Roberto Neira

Estimation of genetic parameters from pedigreed populations: lessons from analysis of alevin weight in Coho salmon (Oncorhynchus kisutch)

Abstract The purpose of the study was to assess the impact of various model structures on REML estimates of variance components using data on alevin weight from two replicate populations from the Genetic Improvement Program for Coho salmon (Chile). Data consisted of 130 d alevin weight from a dams-nested-within-sires mating design over two consecutive generations. Relationship information included direct and collateral relatives but parental individuals lacked records. The construction of a range of animal models considered random effects of direct additive genetic, maternal additive genetic and full-sib family effects as well as the covariance of direct and maternal genetic effects. Fixed effects of year (generation) and spawn date of dams within year were considered and also evaluated. The relative effectiveness of various models in describing the data set were assessed using likelihood ratio tests. The results demonstrated the importance of the correct interpretation of effects in the data set, particularly those effects that can influence the resemblance between relatives. The data structure, as well as the animal model applied, markedly influenced the magnitude of variance component estimates. Models based on year as the only fixed effect did not describe the data nearly as effectively as models containing both year and spawn data of dams within year. Simple models based on animal as the only random effect gave upward biased estimates of additive genetic variance. The most appropriate model for the data set was one based on both year and spawn date as fixed effects, and animal and full-sib family as random effects. The results from models combining maternal genetic and full-sib family effects to exploit the full covariance structure of the data showed that there was confounding between these variance component estimates. The most consistent interpretation of this result was that common environmental effects and non-additive genetic effects were more important sources of variability than maternal genetic effects. The study also demonstrated high variability in parameter estimates for replicate populations.

Disease Resistance in Atlantic Salmon (Salmo salar): Coinfection of the Intracellular Bacterial Pathogen Piscirickettsia salmonis and the Sea Louse Caligus rogercresseyi

Background Naturally occurring coinfections of pathogens have been reported in salmonids, but their consequences on disease resistance are unclear. We hypothesized that 1) coinfection of Caligus rogercresseyi reduces the resistance of Atlantic salmon to Piscirickettsia salmonis; and 2) coinfection resistance is a heritable trait that does not correlate with resistance to a single infection. Methodology In total, 1,634 pedigreed Atlantic salmon were exposed to a single infection (SI) of P. salmonis (primary pathogen) or coinfection with C. rogercresseyi (secondary pathogen). Low and high level of coinfection were evaluated (LC = 44 copepodites per fish; HC = 88 copepodites per fish). Survival and quantitative genetic analyses were performed to determine the resistance to the single infection and coinfections. Main Findings C. rogercresseyi significantly increased the mortality in fish infected with P. salmonis (SI mortality = 251/545; LC mortality = 544/544 and HC mortality = 545/545). Heritability estimates for resistance to P. salmonis were similar and of medium magnitude in all treatments (h 2 SI = 0.23±0.07; h 2 LC = 0.17±0.08; h 2 HC = 0.24±0.07). A large and significant genetic correlation with regard to resistance was observed between coinfection treatments (rg LC-HC = 0.99±0.01) but not between the single and coinfection treatments (rg SI-LC = −0.14±0.33; rg SI-HC = 0.32±0.34). Conclusions/Significance C. rogercresseyi, as a secondary pathogen, reduces the resistance of Atlantic salmon to the pathogen P. salmonis. Resistance to coinfection of Piscirickettsia salmonis and Caligus rogercresseyi in Atlantic salmon is a heritable trait. The absence of a genetic correlation between resistance to a single infection and resistance to coinfection indicates that different genes control these processes. Coinfection of different pathogens and resistance to coinfection needs to be considered in future research on salmon farming, selective breeding and conservation.

GAMETOGENESIS AND SEX STEROID PROFILES IN CULTURED COHO SALMON (ONCORHYNCHUS KISUTCH, WALBAUM)

The gametogenesis of a 2-year-old coho salmon broodstock population cultured in a fish farm in southern Chile was studied. Gonadosomatic index (GSI), microscopic gonadal traits, and serum levels of estradiol-17β(E2), testosterone, and 17α,20β-dihydroxy-4-pregnene-3-one (17,20P) in both sexes were recorded beginning 9 months before spawning in bimonthly samplings. Maximum GSI means were reached during May, the month of spawning, with 16.8 ± 4.1% for females and 8.4 ± 0.8% for males, both values within the range described in the literature. GSI in males, however, was triple that of females during January, showing a faster rate of gonadal growth in males in early summer. Gonadal microscopy for both sexes showed stages corresponding to those described by different authors for other salmonids such as rainbow trout. The secondary vitellogenesis period was 4 to 5 months and corresponded with the short vitellogenesis model described in rainbow trout for broodstocks maturing at 2 years of age. The serum profiles of sex steroids in both sexes are consistent with those described in coho salmon and other salmonid species. In females, E2 and 17,20P show opposite profiles, reaching their maximum levels (E2: 45.13 ± 11.3 ng/ml; 17,20P: 24.47 ± 7.34 ng/ml) during vitellogenesis (March) and ovulation (May), respectively. In both sexes, testosterone concentration shows maximum levels in May (females: 61.68 ± 15.75 ng/ml; males: 107.8 ± 11.6 ng/ml), suggesting the physiological importance of this hormone during maturation, either directly or as a substrate for the synthesis of other hormones. In males, the maximum level of 17,20P (22.33 ± 4.5 ng/ml) also occurs in May during total spermiation, which confirms its role in semen production and semen fluid regulation as described in the literature about this hormone in salmonid males. On the basis of the data obtained, a reproductive pattern is proposed for 2-year-old salmon cultured in southern Chile. J. Exp. Zool. 280:429–438, 1998.

