A first demonstration of realized selection response for fillet yield in fish, in rainbow trout oncorhynchus mykiss

A first demonstration of realized selection response for fillet yield in fish, in rainbow trout oncorhynchus mykiss. 13. International Symposium for Genetics in Aquaculture (ISGA XIII

Can we identify wild-born salmon from parentage assignment data? A case study in the Garonne-Dordogne rivers salmon restoration programme in France

Parentage assignment with genomic markers provides an opportunity to monitor salmon restocking programs. Most of the time, it is used to study the fate of hatchery-born fish in those programs, as well as the genetic impacts of restocking. In such analyses, only fish that are assigned to their parents are considered. In the Garonne-Dordogne river basin in France, native salmon have disappeared, and supportive breeding is being used to try to reinstate a self-sustained population. It is therefore of primary importance to assess the numbers of wild-born returning salmon, which could appear as wrongly assigned or not assigned, depending on the power of the marker set and on the size of the mating plan. We used the genotypes at nine microsatellites of the 5800 hatchery broodstock which were used from 2008 to 2014, and of 884 upstream migrating fish collected from 2008 to 2016, to assess our ability to identify wild-born salmon. We simulated genotypes of hatchery fish and wild-born fish and assessed how they were identified by the parentage assignment software Accurassign. We showed that 98.7% of the fish assigned within the recorded mating plan could be considered hatchery fish, while 93.3% of the fish in other assignment categories (assigned out of the mating plan, assigned to several parent pairs, not assigned) could be considered wild-born. Using a Bayesian approach, we showed that 31.3% of the 457 upstream migrating fish sampled from 2014 to 2016 were wild-born. This approach is thus efficient to identify wild-born fish in a restoration program. It remains dependent on the quality of the recording of the mating plan, which we showed was rather good (<5% mistakes) in this program. To limit this potential dependence, an increase in the number of markers genotyped (17 instead of 9) is now being implemented

Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

International audienceRainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm population at 10 and 15 months post-hatching. The overall masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) on a subsample of 1139 individuals classified as females, intersex or males using either medium-throughput genotyping (31,811 SNPs) or whole-genome sequencing (WGS, 8.7 million SNPs). The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and the number of SNPs used for the estimation. At the 31K SNPs level, we detected four QTL on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTL detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout

How to genetically increase fillet yield in fish: New insights from simulations based on field data

Fillet yield (i.e. the proportion of edible flesh from a given amount of fish) is a trait of high economic interest for species sold as fillets. Improving it by selective breeding is not an easy task, as it is a ratio trait, which causes mathematical difficulties. It is moreover a specific ratio where numerator (fillet weight) and denominator (body weight) are very strongly correlated (genetic and phenotypic correlations in the range 0.89–0.99). This led some authors to conclude that they have the same genetic and phenotypic basis, precluding selection for improved fillet yield. In this study, we propose to study fillet yield as a component of two traits, fillet weight and waste weight (waste weight = body weight-fillet weight, so the sum of head, bones, fins and viscera weight), which we expect to be less correlated. Using data from 5 batches of fish from 3 species (sea bass, sea bream, rainbow trout), we show that as expected, fillet weight and waste weight are less correlated than fillet weight and body weight (on average, rA = 0.91 and rP = 0.88 vs. rA = 0.987, rP = 0.981). We used stochastic simulation to generate genotypes and phenotypes of fish using those genetic parameters for fillet weight and waste weight. We simulated 10 generations of selection for increased fillet yield using nine selection indices. Five indices had rather similar performances, residual fillet weight (the residual of the regression of fillet weight to body weight), fillet yield, fillet to waste ratio, restricted selection index (a linear index aimed at improving fillet weight while keeping waste weight constant) and linear index (optimized to improve fillet/waste ratio). With these indices, the average selection gain was + 0.66% of fillet yield per generation (range 0.30 to 0.95% using real genetic parameters from 5 fish batches). Selection for the difference between fillet weight and waste weight was 30% less efficient, while selection for increased fillet weight or increased body weight was 55–65% less efficient. Selection against waste weight had a null or even negative impact on fillet yield. Factors favorable to higher selection gains are low initial fillet yield, different heritabilities and CVs of fillet weight and waste weight, low genetic correlation and high phenotypic correlation of fillet weight and waste weight. These results suggest that although fillet weight and body weight are strongly correlated and proportional to each other, moderate selection gains on fillet yield are possible. We consider it would be useful to add waste weight in the parameters recorded in future genetic studies on fillet yield

The Size Advantage Model of Sex Allocation in the Protandrous Sex-Changer Crepidula fornicata: Role of the Mating System, Sperm Storage, and Male Mobility

Sequential hermaphroditism is adaptive when the reproductive value of an individual varies with size or age, and this relationship differs between males and females. In this case, theory shows that the lifetime reproductive output of an individual is increased by changing sex (a hypothesis referred to as the size-advantage model). Sex-linked differences in size-fitness curves can stem from differential costs of reproduction, the mating system, and differences in growth and mortality between sexes. Detailed empirical data is required to disentangle the relative roles of each of these factors within the theory. Quantitative data are also needed to explore the role of sperm storage, which has not yet been considered with sequential hermaphrodites. Using experimental rearing and paternity assignment, we report relationships between size and reproductive success of Crepidula fornicata, a protandrous (male-first) gastropod. Male reproductive success increased with size due to the polygamous system and stacking behavior of the species, but females nonetheless had greater reproductive success than males of the same size, in agreement with the size-advantage theory. Sperm storage appeared to be a critical determinant of success for both sexes, and modeling the effect of sperm storage showed that it could potentially accelerate sex change in protandrous species

Development of genomic predictions for female reproduction traits in rainbow trout (Oncorhynchus mykiss)

International audienc

Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing

Background Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90–100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1–49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values. Results The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28–16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19–24% increase when using genomic information. Conclusion The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs.Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencingpublishedVersio

Data from: The size advantage model of sex allocation in the protandrous sex-changer Crepidula fornicata: role of the mating system, sperm storage, and male mobility

Sequential hermaphroditism is adaptive when the reproductive value of an individual varies with size or age, and this relationship differs between males and females. In this case, theory shows that the lifetime reproductive output of an individual is increased by changing sex (a hypothesis referred to as the size-advantage model). Sex-linked differences in size-fitness curves can stem from differential costs of reproduction, the mating system, and differences in growth and mortality between sexes. Detailed empirical data is required to disentangle the relative roles of each of these factors within the theory. Quantitative data are also needed to explore the role of sperm storage, which has not yet been considered with sequential hermaphrodites. Using experimental rearing and paternity assignment, we report relationships between size and reproductive success of Crepidula fornicata, a protandrous (male-first) gastropod. Male reproductive success increased with size due to the polygamous system and stacking behavior of the species, but females nonetheless had greater reproductive success than males of the same size, in agreement with the size-advantage theory. Sperm storage appeared to be a critical determinant of success for both sexes, and modeling the effect of sperm storage showed that it could potentially accelerate sex change in protandrous species