Survival of the currently fittest: genetics of rainbow trout survival across time and space

Selection among critically endangered landlocked salmon (Salmo salar m. sebago) families in survival and growth traits across early life stages and in different environments

Endangered wild fish populations are commonly supported by hatchery propagation. However, hatchery-reared fish experience very different selective pressures compared to their wild counterparts, potentially causing genotype-by-environment interactions (G × E) in essential fitness traits. We experimentally studied early selection in a critically endangered landlocked Atlantic salmon population, first from fertilization to the swim-up stage in a common hatchery setting, and thereafter until the age of 5 months in two contrasting rearing environments. Swim-up progeny were moved either to standard indoor hatchery tanks involving conventional husbandry or to seminatural outdoor channels providing only natural food. After the first summer, sampled survivors were assigned to their families by genotyping. Early survival until the swim-up stage was mostly determined by maternal effects, but also involved significant variation due to sires and full-sib families (potential genetic effects). High on-growing survival in hatchery tanks (88.7%) maintained a more even distribution among families (relative share 1.5%-4.2%) than the seminatural environment (0.0%-5.4%). This heterogeneity was mostly maternal, whereas no independent paternal effect occurred. Heritability estimates were high for body size traits in both environments (0.62-0.69). Genetic correlations between the environments were significantly positive for body size traits (0.67-0.69), and high body condition in hatchery was also genetically linked to rapid growth in the seminatural environment (0.54). Additive and phenotypic growth variation increased in the seminatural environment, but scaling effects probably played a less significant role for G × E, compared to re-ranking of genotypes. Our results suggest that not only maternal effects, but also genetic effects, direct selection according to the environmental conditions experienced. Consistently high genetic variation in growth implies that, despite its low overall genetic diversity and long history in captive rearing (>50 years), this landlocked Atlantic salmon population still possesses adaptive potential for response to change from hatchery rearing back to more natural conditions.

Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus

Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver-operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.

Genetic correlations between challenge tested susceptibility to bacillary necrosis, caused by Edwardsiella ictaluri, and growth performance tested survival and harvest body weight in Mekong striped catfish (Pangasianodon hypophthalmus)

The aim was to carry out a joint genetic analysis of survival and harvest body weight, recorded in a growth performance test in Mekong striped catfish (Pangasianodon hypophthalmus), and susceptibility to bacillary necrosis (caused by Edwardsiella ictaluri), recorded in challenge tests. Data were from two challenge tested year-classes (~6,000 fish in both) that both had growth test data available for survival and body weight (~13,000 fish each year). Data were analysed with a linear tri-variate sire-dam model without the common environmental effect because otherwise genetic correlations were estimated with large standard errors. Susceptibility to bacillary necrosis was found weakly genetically correlated to both growth and survival in the growth test, while growth was found with moderate favourable genetic correlation to growth survival. To defend continued challenge testing of striped catfish in Vietnam, a strong genetic relationship needs to be established between bacillary necrosis and survival under a natural disease outbreak. This requires another field test (in addition to the growth test) with siblings, without antibiotic treatment and the cause of death continuously monitored. Meanwhile, the routine challenge testing with the aim to indirectly improve field survival through selection should continue.

Breeding for improved resistance to Edwardsiella ictaluri in striped catfish (Pangasianodon hypophthalmus): Quantitative genetic parameters

Bacillary necrosis of Pangasius (BNP), caused by Edwardsiella ictaluri, is one of the most devastating diseases in striped catfish farming. To date, quantitative genetic inheritance of BNP resistance is not known in striped catfish Pangasianodon hypophthalmus. The main aim of this study was to estimate genetic parameters for BNP resistance in a breeding population of striped catfish undergoing four generations of selection for high growth. Specifically, the study examined whether BNP resistance is heritable to enable family selection and whether genetic improvement for enhanced BNP resistance may have detrimental effects on growth and survival rate. To test these hypotheses, 720 full- and half-sib families were challenged with E. ictaluri pathogen using injection and cohabitation methods over four years, from 2010 to 2012 and 2015. In total, the data included 398,234 animals in the pedigree, from which 18,849 animals had disease challenge test records and 39,103 siblings had growth performance. Both univariate and bivariate sire-dam linear and threshold mixed models were used to estimate (co)variance components for BNP resistance, survivals and growth traits. The estimates of heritability for the BNP resistance recorded as death or survival were low regardless of models used (0.10-0.16), whereas survival time (days post-challenge test) showed moderate heritability (0.35). The survival rate during hapa rearing had medium heritability (0.33-0.52). The genetic correlations of BNP resistance with body weight and survival were all positive (0.03-0.53), suggesting that selection of increased BNP resistance may have positive impacts on growth and survival traits, and these traits could be easily improved simultaneously in the selective breeding programme for striped catfish.