The consequences of including non-additive effects on the genetic evaluation of harvest body weight in Coho salmon (Oncorhynchus kisutch)

BackgroundIn this study, we used different animal models to estimate genetic and environmental variance components on harvest weight in two populations of Oncorhynchus kisutch, forming two classes i.e. odd- and even-year spawners.MethodsThe models used were: additive, with and without inbreeding as a covariable (A + F and A respectively); additive plus common environmental due to full-sib families and inbreeding (A + C + F); additive plus parental dominance and inbreeding (A + D + F); and a full model (A + C + D + F). Genetic parameters and breeding values obtained by different models were compared to evaluate the consequences of including non-additive effects on genetic evaluation.ResultsIncluding inbreeding as a covariable did not affect the estimation of genetic parameters, but heritability was reduced when dominance or common environmental effects were included. A high heritability for harvest weight was estimated in both populations (even = 0.46 and odd = 0.50) when simple additive models (A + F and A) were used. Heritabilities decreased to 0.21 (even) and 0.37 (odd) when the full model was used (A + C + D + F). In this full model, the magnitude of the dominance variance was 0.19 (even) and 0.06 (odd), while the magnitude of the common environmental effect was lower than 0.01 in both populations. The correlation between breeding values estimated with different models was very high in all cases (i.e. higher than 0.98). However, ranking of the 30 best males and the 100 best females per generation changed when a high dominance variance was estimated, as was the case in one of the two populations (even).ConclusionsDominance and common environmental variance may be important components of variance in harvest weight in O. kisutch, thus not including them may produce an overestimation of the predicted response; furthermore, genetic evaluation was seen to be partially affected, since the ranking of selected animals changed with the inclusion of non-additive effects in the animal model.

Analysis of Reproductive Performance of Rainbow Trout in a Hatchery in Chile

Abstract Reproductive variables of 986 female rainbow trout (Oncorhynchus mykiss) spawned during 1990 in a hatchery in central Chile were evaluated. Data were recorded on individual females. Fish were spawned over a 9-month period, from March to November. The data indicated the coexistence of different strains of fish with different spawning times. There was a direct relationship between body weight and total fecundity (r = 0.71; P < 0.001, n = 905). The correlation between body weight and egg diameter was low (r = 0.16; P < 0.001; N = 890). The correlation between body weight and relative fecundity was not only low, but slightly negative (r = -0.14; P < 0.001; N = 906). There was a high correlation between fertilization rate and survival of the embryo to the eyed stage (r = 0.75; P < 0.001; N = 903). Embryo survival to the eyed stage appeared to be closely related to incubation temperature, with highest yields obtained during months that average water temperature was 8°C or lower. Egg diameter was not po...

Growth response and expression of muscle growth-related candidate genes in adult zebrafish fed plant and fishmeal protein-based diets.

The main objective of this study was to examine the effects of a plant protein- vs. fishmeal-based diet on growth response in a population of 24 families, as well as expression of growth-related genes in the muscle of adult zebrafish (Danio rerio). Each family was split to create two fish populations with similar genetic backgrounds, and the fish were fed either fishmeal (FM diet) or plant protein (PP diet) as the unique protein source in their diets from 35 to 98 days postfertilization (dpf). To understand the effect of the PP diet on gene expression, individuals from three families, representative of the mean weight in both populations, were selected. To understand the effect of familiar variation on gene expression, the same families were evaluated separately. At 98 dpf, growth-related genes Igf1a, Igf2a, mTOR, Pld1a, Mrf4, Myod, Myogenin, and Myostatin1b were evaluated. In males, Myogenin, Mrf4, and Igf2a showed changes attributable to the PP diet. In females, the effect of the PP diet did not modulate the expression in any of the eight genes studied. The effect of familiar variation on gene expression was observed among families. This study shows that PP diet and family variation have effects on gene expression in fish muscle.

Reproductive Performance of Cultured Female Coho Salmon in Chile

Abstract Data on reproductive traits from 1,229 mature 2-year-old female coho salmon Oncorhynchus kisutch were collected during 2 years at four salmon farms in southern Chile. Spawning periods were similar in 1993 and 1994 (39 and 41 d, respectively). The spawning period of May–June, corresponded to the full reproductive period in the northern hemisphere. The mean weight of mature females (about 4 kg) was almost double the weight reported in the northern hemisphere for 2-year-old maturing females. The pigmented eyed stage was reached approximately 270 accumulated temperature units (ATU days × °C above 0°C after fertilization. Averages for total fecundity (3,802 ± 956 eggs/female, mean ± SD; N = 1, 188), relative fecundity (986 ± 274 eggs/ kg; N = 1,170), and egg diameter (7.11 ± 0.51 mm; N = 1,185) were higher than corresponding values reported for coho salmon hatchery stocks in the northern hemisphere. Survival to the eyedegg stage averaged 74.3 ± 24.2% (N = 1,147). Correlations of female body weight wit...

Applications in the search for genomic selection signatures in fish

Selection signatures are genomic regions harboring DNA sequences functionally involved in the genetic variation of traits subject to selection. Selection signatures have been intensively studied in recent years because of their relevance to evolutionary biology and their potential association with genes that control phenotypes of interest in wild and domestic populations. Selection signature research in fish has been confined to a smaller scale, due in part to the relatively recent domestication of fish species and limited genomic resources such as molecular markers, genetic mapping, DNA sequences, and reference genomes. However, recent genomic technology advances are paving the way for more studies that may contribute to the knowledge of genomic regions underlying phenotypes of biological and productive interest in fish.