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Plateforme SYSAAF-ANSES Fortior Genetics; National audience; Depuis 2018, et grâce aux projets de R&D Fild’Or et GèneSea (FEAMP), les écloseries FMDS et EMGI ont commencé à indexer leurs candidats en utilisant la ressemblance des génomes (sélection génomique - SG) plutôt que l’appartenance familiale (pedigree), en particulier pour des caractères de résistance à des pathologies ou pour sélectionner des candidats élevés à terre sur les performances d’apparentés élevés en cages. Le coût de génotypage (20-25 € /individu) avec une puce moyenne densité (MD) d’environ 57 000 marqueurs génétiques SNP (57K) constitue un frein concurrentiel réel pour les entreprises de sélection. Les travaux antérieurs sur les espèces terrestres et le saumon ainsi que l’arrivée du génotypage par séquençage pourraient cependant permettre de réduire ce coût en génotypant les candidats et apparentés à plus basse densité (LD, 200 à 3000 marqueurs) et en imputant les marqueurs manquants entre ces marqueurs génotypés à partir du génotype de leurs parents obtenu en MD (sélection génomique par imputation). L’objectif de l’étude réalisée dans le projet européen AquaIMPACT était d’évaluer l’efficacité relative d’une sélection génomique par imputation chez le bar et la daurade avec des panels LD par rapport à une sélection sur pedigree ou génomique avec une puce MD pour évaluer le meilleur compromis entre efficacité de la sélection et prix du génotypage. Ce travail a été mené pour deux espèces marines de deux entreprises de sélection française : EMGI (bar) et FMDS (daurade). Un total de 1646 bars a été génotypé à l’aide de la puce MD 57K SNP Axiom DlabCHIP à raison de 942 bars phénotypés pour la résistance à vibrio harveyi par la plateforme SYSAAF-ANSES Fortior Genetics et de 704 bars phénotypés pour des caractères de découpe (poids, poids éviscéré et étêté ajusté par le poids). 919 daurades ont été génotypées avec la puce 60K SNP Axiom SaurCHIP et phénotypées pour différents caractères de découpe (poids, poids éviscéré et étêté ajusté par le poids, poids du filet ajusté par le poids). Pour chaque espèce, l’efficacité de la sélection génomique a été évaluée avec les puces MD et pour 10 panels LD de tailles différentes : 300, 500, 700, 1 000, 3 000, 5 000, 10 000, 15 000, 20 000 marqueurs. La qualité de l’imputation augmente avec le nombre de marqueurs sur les panels LD. Elle atteint rapidement un plateau entre 3 000 et 5 000 marqueurs, pour les deux espèces. Les résultats montrent une efficacité proche, en moyenne, de la sélection avec une puce 57K en utilisant un panel LD avec 3 000 marqueurs sans imputation ou avec un panel 1 000 marqueurs avec imputation pour les deux espèces et les différents caractères. Ces résultats permettent d’envisager la création de panels LD pour les différentes entreprises de sélection françaises pour réduire les coûts de la sélection génomique tout en conservant un niveau d’efficacité équivalent à une puce 57K.

International audience; Hypoxia is one of the major threats to the aquaculture sector resulting in substantial economic losses to the fish farmers. Thus, tolerance to hypoxia is of high economic interest to be genetically improved by breeding programs. Rainbow trout (Oncorhynchus mykiss) is one of the most cultured salmonid species worldwide, with welldeveloped breeding programs. Still, studies of genetic potential to improve hypoxia tolerance in this species are rare. In the present study, 1320 individuals of rainbow trout were used for a genome-wide association study of acute hypoxia tolerance based on imputed high-density genotypes to explore the genetic architecture and related candidate genes affecting hypoxia response. Three significant (Omy31_1, Omy31_2, Omy20) and two putative (Omy15, Omy28) quantitative trait loci (QTLs) were detected, but each of them only explained between 0.2% and 0.8% of the genetic variance of acute hypoxia tolerance. However, heritability was estimated at a moderate value of 0.24-0.28, that suggests a solid potential to improve hypoxia tolerance in the studied rainbow trout population by genetic selection. Moreover, it was shown that genomic prediction for hypoxia tolerance would lead to a relative increase of ~11% for genomic selection (GS) accuracy compared to the pedigree-based selection, considering a reference population of 1000 individuals. Finally, fifteen genes (ids, fmr1, arx, lonrf3, commd5, map4k4, smu1, b4galt1, re1, abca1, noa1, igfbp7, noxo1, bcl2a, mylk3) were proposed as potential functional candidates involved in hypoxia tolerance. Taking all proposed candidate genes (6 out of 15 genes) and high linkage disequilibrium (r 2) values within the main QTL (Omy31_1), we may hypothesize that the complex response to acute hypoxia in rainbow trout, i.e., the interplay between behavioural, morphological, and physiological responses, is primarily encoded by a supergene. However, further functional validation of their effects may help to specify the biological mechanisms triggering a response to acute hypoxia in rainbow trout.