Can metamorphosis survival during larval development in spiny lobster Sagmariasus verreauxi be improved through quantitative genetic inheritance?

Background

One of the major impediments to spiny lobster aquaculture is the high cost of hatchery production due to the long and complex larval cycle and poor survival during the many moult stages, especially at metamorphosis. We examined if the key trait of larval survival can be improved through selection by determining if genetic variance exists for this trait. Specifically, we report, for the first time, genetic parameters (heritability and correlations) for early survival rates recorded at five larval phases; early-phyllosoma stages (instars 1–6; S1), mid-phyllosoma stages (instars; 7–12; S2), late-phyllosoma stages (instars 13–17; S3), metamorphosis (S4) and puerulus stage (S5) in hatchery-reared spiny lobster Sagmariasus verreauxi.

Results

The data were collected from a total of 235,060 larvae produced from 18 sires and 30 dams over nine years (2006 to 2014). Parentage of the offspring and full-sib families was verified using ten microsatellite markers. Analysis of variance components showed that the estimates of heritability for all the five phases of larval survival obtained from linear mixed model were generally similar to those obtained from threshold logistic generalised models (0.03–0.47 vs. 0.01–0.50). The heritability estimates for survival traits recorded in the early larval phases (S1 and S2) were higher than those estimated in later phases (S3, S4 and S5). The existence of the additive genetic component in larval survival traits indicate that they could be improved through selection. Both phenotypic and genetic correlations among the five survival measures studied were moderate to high and positive. The genetic associations between successive rearing periods were stronger than those that are further apart.

Conclusions

Our estimates of heritability and genetic correlations reported here in a spiny lobster species indicate that improvement in the early survival especially during metamorphosis can be achieved through genetic selection in this highly economic value species.

Electronic supplementary material

The online version of this article (10.1186/s12863-018-0621-z) contains supplementary material, which is available to authorized users.

Genetically influenced resistance to stress and disease in salmonids in relation to present-day breeding practice - a short review

While intensive fish production has many advantages, it also has a number of drawbacks as regards disease and stress. To date, there has been no conclusive review of disease resistance at Czech fish farms. The aim of the study was to describe briefly the existing salmonid breeding practice in the Czech Republic and to point out the trends and new possibilities gaining ground around Europe. However, the present situation in the Czech stocks is not rare at all and therefore it is used here as a model example representing numerous breeding practices in Europe. Stress and disease resistance in fish is polygenic and quantitative, making selection for such traits difficult. In recent years, however, fish breeding methods have developed rapidly, with the use of genetic analysis tools, for example, now allowing much greater selection accuracy. Gradual progress in understanding the importance of individual genetic markers offers many new options that can be utilised in breeding practice. New selection methods, such as quantitative trait loci (QTLs) and genomic selection, are increasingly employed in European aquaculture. Next generation sequencing techniques now help in the finding of new and promising QTLs that can be used in assisted selection. This review maps the current progress in improving salmonid resistance to stress and disease in aquaculture and at the same time provides the breeders with a short overview of the latest tools of genetically controlled breeding and of the newest products available at the European market.

Cost-benefit analysis of aquaculture breeding programs

Background

Profitability of breeding programs is a key determinant in the adoption of selective breeding, and can be evaluated using cost-benefit analysis. There are many options to design breeding programs, with or without a multiplier tier. Our objectives were to evaluate different breeding program designs for aquaculture and to optimize the number of selection candidates for these programs.

Methods

The baseline was based on an existing breeding program for gilthead seabream, where improvement of the nucleus had priority over improvement of the multiplier tier, which was partly replaced once every 3 years. Alternative breeding programs considered were annual multiplier tier replacement, annual multiplier tier replacement with priority on improvement of the multiplier tier, and a program without a multiplier tier. Cost-benefit analyses were performed to compare breeding programs. The outcomes were used to describe relationships between profitability and the number of selection candidates, length of the time horizon, and production output, and to estimate the optimum numbers of selection candidates.

