Family growth response to different laboratory culture environments shows genotype–environment interaction in the sea urchin Strongylocentrotus intermedius

This study investigated the genetic variation and genotype–environment interaction (GEI) in the early growth stage among seven full‐sib families of the sea urchin Strongylocentrotus intermedius. From each of the seven families, 180 or 270 sea urchins of the same size were exposed to three laboratory environments (E₁, E₂ and E₃). These environments were commonly used in breeding programs for S. intermedius. After a 102 days trial, test height, test diameter, body weight and the coefficient of variation of body weight were determined. The results revealed significant family effects on most growth traits in all the three environments (except for test diameter in environment E₂), and significant environmental effects on growth in several families (family 1, 5, 6, 7). The study also revealed that the coefficient of variation in body weight varied significantly among the families (P < 0.01) but not among the environments. Highly significant GEI effects were also recorded for all growth traits (P ≤ 0.001), except for the coefficient of variation in body weight (P > 0.05). Variances of GEI accounted for about 0–2.742% of phenotypic variances for the investigated traits. Significant GEI caused a certain degree family ranking inversions for the growth traits. The present study provides evidence for the existence of GEI in the family selection of sea urchin S. intermedius. More attention should be paid to the GEI to obtain satisfactory genetic gain in S. intermedius.     

Experimental evaluation of mass selection to improve red body colour in Fijian hybrid tilapia (Oreochromis niloticus × Oreochromis mossambicus)

Mass selection was trialed on Fijian hybrid tilapia (Oreochromis niloticus × Oreochromis mossambicus) to reduce the amount of black spots on otherwise red phenotypes. The responses of two selection intensities (low‐selection line, top 50% – L) and (high‐selection line, top 30% – H) were compared with that of a control line (no selection – C) across three generations. The relative growth performance of treatments (C, L and H) was examined in parallel in each generation to assess whether mass selection had a correlated negative effect on growth performance. The results show clearly that red phenotype can be improved significantly by applying mass selection, without affecting growth performance. We propose that black spots on an otherwise red phenotype could represent the allelic products of a second genetic locus influencing skin colour, which can be expressed in red individuals (genotype Rr) but which may be masked in black individuals (genotype rr).     

Estimates of heritabilities and genetic correlations for growth and gonad traits in the sea urchin Strongylocentrotus intermedius

The present study is the first estimate for the sea urchin, Strongylocentrotus intermedius, of genetic parameters for growth and gonad traits during the entire reproductive period. 2165–5764 sea urchins were sampled from 74 to 120 families at six different growth stages. Six hundred individuals were sampled from 20 randomly chosen families at harvest. Coefficients of variation for most growth and gonad traits were high (18.08–78.66%) suggesting a good variation foundation for breeding. Point estimate for heritabilities based on the sire components of variance were moderate to high for test height (0.24–0.39), test diameter (0.21–0.48) and body weight (0.16–0.49). Heritabilities of gonad wet weight, gonad index and gonad moisture at harvest were 0.17, 0.41 and 0.50 respectively (moderate or high). Gonad colour parameters, L^* (lightness) and a^* (redness) have a heritability of 0, while b^* (yellowness) and colour difference ΔE₁ and ΔE₂ have very similar heritabilities of 0.2, 0.18 and 0.21 respectively. Heritabilities of β‐carotene concentration and content were 0.89 and 0.44 respectively. The genetic correlations between the two measured traits ranged from ?0.984 to 0.999. Gonad wet weight, L^*, b^*, β‐carotene concentration and β‐carotene content had significant positive genetic correlations with all the growth traits. However, gonad index, gonad moisture and colour differences ΔE₁ and ΔE₂ had significant negative genetic correlations with growth traits. The present study indicates that growth, gonad yield and most gonad quality traits could be improved by selection with moderate to high potential. Indirect selection should be applied on gonad traits using growth traits as secondary traits. The present study provides important theoretical guidance for future selective breeding programmes for S. intermedius.     

