the low-density panel used. For the best scenario with the lowest number of animals in reference population (Group B), the accuracy of imputation ranged from 0.94 to 0.98 depending on the low-density panel used. In general, the number of SNPs in the low-density panels had a greater influence on the accuracy of imputation than the size of the reference set. The accuracies of genomic predictions using imputed genotypes, ranging from 0.71 to 0.73, outperformed PBLUP (0.66) and were identical or very similar to the use of all true genotype data (0.73). The high imputation and genomic prediction accuracy suggest that the imputation of genotypes from low density (0.5 to 3 K) to high density (50 K) could be a cost-effective strategy for the feasibility of the practical implementation of genomic selection in Atlantic salmon. Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile, Av. Santa Rosa 11735 School of Agricultural and Veterinarian Sciences São Paulo State University (UNESP), Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane Aquainnovo, Cardonal S/N The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh Núcleo Milenio INVASAL School of Agricultural and Veterinarian Sciences São Paulo State University (UNESP), Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane

Made available in DSpace on 2018-11-26T15:47:47Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-04-01 National Commission of Scientific and Technologic Research (CONICYT) Government of Canada U-Inicia grant, from the Vicerrectoria de Investigacion y Desarrollo, Universidad de Chile grant FON-DEF NEWTON-PICARTE - CONICYT (Government of Chile) Newton Fund - The British Council (Government of United Kingdom) Nucleo Milenio INVASAL from Iniciativa Cientifica Milenio (Ministerio de Economia, Fomento y Turismo, Gobierno de Chile) government of Canada through Genome Canada Genome British Columbia Genome Quebec 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. Univ Chile, Fac Ciencias Vet & Pecuarias, Santiago 8820808, Chile Pontificia Univ Catolica Valparaiso, Programa Cooperat Univ Chile, Univ Catolica Norte, Acuicultura, Valparaiso 8820808, Chile Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC V5A 1S6, Canada Univ Estadual Paulista, Dept Anim Sci, Fac Ciencias Agr & Vet, Campus Jaboticabal, BR-14884900 Jaboticabal, Brazil Aquainnovo SA, Puerto Montt 5503032, Chile Nucleo Milenio INVASAL, Concepcion 4070386, Chile Govt Canada, Marine Ecosyst & Aquaculture Div, Sci Branch Fisheries & Oceans Canada, 4160 Marine Dr, W Vancouver, BC V7V 1N6, Canada Univ Estadual Paulista, Dept Anim Sci, Fac Ciencias Agr & Vet, Campus Jaboticabal, BR-14884900 Jaboticabal, Brazil grant FON-DEF NEWTON-PICARTE - CONICYT (Government of Chile): IT14I10100

Made available in DSpace on 2018-11-26T15:47:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-02-01 Aguas Claras S.A. Corporacion de Fomento de la Produccion Fondo Nacional de Desarrollo Cientifico y Tecnologico Regular Nucleo Milenio de Salmonidos Invasores Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) National Council for Scientific and Technological Development fellowship Salmonid rickettsial syndrome (SRS), caused by the intracellular bacterium Piscirickettsia salmonis, is one of the main diseases affecting rainbow trout (Oncorhynchus mykiss) 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 (0.5, 3, 10, 20, and 27 K) for resistance against P. salmonis in rainbow trout. Phenotypes were recorded as number of days to death (DD) and binary survival (BS) from 2416 fish challenged with P. salmonis. A total of 1934 fish were genotyped using a 57 K single-nucleotide polymorphism (SNP) array. All genomic prediction methods achieved higher accuracies than PBLUP. The relative increase in accuracy for different genomic models ranged from 28 to 41% for both DD and BS at 27 K SNP. Between different genomic models, the highest relative increase in accuracy was obtained with Bayes C (approximate to 40%), where 3 K SNP was enough to achieve a similar accuracy to that of the 27 K SNP for both traits. For resistance against P. salmonis in rainbow trout, we showed that genomic predictions using GBLUP, ssGBLUP, Bayes C, and LASSO can increase accuracy compared with PBLUP. Moreover, it is possible to use relatively low-density SNP panels for genomic prediction without compromising accuracy predictions for resistance against P. salmonis in rainbow trout. Univ Chile, Fac Ciencias Vet & Pecuarias, Santiago 8820808, Chile Sao Paulo State Univ, Sch Agr & Veterinarian Sci, Dept Anim Sci, Campus Jaboticabal, BR-14884900 Jaboticabal, Brazil Akvaforsk Genet, N-6600 Sunndalsora, Norway Aquainnovo, Puerto Montt, Chile Nucleo Milenio Salmonidos Invasores, Concepcion, Chile Sao Paulo State Univ, Sch Agr & Veterinarian Sci, Dept Anim Sci, Campus Jaboticabal, BR-14884900 Jaboticabal, Brazil Corporacion de Fomento de la Produccion: 11IEI-12843 Fondo Nacional de Desarrollo Cientifico y Tecnologico Regular: 1171720 FAPESP: 2014/20626-4 FAPESP: 2015/25232-7 National Council for Scientific and Technological Development fellowship: 308636/2014-7