Results

The baseline breeding program was profitable after 5 years and reached a net present value of 2.9 million euro in year 10. All alternative programs were more profitable up to year 17. The program without a multiplier tier was the most profitable one up to year 22, followed by the program with annual multiplier tier replacement and nucleus priority. The optimum number of selection candidates increased with the length of the time horizon and production output.

Conclusions

The baseline breeding program was profitable after 5 years. For a short time horizon, putting priority on improvement of the multiplier tier over the nucleus is more profitable than putting priority on nucleus improvement, and vice versa for a long time horizon. Use of a multiplier tier increases the delay between costs made for selection and resulting benefits. Thus, avoiding the use of a multiplier tier will increase the profitability of the breeding program in the short term. The optimum number of selection candidates increases with the length of the time horizon and production output. Using too many selection candidates relative to the optimum leads to less reduction in profitability than using too few selection candidates.

The genetics of overwintering performance in two-year old common carp and its relation to performance until market size

Using farmed common carp, we investigated the genetic background of the second year overwintering performance and its relation to the performance during the third growing season and at market size. The experimental stock was established by partial factorial design with a series of 4 factorial matings of 5 dams and 10 sires each. The families were reared communally and pedigree was re-constructed with 93.6% success using 12 microsatellites on 2008 offspring. Three successive recordings (second autumn, third spring, and third autumn—market size) covering two periods (second overwintering, third growing season) were included. Body weight, Fulton’s condition factor and percent muscle fat content were recorded at all times and headless carcass yield and fillet yield were recorded at market size. Specific growth rate, absolute and relative fat change and overall survival were calculated for each period. Heritability estimates were significantly different from zero and almost all traits were moderately to highly heritable (h² = 0.36–1.00), except survival in both periods and fat change (both patterns) during overwintering (h² = 0.12–0.15). Genetic and phenotypic correlations imply that selection against weight loss and fat loss during overwintering is expected to lead to a better winter survival, together with a positive effect on growth in the third growing season. Interestingly, higher muscle fat content was genetically correlated to lower survival in the following period (r_g = -0.59; -0.53, respectively for winter and the third summer). On the other hand, higher muscle fat was also genetically linked to better slaughter yields. Moreover, selection for higher condition factor would lead to better performance during winter, growing season and at market size.

Genetic analysis of a red tilapia (Oreochromis spp.) population undergoing three generations of selection for increased body weight at harvest

Quantitative genetic analysis was performed on 10,919 data records collected over three generations from the selection programme for increased body weight at harvest in red tilapia (Oreochromis spp.). They were offspring of 224 sires and 226 dams (50 sires and 60 dams per generation, on average). Linear mixed models were used to analyse body traits (weight, length, width and depth), whereas threshold generalised models assuming probit distribution were employed to examine genetic inheritance of survival rate, sexual maturity and body colour. The estimates of heritability for traits studied (body weight, standard length, body width, body depth, body colour, early sexual maturation and survival) across statistical models were moderate to high (0.13-0.45). Genetic correlations among body traits and survival were high and positive (0.68-0.96). Body length and width exhibited negative genetic correlations with body colour (- 0.47 to - 0.25). Sexual maturity was genetically correlated positively with measurements of body traits (weight and length). Direct and correlated genetic responses to selection were measured as estimated breeding values in each generation and expressed in genetic standard deviation units (σ_G). The cumulative improvement achieved for harvest body weight was 1.72 σ_G after three generations or 12.5% per generation when the gain was expressed as a percentage of the base population. Selection for improved body weight also resulted in correlated increase in other body traits (length, width and depth) and survival rate (ranging from 0.25 to 0.81 genetic standard deviation units). Avoidance of black spot parent matings also improved the overall red colour of the selected population. It is concluded that the selective breeding programme for red tilapia has succeeded in achieving significant genetic improvement for a range of commercially important traits in this species, and the large genetic variation in body colour and survival also shows that there are prospects for future improvement of these traits in this population of red tilapia.