Selective breeding is a promising solution to reduce fish farms vulnerability to heat peaks.Objectives of this study were to give a new insight on the genetic architecture of resistance toacute hyperthermia stress in rainbow trout. At 275 days post-fertilization, 1,384 fish werephenotyped for acute hyperthermia resistance and body weight. Challenged fish weregenotyped for 57K SNP and their genotypes were imputed at high-density thanks to theirparents being genotyped on a 665K SNP array. Heritability estimate of resistance to acutehyperthermia was 0.32 ± 0.04. This trait was genetically negatively correlated with body weight(-0.58 ± 0.17). The genome-wide association study revealed that resistance to acutehyperthermia is highly polygenic as altogether the 5 detected QTLs explained less than 5% ofthe genetic variance. The main QTL region explained 3% of the genetic variance and containedtwo candidate genes previously described to be associated with temperature resistance.

International audience; One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1–4% of the genetic variance. Within these regions, we identified several genes (htr1, gnpat, ephx1, bcmo1, and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits.

Additional file 2. Estimates of phenotypic correlations between proportions of fatty acids and production or quality traits.

International audience

Additional file 4. Summary statistics for 11 production and quality traits in rainbow trout.

Selection for production traits in closed and small broodstock populations of rainbow trout over the last 30 years have induced significant levels of inbreeding [1]. Inbreeding can be derived from the identification of homozygous genomic segments, named ROH for run of homozygozity [2]. The size of the ROHs makes it possible to estimate how long there has been inbreeding in the population. From this ROH property, the aim of the study was to assess the age of inbreeding events affecting rainbow trout size and reproduction traits in a French selected line. We analyzed the performance of 1,366 females under mixed linear animal model including the fixed effects of the two study cohorts and the spawn week within cohort. A first model fitted the pangenomic inbreeding coefficient as a unique covariate and a second model fitted altogether the chromosomal inbreeding coefficients as 30 covariates explaining performance. For both models, we consider the cumulated effects of inbreeding over all generations (F all) or only the effects of recent inbreeding events (F rec) through ROH sizes longer than 10Mb, which correspond to inbreeding approximatively occurring the 3 last generations. The study traits were the female post-spawning weight (PW), the spawning date (SD), the spawn weight (SW), and the egg average weight (EW). At the all genome scale, we observed significant effects of inbreeding only for SD and EW, with +10% in F level leading to performance variations of +12.3% and-3.8%, respectively. While both recent and ancient inbreeding effects were significant for SD, only recent inbreeding events affected EW. At the chromosome scale, both recent and ancient events of inbreeding affected all the study traits with negative but also positive effects (Fig1). As largely described in the literature, the main observed effects for all traits were negative impacts of recent inbreeding. However some positive effects of recent inbreeding (see Omy17 for SW) or old inbreeding (see Omy28 for PW) were also observed (Fig1). A unique case of inbreeding depression due to ancient inbreeding events (see Omy28 for SW) was detected (Fig1). To conclude, for all traits, both recent and ancient inbreeding events affect female size and reproduction traits in rainbow trout. Despite a global trend towards inbreeding depression due to recent inbreeding events, positive impacts of local inbreeding are also commonly encountered for all traits. These results shed light on the genetic architecture of inbreeding depression for female size and reproduction traits and its evolution along the genome and over generations. Fig1. Effect of a +10% increase in inbreeding coefficients for Omy28 and Omy17 on SW and PW performance. Material was provided by the breeding company Viviers de Sarrance and funded by the European Maritime and Fisheries Fund and FranceAgrimer (SG-Truite project, n° RFEA47 0016 FA 1000016).

Additional file 1. Fatty acid composition of the two final diets (% total FAs).

GWAS reveals several genomic regions governing spontaneous XX-maleness in rainbow trout. Aquaculture Europe 2019

National audience; Estimation de la diversité génétique entre et intra lignées françaises de truite arc en ciel. 6. Journées de la Recherche Filière Piscicole

International audience

Additional file 1. Table S1: Number of SNPs per minimum allele frequency (MAF) category in each line. Table S2: Average r2 ± SD between SNPs according to different distances. Table S3: Sensitivity analysis of ROH estimates to MAF and maximal distance gap between two SNPs and derived inbreeding coefficient. Table S4: Estimates of effective population size (standard errors in brackets) for each line with or without Omy5 and Omy20.