This study examined four commercial lines of Nile tilapia ( Oerochromis niloticus ) ultimately to implement a breeding program to produce clean fillets from an all-male fish population that is grown to 1 kg. Contemporary progenies were produced to perform a complete 4 × 4 diallel cross. Two experimental populations were studied: (1) a set of hormonal sex-reversed (SR) progeny populations that were processed at 1 kg to obtain carcass quality data and (2) a set of populations that did not receive hormone treatment (no hormone, NH) that were used to assess growth between 100 g to 400 g. The growth traits of 3997 NH fish from 124 families were recorded at 400 g, and the processing plant traits were obtained from 2721 SR fish from 99 families. In general, all sources of variation were highly significant for most traits with the effect of linebreeding explaining the largest (from 35 to 50%) fraction of the explained variance (FEV) for all traits, except for the dressing percentage, for which the effect of the general combining ability (gca) was the most important source of variation (51%). The gca exerted the second most important effect on the body weight, fillet weight, and abdominal fat percentage, and reciprocal effects constituted the second most important influence on the head, dressing and fillet percentages, with an FEV of 20% to 35% being observed. The maternal effect was relatively important only for the specific growth rate (SGR), explaining 26% of the total variance. The effect of heterosis was highly significant for all traits but corresponded to only 5% or less of the explained variance for almost all traits, except for the fillet percentage and for days to 1000 g with FEVs of 16% and 9%, respectively. In the NH population, the heterosis for all traits indicates a favorable effect of crossbreeding, particularly the heterosis for body weight (6.7%) and average daily gain (6.8%). In the SR population, the levels of heterosis demonstrated the favorable moderate effects of crossbreeding on the body wt. at 400 g (4.0%), days to 1 kg (− 6.3%), average abdominal fat % (− 7.4%), and fillet yield (1.6%). These results suggest that crossbreeding does not further improve the exploitation of genetic variation for single traits in this particular farmed tilapia population; however, the observed composite trait fillet productivity, i.e., the total biomass of fillet produced per number of farmed fish,yielded promising levels of heterosis with levels that reached 38% and 43% in specific crosses. Furthermore, four of six cases exhibited a cross that was better than the best pure line, demonstrating that profit heterosis is a relevant parameter to consider for assessing breeding strategies. Statement of relevance Total biomass of fillet produced, yielded promising levels of heterosis.