Derivation of economic values for production traits in aquaculture species

BACKGROUND

In breeding programs for aquaculture species, breeding goal traits are often weighted based on the desired gains but economic gain would be higher if economic values were used instead. The objectives of this study were: (1) to develop a bio-economic model to derive economic values for aquaculture species, (2) to apply the model to determine the economic importance and economic values of traits in a case-study on gilthead seabream, and (3) to validate the model by comparison with a profit equation for a simplified production system.

METHODS

A bio-economic model was developed to simulate a grow-out farm for gilthead seabream, and then used to simulate gross margin at the current levels of the traits and after one genetic standard deviation change in each trait with the other traits remaining unchanged. Economic values were derived for the traits included in the breeding goal: thermal growth coefficient (TGC), thermal feed intake coefficient (TFC), mortality rate (M), and standard deviation of harvest weight ([Formula: see text]). For a simplified production system, improvement in TGC was assumed to affect harvest weight instead of growing period. Using the bio-economic model and a profit equation, economic values were derived for harvest weight, cumulative feed intake at harvest, and overall survival.

RESULTS

Changes in gross margin showed that the order of economic importance of the traits was: TGC, TFC, M, and [Formula: see text]. Economic values in € (kg production)^-1 (trait unit)^-1 were: 0.40 for TGC, -0.45 for TFC, -7.7 for M, and -0.0011 to -0.0010 for [Formula: see text]. For the simplified production system, similar economic values were obtained with the bio-economic model and the profit equation. The advantage of the profit equation is its simplicity, while that of the bio-economic model is that it can be applied to any aquaculture species, because it can include any limiting factor and/or environmental condition that affects production.

CONCLUSIONS

We confirmed the validity of the bio-economic model. TGC is the most important trait to improve, followed by TFC and M, and the effect of [Formula: see text] on gross margin is small.

Very low levels of direct additive genetic variance in fitness and fitness components in a red squirrel population

A trait must genetically correlate with fitness in order to evolve in response to natural selection, but theory suggests that strong directional selection should erode additive genetic variance in fitness and limit future evolutionary potential. Balancing selection has been proposed as a mechanism that could maintain genetic variance if fitness components trade off with one another and has been invoked to account for empirical observations of higher levels of additive genetic variance in fitness components than would be expected from mutation–selection balance. Here, we used a long-term study of an individually marked population of North American red squirrels (Tamiasciurus hudsonicus) to look for evidence of (1) additive genetic variance in lifetime reproductive success and (2) fitness trade-offs between fitness components, such as male and female fitness or fitness in high- and low-resource environments. “Animal model” analyses of a multigenerational pedigree revealed modest maternal effects on fitness, but very low levels of additive genetic variance in lifetime reproductive success overall as well as fitness measures within each sex and environment. It therefore appears that there are very low levels of direct genetic variance in fitness and fitness components in red squirrels to facilitate contemporary adaptation in this population.

Merino ewes can be bred for body weight change to be more tolerant to uncertain feed supply

Sheep in Australia experience periods with different feed supply causing them to gain and lose BW during the year. It is more efficient if ewes lose less BW during periods of poor nutrition and gain more BW during periods of good nutrition. We investigated whether BW loss during periods of poor nutrition and BW gain during periods of good nutrition are genetically different traits. We used BW measurements from 2,336 adult Merino ewes managed over 5 yr in a Mediterranean climate in Katanning, Australia. Body weight loss is the difference between 2 BW measured 42 d apart during mating, a period of poor nutrition. Body weight gain is the difference between 2 BW measured 131 d apart during a period of good nutrition between prelambing and weaning. We estimated variance compnents of BW change using 3 methods: 1) as a trait calculated by subtracting the first BW from the second, 2) multivariate analysis of BW traits, and 3) random regression analysis of BW. The h(2) and genetic correlations (rg) estimated using the multivariate analysis of BW and the BW change trait were very similar whereas the random regression analysis estimated lower heritabilities and more extreme negative genetic correlations between BW loss and gain. The multivariate model fitted the data better than random regression based on Akaike and Bayesian information criterion so we considered the results of the multivariate model to be more reliable. The heritability of BW loss (h(2) = 0.05-0.16) was smaller than that of BW gain (h(2) = 0.14-0.37). Body weight loss and gain can be bred for independently at 2 and 4 yr of age (rg = 0.03 and -0.04) whereas at 3 yr of age ewes that genetically lost more BW gained more BW (rg = -0.41). Body weight loss is genetically not the same trait at different ages (rg range 0.13-0.39). Body weight gain at age 3 yr is genetically the same trait at age 4 yr (rg = 0.99) but is different between age 2 yr and the older ages (rg = 0.53 and 0.51). These results suggest that as the ewes reach their mature BW, BW gain at different ages becomes the same trait. This does not apply to BW loss. We conclude that BW change could be included in breeding programs to breed adult Merino ewes that are more tolerant to variation in feed supply.

The genetic analysis of tolerance to infections: a review

Tolerance to infections is defined as the ability of a host to limit the impact of a given pathogen burden on host performance. Uncoupling resistance and tolerance is a challenge, and there is a need to be able to separate them using specific trait recording or statistical methods. We present three statistical methods that can be used to investigate genetics of tolerance-related traits. Firstly, using random regressions, tolerance can be analyzed as a reaction norm slope in which host performance (y-axis) is regressed against an increasing pathogen burden (x-axis). Genetic variance in tolerance slopes is the genetic variance for tolerance. Variation in tolerance can induce genotype re-ranking and changes in genetic and phenotypic variation in host performance along the pathogen burden trajectory, contributing to environment-dependent genetic responses to selection. Such genotype-by-environment interactions can be quantified by combining random regressions and covariance functions. To apply random regressions, pathogen burden of individuals needs to be recorded. Secondly, when pathogen burden is not recorded, the cure model for time-until-death data allows separating two traits, susceptibility and endurance. Susceptibility is whether or not an individual was susceptible to an infection, whereas endurance denotes how long time it took until the infection killed a susceptible animal (influenced by tolerance). Thirdly, the normal mixture model can be used to classify continuously distributed host performance, such as growth rate, into different sub-classes (e.g., non-infected and infected), which allows estimation of host performance reduction specific to infected individuals. Moreover, genetics of host performance can be analyzed separately in healthy and affected animals, even in the absence of pathogen burden and survival data. These methods provide novel tools to increase our understanding on the impact of parasites, pathogens, and production diseases on host traits.

Untangling the positive genetic correlation between rainbow trout growth and survival

Explanations for positive and negative genetic correlations between growth and fitness traits are essential for life-history theory and selective breeding. Here, we test whether growth and survival display genetic trade-off. Furthermore, we assess the potential of third-party traits to explain observed genetic associations. First, we estimated genetic correlations of growth and survival of rainbow trout. We then explored whether these associations are explained by genetic correlations with health, body composition and maturity traits. Analysis included 14 traits across life stages and environments. Data were recorded from 249 166 individuals belonging to 10 year classes of a pedigreed population. The results revealed that rapid growth during grow-out was genetically associated with enhanced survival (mean r_G = 0.17). This resulted because genotypes with less nematode caused cataract grew faster and were more likely to survive. Fingerling survival was not genetically related to weight or to grow-out survival. Instead, rapid fingerling growth made fish prone to deformations (r_G = 0.18). Evolutionary genetics provides a theoretical framework to study variation in genetic correlations. This study demonstrates that genetic correlation patterns of growth and survival can be explained by a set of key explanatory traits recorded at different life stages and that these traits can be simultaneously improved by selective breeding.

Genetics of microenvironmental sensitivity of body weight in rainbow trout (Oncorhynchus mykiss) selected for improved growth

Microenvironmental sensitivity of a genotype refers to the ability to buffer against non-specific environmental factors, and it can be quantified by the amount of residual variation in a trait expressed by the genotype's offspring within a (macro)environment. Due to the high degree of polymorphism in behavioral, growth and life-history traits, both farmed and wild salmonids are highly susceptible to microenvironmental variation, yet the heritable basis of this characteristic remains unknown. We estimated the genetic (co)variance of body weight and its residual variation in 2-year-old rainbow trout (Oncorhynchus mykiss) using a multigenerational data of 45,900 individuals from the Finnish national breeding programme. We also tested whether or not microenvironmental sensitivity has been changed as a correlated genetic response when genetic improvement for growth has been practiced over five generations. The animal model analysis revealed the presence of genetic heterogeneity both in body weight and its residual variation. Heritability of residual variation was remarkably lower (0.02) than that for body weight (0.35). However, genetic coefficient of variation was notable in both body weight (14%) and its residual variation (37%), suggesting a substantial potential for selection responses in both traits. Furthermore, a significant negative genetic correlation (-0.16) was found between body weight and its residual variation, i.e., rapidly growing genotypes are also more tolerant to perturbations in microenvironment. The genetic trends showed that fish growth was successfully increased by selective breeding (an average of 6% per generation), whereas no genetic change occurred in residual variation during the same period. The results imply that genetic improvement for body weight does not cause a concomitant increase in microenvironmental sensitivity. For commercial production, however, there may be high potential to simultaneously improve weight gain and increase its uniformity if both criteria are included in a selection index.

