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

Déterminisme génétique et sélection génomique des caractères de reproduction femelle chez la truite arc-en-ciel

Déterminisme génétique et sélection génomique des caractères de reproduction femelle chez la truite arc-en-ciel. 6. Journées de la Recherche Piscicol

Déterminisme génétique et sélection génomique des caractères de reproduction femelle chez la truite arc-en-ciel

Déterminisme génétique et sélection génomique des caractères de reproduction femelle chez la truite arc-en-ciel. 6. Journées de la Recherche Piscicol

Genetic architecture and genomic selection of female reproduction traits in rainbow trout

International audienceBackground: Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, to determine the genetic architecture of these traits by the identification of quantitative trait loci (QTL), and to assess the expected efficiency of a pedigree-based selection (BLUP) or genomic selection for these traits.Results: A pedigreed population of 1343 trout were genotyped for 57,000 SNP markers and phenotyped for seven traits at 2years of age: spawning date, female body weight before and after spawning, the spawn weight and the egg number of the spawn, the egg average weight and average diameter. Genetic parameters were estimated in multi-trait linear animal models. Heritability estimates were moderate, varying from 0.27 to 0.44. The female body weight was not genetically correlated to any of the reproduction traits. Spawn weight showed strong and favourable genetic correlation with the number of eggs in the spawn and individual egg size traits, but the egg number was uncorrelated to the egg size traits. The genome-wide association studies showed that all traits were very polygenic since less than 10% of the genetic variance was explained by the cumulative effects of the QTLs: for any trait, only 2 to 4 QTLs were detected that explained in-between 1 and 3% of the genetic variance. Genomic selection based on a reference population of only one thousand individuals related to candidates would improve the efficiency of BLUP selection from 16 to 37% depending on traits.Conclusions: Our genetic parameter estimates made unlikely the hypothesis that selection for growth could induce any indirect improvement for female reproduction traits. It is thus important to consider direct selection for spawn weight for improving egg production traits in rainbow trout breeding programs. Due to the low proportion of genetic variance explained by the few QTLs detected for each reproduction traits, marker assisted selection cannot be effective. However genomic selection would allow significant gains of accuracy compared to pedigree-based selection

Morphological predictors of slaughter yields using 3D digitizer and their utilization in common carp breeding program

Morphological predictors of slaughter yields using 3D digitizer and their utilization in common carp breeding program. Aquaculture Europe 201

QTLs linked to survival and growth of rainbow trout fed a 100% plant-based diet in rainbow trout since the first meal

eposterQTLs linked to survival and growth of rainbow trout fed a 100% plant-based diet in rainbow trout since the first meal. Aquaculture Europe 201

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Background: Yellow perch, Perca flavescens, is an ecologically and commercially important species native to a large portion of the northern United States and southern Canada. It is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquaculture management practices. Findings: By combining Oxford Nanopore Technologies long-reads, 10X genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). Genome annotation identified 41.7% (366 Mb) of repeated elements and 24,486 genes including 16,579 genes (76.3%) significantly matching with proteins in public databases. We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping test which accurately differentiates XY genetic males (amhr2by+) from XX genetic females (amhr2by−). Conclusions: Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries, and aquaculture research. In addition, the characterization of the amhr2by gene as a candidate sex determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes