Potential of low-density genotype imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss)

Background Flavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease that afects rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of the host resistance. However, genomic selection is expensive partly because of the cost of genotyping large numbers of animals using high-density single nucleotide polymorphism (SNP) arrays. The objective of this study was to assess the efciency of genomic selection for resistance to F. columnare using in silico low-density (LD) panels combined with imputation. After a natural outbreak of columnaris disease, 2874 challenged fsh and 469 fsh from the parental generation (n=81 parents) were genotyped with 27,907 SNPs. The efciency of genomic prediction using LD panels was assessed for 10 panels of diferent densities, which were created in silico using two sampling methods, random and equally spaced. All LD panels were also imputed to the full 28K HD panel using the parental generation as the reference population, and genomic predictions were re-evaluated. The potential of prioritizing SNPs that are associated with resistance to F. columnare was also tested for the six lower-density panels. Results The accuracies of both imputation and genomic predictions were similar with random and equally-spaced sampling of SNPs. Using LD panels of at least 3000 SNPs or lower-density panels (as low as 300 SNPs) combined with imputation resulted in accuracies that were comparable to those of the 28K HD panel and were 11% higher than the pedigree-based predictions. Conclusions Compared to using the commercial HD panel, LD panels combined with imputation may provide a more afordable approach to genomic prediction of breeding values, which supports a more widespread adoption of genomic selection in aquaculture breeding programme

Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions.

BACKGROUND: Bacterial cold-water disease, which is caused by Flavobacterium psychrophilum, is one of the major diseases that affect rainbow trout (Oncorhynchus mykiss) and a primary concern for trout farming. Better knowledge of the genetic basis of resistance to F. psychrophilum would help to implement this trait in selection schemes and to investigate the immune mechanisms associated with resistance. Various studies have revealed that skin and mucus may contribute to response to infection. However, previous quantitative trait loci (QTL) studies were conducted by using injection as the route of infection. Immersion challenge, which is assumed to mimic natural infection by F. psychrophilum more closely, may reveal different defence mechanisms. RESULTS: Two isogenic lines of rainbow trout with contrasting susceptibilities to F. psychrophilum were crossed to produce doubled haploid F2 progeny. Fish were infected with F. psychrophilum either by intramuscular injection (115 individuals) or by immersion (195 individuals), and genotyped for 9654 markers using RAD-sequencing. Fifteen QTL associated with resistance traits were detected and only three QTL were common between the injection and immersion. Using a model that accounted for epistatic interactions between QTL, two main types of interactions were revealed. A "compensation-like" effect was detected between several pairs of QTL for the two modes of infection. An "enhancing-like" interaction effect was detected between four pairs of QTL. Integration of the QTL results with results of a previous transcriptomic analysis of response to F. psychrophilum infection resulted in a list of potential candidate immune genes that belong to four relevant functional categories (bacterial sensors, effectors of antibacterial immunity, inflammatory factors and interferon-stimulated genes). CONCLUSIONS: These results provide new insights into the genetic determinism of rainbow trout resistance to F. psychrophilum and confirm that some QTL with large effects are involved in this trait. For the first time, the role of epistatic interactions between resistance-associated QTL was evidenced. We found that the infection protocol used had an effect on the modulation of defence mechanisms and also identified relevant immune functional candidate genes

Conserved QTL and chromosomal inversion affect resistance to columnaris disease in two rainbow trout (Oncorhyncus mykiss) populations

We present a comparative genetic analysis of the quantitative trait loci underlying resistance to warm water columnaris disease in 2 farmed rainbow trout (Oncorhynchus mykiss) populations. We provide evidence for the conservation of a major quantitative trait loci on Omy03, and the putative role played by a chromosomal rearrangement on Omy05. A total of 3,962 individuals from the 2 populations experienced a natural Flavobacterium columnare outbreak. Data for 25,823 genome-wide SNPs were generated for both cases (fatalities) and controls (survivors). F(ST) and pairwise additive genetic relationships suggest that, despite being currently kept as separate broodstocks, the 2 populations are closely related. Association analyses identified a major quantitative trait loci on chromosome Omy03 and a second smaller quantitative trait loci on Omy05. Quantitative trait loci on Omy03 consistently explained 3–11% of genetic variation in both populations, whereas quantitative trait loci on Omy05 showed different degree of association across populations and sexes. The quantitative trait loci on Omy05 was found within a naturally occurring, 54.84 cM long inversion which is easy to tag due to a strong linkage disequilibrium between the 375 tagging SNPs. The ancestral haplotype on Omy05 was associated with decreased mortality. Genetic correlation between mortality in the 2 populations was estimated at 0.64, implying that the genetic basis of resistance is partly similar in the 2 populations. Our quantitative trait loci validation identifies markers that can be potentially used to complement breeding value evaluations to increase resistance against columnaris disease, and help to mitigate effects of climate change on aquaculture

RAINBOW TROUT RESISTANCE TO Flavobacterium psychrophilum: A GENOME WIDE ASSOCIATION STUDY IN A FRENCH POPULATION AFTER A NATURAL DISEASE OUTBREAK

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

Rainbow trout resistance to bacterial cold water disease: two new quantitative trait loci identified after a natural disease outbreak on a French farm

In rainbow trout farming, Flavobacterium psychrophilum, the causative agent of bacterial cold water disease, is responsible for important economic losses. Resistance to F. psychrophilum is heritable, and several quantitative trait loci (QTL) with moderate effects have been detected, opening up promising perspectives for the genetic improvement of resistance. In most studies however, resistance to F. psychrophilum was assessed in experimental infectious challenges using injection as the infection route, which is not representative of natural infection. Indeed, injection bypasses external barriers, such as mucus and skin, that likely play a protective role against the infection. In this study, we aimed at describing the genetic architecture of the resistance to F. psychrophilum after a natural disease outbreak. In a 2000-fish cohort, reared on a French farm, 720 fish were sampled and genotyped using the medium-throughput Axiom (TM) Trout Genotyping Array. Overall mortality at the end of the outbreak was 25%. Genome-wide association studies were performed under two different models for time to death measured on 706 fish with validated genotypes for 30 060 SNPs. This study confirms the polygenic inheritance of resistance to F. psychrophilum with a few QTL with moderate effects and a large polygenic background, the heritability of the trait being estimated at 0.34. Two new chromosome-wide significant QTL and three suggestive QTL were detected, each of them explaining between 1% and 4% of genetic variance

Genomic estimates of diversity between and within french rainbow trout populations

Genomic estimates of diversity between and within french rainbow trout populations. Aqua 2018 - World Aquaculture Society Meetin

Estimation de la diversité génétique entre et intra lignées françaises de truite arc en ciel

Estimation de la diversité génétique entre et intra lignées françaises de truite arc en ciel. 6. Journées de la Recherche Filière Piscicol