BackgroundSea lice are parasitic copepods that cause large economic losses to salmon aquaculture worldwide. Frequent chemotherapeutic treatments are typically required to control this parasite, and alternative measures such as breeding for improved host resistance are desirable. Insight into the host-parasite interaction and mechanisms of host resistance can lead to improvements in selective breeding, and potentially novel treatment targets. In this study, RNA sequencing was used to study the skin transcriptome of Atlantic salmon parasitized with sea lice (C. rogercresseyi). The overall aims were to compare the transcriptomic profile of skin at louse attachment sites and ‘healthy’ skin, and to assess differences between animals with varying levels of resistance to the parasite.ResultsAtlantic salmon were challenged with C. rogercresseyi, growth and lice count measurements were taken for each fish. 21 animals were selected and RNA-Seq was performed on skin from a louse attachment site, and skin distal to attachment sites for each animal. These animals were classified into family-balanced groups according to the traits of resistance (high vs low lice count), and growth during infestation (an indication of tolerance). Overall comparison of skin from louse attachment sites versus healthy skin showed that 4,355 genes were differentially expressed, indicating local up-regulation of several immune pathways and activation of tissue repair mechanisms. Comparison between resistant and susceptible animals highlighted expression differences in several immune response and pattern recognition genes, and also myogenic and iron availability factors. Genomic regions showing signs of differentiation between resistant and susceptible fish were identified using an Fst analysis.ConclusionsComparison of the skin transcriptome between louse attachment sites and healthy skin has yielded a detailed profile of genes and pathways with putative roles in the local host immune response to C. rogercresseyi. The difference in skin gene expression profile between resistant and susceptible animals led to the identification of several immune and myogenic pathways potentially involved in host resistance. Components of these pathways may be targets for studies aimed at improved or novel treatment strategies, or to prioritise candidate functional polymorphisms to enhance genomic selection for host resistance in commercial salmon farming.

Breeding for disease resistance has become a highly desirable strategy for mitigating infectious disease problems in aquaculture. However, knowledge of the genetic relationship between resistance and other economically important traits, such as growth, is important to assess prior to including disease resistance into the breeding goal. Our study assessed the genetic correlations between growth and survival traits in a large bacterial infection challenge experiment. A population of 2606 coho salmon individuals from 107 full-sibling families were challenged with the bacteria Piscirickettsia salmonis. Growth was measured as average daily gain prior (ADG0) and during (ADGi) the experimental infection and as harvest weight (HW). Resistance was measured as Survival time (ST) and binary survival (BS). Furthermore, individual measures of bacterial load (BL) were assessed as new resistance phenotypes and to provide an indication of genetic variation in tolerance in salmonid species. Resistant families showed lower bacterial load than those susceptible to P. salmonis. Furthermore, some surviving fish belonging to resistant families, were considered as bacterial-free because their bacterial load was below the detection threshold. Adding logBL as a covariate into the models for growth under infection and survival indicated significant genetic variation in tolerance.Significant moderate heritabilities were estimated for ADG0 (0.30 ± 0.05), HW (0.38 ± 0.03), and for the survival traits ST (0.16 ± 0.03) and BS (0.18 ± 0.03). In contrast, heritabilities for ADGi and log-transformed BL were low (0.07 ± 0.02 (significant) and 0.04 ± 0.03, respectively), although these increased to moderate significant levels (0.20 ± 0.09 and 0.12 ± 0.05, respectively) when traits were assessed in survivors only. Significant favorable genetic correlations were found between ADG0 and ADGi (0.40 ± 0.16), HW (0.64 ± 0.09), and with resistance as ST (0.43 ± 0.18), indicating that fish with higher genetic growth rate early on and prior to infection not only tend to maintain their genetic growth advantage until harvest, but also tend to grow faster and survive longer during infection. Although a significant unfavorable correlation (−0.50 ± 0.13) between HW and ST was found, this value decreased to −0.35 ± 0.20 using uncensored data from non-survivors only. Similarly, no robust unfavorable genetic correlations between ADG0 and LogBL, or ADG0 and any of the other traits considered in this study, was identified. These results suggest that selective breeding for early growth, in the current coho salmon population, would be expected to simultaneously increase survival time and growth performance during an infection with Piscirickettsia salmonis, without negatively impacting on pathogen burden