Genetics of ascites resistance and tolerance in chicken: a random regression approach

Resistance and tolerance are two complementary mechanisms to reduce the detrimental effects of parasites, pathogens, and production diseases on host performance. Using body weight and ascites data on domesticated chicken Gallus gallus domesticus, we demonstrate the use of random regression animal model and covariance functions to estimate genetic parameters for ascites resistance and tolerance and illustrate the way individual variation in resistance and tolerance induce both genotype re-ranking and changes in variation of host performance along increasing ascites severity. Tolerance to ascites displayed significant genetic variance, with the estimated breeding values of tolerance slope ranging from strongly negative (very sensitive genotype) to weakly negative (less sensitive). Resistance to ascites had heritability of 0.34. Both traits are hence expected to respond to selection. The two complementary defense strategies, tolerance and resistance, were genetically independent. Ascites induced changes to the correlations between ascites resistance and body weight, with the genetic correlations being weak when birds were ascites-free but moderately negative when both healthy and affected birds were present. This likely results because ascites reduces growth, and thus high ascites incidence is genetically related to low adult body weight. Although ascites induced elevated phenotypic and genetic variances in body weight of affected birds, heritability displayed negligible changes across healthy and affected birds. Ascites induced moderate genotype re-ranking in body weight, with the genetic correlation of healthy birds with mildly affected birds being unity but with severely affected birds 0.45. This study demonstrates a novel approach for exploring genetics of defense traits and their impact on genotype-by-environment interactions.

Defining desired genetic gains for rainbow trout breeding objective using analytic hierarchy process

Distributing animals from a single breeding program to a global market may not satisfy all producers, as they may differ in market objectives and farming environments. Analytic hierarchy process (AHP) is used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The aim of this study was to use an AHP-WGP based approach to derive desired genetic gains for rainbow trout breeding and to study whether breeding trait preferences vary depending on commercial products and farming environments. Two questionnaires were sent out. Questionnaire-A (Q-A) was distributed to 178 farmers from 5 continents and used to collect information on commercial products and farming environments. In this questionnaire, farmers were asked to rank the 6 most important traits for genetic improvement from a list of 13 traits. Questionnaire B (Q-B) was sent to all farmers who responded to Q-A (53 in total). For Q-B, preferences of the 6 traits were obtained using pairwise comparison. Preference intensity was given to quantify (in % of a trait mean; G%) the degree to which 1 trait is preferred over the other. Individual preferences, social preferences, and consensus preferences (Con-P) were estimated using AHP and WGP. Desired gains were constructed by multiplying Con-P by G%. The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (FIL%), and late maturation (LMat). Ranking of traits based on average Con-P values were Surv (0.271), FCR (0.246), TGC (0.246), LMat (0.090), FIL% (0.081), and CF (0.067). Corresponding desired genetic gains (in % of trait mean) were 1.63, 1.87, 1.67, 1.29, 0.06, and 0.33%, respectively. The results from Con-P values show that trait preferences may vary for different types of commercial production or farming environments. This study demonstrated that combination of AHP and WGP can be used to derive desired gains for a breeding program and to quantify differences due to variations market demand or production environment.

Genetic analysis of tolerance to infections using random regressions: a simulation study

Tolerance to infections is the ability of a host to limit the impact of a given pathogen burden on host performance. This simulation study demonstrated the merit of using random regressions to estimate unbiased genetic variances for tolerance slope and its genetic correlations with other traits, which could not be obtained using the previously implemented statistical methods. Genetic variance in tolerance was estimated as genetic variance in regression slopes of host performance along an increasing pathogen burden level. Random regressions combined with covariance functions allowed genetic variance for host performance to be estimated at any point along the pathogen burden trajectory, providing a novel means to analyse infection-induced changes in genetic variation of host performance. Yet, the results implied that decreasing family size as well as a non-zero environmental or genetic correlation between initial host performance before infection and pathogen burden led to biased estimates for tolerance genetic variance. In both cases, genetic correlation between tolerance slope and host performance in a pathogen-free environment became artificially negative, implying a genetic trade-off when it did not exist. Moreover, recording a normally distributed pathogen burden as a threshold trait is not a realistic way of obtaining unbiased estimates for tolerance genetic variance. The results show that random regressions are suitable for the genetic analysis of tolerance, given suitable data structure collected either under field or experimental conditions.