Background: Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a signifcant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fxation index (FST), linkage disequilibrium (LD), efective population size (Ne) and inbreeding coefcient derived from runs of homozygosity (ROH). Results: Our results showed a moderate level of genetic diferentiation between selected lines (FST ranging from 0.08 to 0.15). LD declined rapidly over the frst 100 kb, but then remained quite high at long distances, leading to low estimates of Ne in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to diferences in local rates of recombination or due to key genes that tended to have fxed favorable alleles for domestication or production. Conclusions: This is the frst report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder efects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efcient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fsh genome.

Additional file 2. Figure S1: Line mean linkage disequilibrium at 50Â kb for each chromosome. Figure S2: Proportion of individuals per line with a SNP in a ROH along the genome. Figure S3: Proportion of individuals per line with a SNP in a ROH along chromosome 10.

Health management is a major issue for sustainable aquaculture. Flavobacterium psychrophilum (Fp), the causative agent of bacterial cold water disease (BCWD) is responsible of important economic losses in rainbow trout farming. Resistance to the disease is heritable and several Quantitative Trait Loci (QTL) with moderate effects have been detected, indicating that selective breeding may be efficient. However, in most studies, the resistance to Fp was assessed after experimental infectious challenges using injection as route of infection, which is not representative of the natural infection as it bypasses external barriers (e.g. skin, mucus) likely to play a protective role. In this study, we aimed at describing the genetic architecture of the resistance after a field outbreak in a French trout population, using a medium-throughput genotyping array (Affymetrix OD Axiom 57K SNP array). A natural outbreak of BCWD occurred in a farm from Les Aquaculteurs Bretons, a French breeding company in a cohort of 2,000 fish derived from 10 factorial mating design (69 dams, 97 sires in total). Dead fish were removed daily. At day 95 surviving fish were euthanized. All fish were stored for further genotyping. The presence of Fp in dead fish was checked at different time points until day 60, when mortality reached a plateau (30%) and Fp was no longer detected. Fish that died after day 60 were thus considered as resistant. Resistance was assessed as STATUS, a binary trait (dead/alive-resistant), and as time to death (TTD), the number of days between the onset of the disease and the day fish succumbed to the disease (value of 61 assigned for resistant fish). Using microsatellite genotyping, 1,733 fish were correctly assigned to a single mating pair. Those fish were used to estimate pedigree-based heritability for the two traits. For the genome wide association study, 720 individuals were sampled (290 resistant and 430 dead fish) and genotyped with the 57K SNP array. After genotype quality control, 706 fish genotyped for 30,030 validated SNP could be used. The association analysis was carried out using BLUPF90 software on TTD and STATUS separately. Heritability was 0.33 for TTD and 0.27 for STATUS. We detected seven low-effect and two moderate-effect QTL and several relevant candidate genes involved in the inflammatory immune response were located inside those QTL. Our study confirms the main features of the genetic architecture of resistance to Fp (no major QTL, several QTL with moderate effects) and that implementing genomic selection should improve resistance. Moreover, some QTL were the same as the ones detected previously in other trout populations infected experimentally with different bacterial isolates, confirming that they may drive a core set of resistance mechanisms.

Changes in host-parasite ecological interactions during biological invasion events may affect both the outcome of invasions and the dynamics of exotic and/or endemic infections. We tested these hypotheses, by investigating ongoing house mouse (Mus musculus domesticus) and black rat (Rattus rattus) invasions in Senegal (West Africa). We used a 16S gene rRNA amplicon sequencing approach to study potentially zoonotic bacterial communities in invasive and native rodents sampled along two well-defined independent invasion routes. We found that individual host factors (body mass and sex) were important drivers of these bacterial infections in rodents. We observed that the bacterial communities varied along invasion routes and differed between invasive and native rodents, with native rodents displaying higher overall bacterial diversity than invasive rodents. Differences in prevalence levels for some bacterial Operational Taxonomic Units (OTUs) provided support for ecological processes connecting parasitism and invasion success. Finally, our results indicated that rodent invasions may lead to the introduction of exotic bacterial genera and/or to changes in the prevalence of endemic ones. This study illustrates the difficulty of predicting the relationship between biodiversity and disease risks, and advocate for public health prevention strategies based on global pathogen surveillance followed by accurate characterization of potential zoonotic agents.

International audience