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. Our aim was to compare the accuracy, in terms of reliability of genome-enabled prediction, from different GS methods with PBLUP for resistance to SRS in an Atlantic salmon breeding program. Number of days to death (DAYS), binary survival status (STATUS) phenotypes, and 50 K SNP array genotypes were obtained from 2601 smolts challenged with P. salmonis. The reliability of different GS methods at different SNP densities with and without pedigree were compared to PBLUP using a five-fold cross validation scheme. Results Heritability estimated from GS methods was significantly higher than PBLUP. Pearson’s correlation between predicted GEBV from PBLUP and GS models ranged from 0.79 to 0.91 and 0.79–0.95 for DAYS and STATUS, respectively. The relative increase in reliability from different GS methods for DAYS and STATUS with 50 K SNP ranged from 8 to 25% and 27–30%, respectively. All GS methods outperformed PBLUP at all marker densities. DAYS and STATUS showed superior reliability over PBLUP even at the lowest marker density of 3 K and 500 SNP, respectively. 20 K SNP showed close to maximal reliability for both traits with little improvement using higher densities. Conclusions These results indicate that genomic predictions can accelerate genetic progress for SRS resistance in Atlantic salmon and implementation of this approach will contribute to the control of SRS in Chile. We recommend GBLUP for routine GS evaluation because this method is computationally faster and the results are very similar with other GS methods. The use of lower density SNP or the combination of low density SNP and an imputation strategy may help to reduce genotyping costs without compromising gain in reliability. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3487-y) contains supplementary material, which is available to authorized users.

International audience; AbstractSea 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.

We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)

We describe an emerging initiative - the ‘Functional Analysis of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, through to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Selective breeding practices in Atlantic salmon aquaculture have been carried out intensively since the 1970s. Along with the phenotypic improvement of fish, we expect to observe genomic regions showing evidence of selection for traits related to growth and age at sexual maturation, as well as traits involved in the domestication process. This is mainly linked to the increase in the frequency of favourable alleles at loci that affect the traits of interest in the breeding population. In this study we searched for signatures of selection in the Cermaq Atlantic salmon broodstock, a Mowi strain, which was derived from wild Norwegian populations, and is now farmed in British Columbia, Canada. A 6.5K SNP array was used to genotype 202 fish from the Cermaq population, and the genotypes were compared with four wild populations from Norway. We used three methods based on FST values to detect signatures of selection. Forty four markers showing divergence in allele frequency were identified as outliers by the three detection methods, suggesting the presence of signatures of selection in the Cermaq population relative to their wild counterparts. Markers identified as outliers are associated with molecular functions that could be related to the selection for economically important traits (e.g., growth) as well as the domestication process (e.g., response to pathogens and environmental stressors). Of particular interest were three outlier markers that had been previously associated with grilsing (i.e., early sexual maturation) an undesirable trait, which has been heavily selected against in Atlantic salmon aquaculture. This study provides clear evidence of the presence of signatures of selection and domestication in a farmed Atlantic salmon population.

Background: Mastitis resistance is a complex and multifactorial trait, and its expression depends on both genetic and environmental factors, including infection pressure. The objective of this research was to determine the genetic basis of mastitis resistance to specific pathogens using a repeatability threshold probit animal model. Results: The most prevalent isolated pathogens were coagulase-negative staphylococci (CNS); 39 % of records and 77 % of the animals infected at least one time in the whole period of study. There was significant genetic variation only for Streptococci (STR). In addition, there was a positive genetic correlation between STR and all pathogens together (ALL) (0.36 ± 0.22), and CNS and ALL (0.92 ± 0.04). Conclusion: The results of our study support the presence of significant genetic variation for mastitis caused by Streptococci and suggest the importance of discriminating between different pathogens causing mastitis due to the fact that they most likely influence different genetic traits. Low heritabilities for pathogen specific-mastitis resistance may be considered when including bacteriological status as a measure of mastitis presence to implement breeding strategies for improving udder health in dairy ewes.