Reducing mutation load through sexual selection on males

Mutation load is a key parameter in evolutionary theories, but relatively little empirical information exists on the mutation load of populations, or the elimination of this load through selection. We manipulated the opportunity for sexual selection within a mutation accumulation divergence experiment to determine how sexual selection on males affected the accumulation of mutations contributing to sexual and nonsexual fitness. Sexual selection prevented the accumulation of mutations affecting male mating success, the target trait, as well as reducing mutation load on productivity, a nonsexual fitness component. Mutational correlations between mating success and productivity (estimated in the absence of sexual selection) were positive. Sexual selection significantly reduced these fitness component correlations. Male mating success significantly diverged between sexual selection treatments, consistent with the fixation of genetic differences. However, the rank of the treatments was not consistent across assays, indicating that the mutational effects on mating success were conditional on biotic and abiotic context. Our experiment suggests that greater insight into the genetic targets of natural and sexual selection can be gained by focusing on mutational rather than standing genetic variation, and on the behavior of trait variances rather than means.

Quantitative genetic architecture of parasite-induced cataract in rainbow trout, Oncorhynchus mykiss

Parasites impose costs on their hosts. The capability to fight against them is of great advantage, but may also be traded off with other traits. Although often observed at the phenotypic level, our knowledge of the extent to which such trade-offs are genetically determined is relatively poor. We tested this possibility with a farmed rainbow trout population suffering from natural Diplostomum spp. infections that cause cataracts in fish. We estimated the heritability of cataract severity and examined phenotypic and genetic correlations between cataract and a set of performance traits measured three times during a 3-year rearing period. A cataract score was used as an indicator of the host's capability to resist and/or tolerate the parasite. Our results showed moderate heritability for the cataract. Nevertheless, we found no evidence for a genetic or phenotypic trade-off between parasite resistance/tolerance and the measured performance traits. Initial body weight was not correlated with the cataract score. Phenotypic and genetic correlations of cataract severity with body mass and condition measured in the second and third year were strongly negative, indicating reduced growth and condition in fish with a high cataract score. The reduced body size and condition in cataract-bearing fish were probably reflected in the phenotypic association between a high cataract score and delayed maturity age in females. Put together, our study did not provide evidence of genetic or phenotypic trade-offs between Diplostomum resistance/tolerance and a number of performance traits. Therefore, selection for lessened Diplostomum-caused cataracts is unlikely to have a negative impact on the studied performance traits.

Genetic architecture of rainbow trout survival from egg to adult

Survival from birth to a reproductive adult is a challenge that only robust individuals resistant to a variety of mortality factors will overcome. To assess whether survival traits share genetic architecture throughout the life cycle, we estimated genetic correlations for survival within fingerling stage, and across egg, fingerling and grow-out stages in farmed rainbow trout. Genetic parameters of survival at three life cycle stages were estimated for 249 166 individuals originating from ten year classes of a pedigreed population. Despite being an important fitness component, survival traits harboured significant but modest amount of genetic variation (h2=0.07-0.27). Weak associations between survival during egg-fry and fingerling periods, between early and late fingerling periods (rG=0.30) and generally low genetic correlations between fingerling and grow-out survival (mean rG=0.06) suggested that life-stage specific survival traits are best regarded as separate traits. However, in the sub-set of data with detailed time of death records, positive genetic correlations between early and late fingerling survival (rG=0.89) showed that during certain years the best genotypes in the early period were also among the best in the late period. That survival across fingerling period can be genetically the same, trait was indicated also by only slightly higher heritability (h2=0.15) estimated with the survival analysis of time to death during fingerling period compared to the analysis treating fingerling survival as a binary character (h2=0.11). The results imply that (1) inherited resistance against unknown mortality factors exists, but (2) ranking of genotypes changes across life stages.