Heritability and genotype by environment interactions for growth and survival in Litopenaeus vannamei at low and high densities

Genetic parameters and genotype by rearing density interactions for growth traits and survival were investigated in Litopenaeus vannamei. A total of 3626 shrimps from 40 families in two densities (low density, 80 shrimps m^?2; high density, 160 shrimps m^?2) were measured for four growth traits, body length, body weight, cephalothorax length and abdominal segment length. Variance components and genetic parameters for growth and survival were estimated using a two‐trait animal model or a threshold (probit) sire and dam model. The common environment effect was excluded because it could not be partitioned effectively, likely because of high heritability. The heritability for growth traits varied from 0.21 to 0.44, indicating a moderate level. For survival, the back‐transformed heritability () was 0.36 ± 0.06 and 0.22 ± 0.04 for the low and high densities respectively. There were no significant differences in heritability for growth traits and survival between the two densities (P > 0.05). High genetic correlations (0.94–0.98) between the two densities for growth traits indicated a low genotype by density interaction and ranking effect across the environments, which suggested that these traits were controlled mostly by the same genes over the two densities. Therefore, selection in a low‐density environment should produce desired correlated responses for growth at a high density. Genetic correlation (0.77 ± 0.09) between the two densities for survival was moderate and significant, which indicated that the genotype by density interaction effect was moderate and low for survival under the two densities. Our results provide crucial information for use in L. vannamei breeding programmes in China.     

Strain differences in feed efficiency measured as residual feed intake in individually reared rainbow trout, Oncorhynchus mykiss (Walbaum)

The efficient use of feed for growth and meat production is important for all animal production industries including aquaculture. Residual feed intake (RFI) is an alternative measure of feed efficiency that has been widely used in livestock production. Residual feed intake was calculated as the difference between intake observed and intake predicted on the basis of a bioenergetics model; a low RFI indicates greater efficiency. Residual feed intake offers some advantages as a selection criterion for improving production efficiency over traditional feed efficiency statistics because it is not a ratio and it typically has a larger coefficient of variation. The RFI of individually reared rainbow trout progeny from six different genetic cross‐types was examined for genetic variation. Proximate analysis and nitrogen retention were also evaluated to determine if differences in RFI correlate to differences in body composition and nutrient retention and varied by cross‐type. Differences between cross‐types indicated a genetic component for RFI, with the most efficient fish of approximately 160 g consuming 0.99 g less and inefficient fish consuming 0.05 g more feed per day than expected. Lower RFI was associated with higher growth rates (r=?0.38, P<0.05) and greater nitrogen retention (r=?0.82 P<0.001).     

Genetic effects on carcass-quality traits in hybrid striped bass (Morone chrysops♀×Morone saxatilis♂)

A 10 × 10 factorial mating design was used to examine the genetic effects on various carcass‐quality traits in hybrid striped bass (Morone chrysops♀×Morone saxatilis♂). A total of 448 offspring were raised in a ‘common‐garden’ environment and carcass‐quality traits were assessed at 389 days post fertilization; parentage of each fish was inferred from genotypes at 5–10 nuclear‐encoded microsatellites. There was a significant effect of dam and sire on body weight and fillet weight and a significant effect of dam on viscera weight and condition factor. When carcass‐quality traits were standardized to body weight, there was a significant effect of dam, sire and dam × sire interaction on viscera percentage (proportion of viscera weight to body weight). Phenotypic correlations between body weight and non‐standardized carcass‐quality traits were high (r_p=0.80–0.92), whereas phenotypic correlations between body weight and standardized carcass‐quality traits were low (r_p=0.13–0.19). Genetic correlations between body weight and fillet weight (dams and sires), and body weight and viscera weight (dams only) were significant and positive, while the genetic correlations between body weight and viscera percentage (dams and sires) were significant and negative. Significant general combining ability values for favourable carcass‐quality traits in the same breeder (dam or sire) occurred only in one or two of 20 (dams and sires) used in this study, suggesting that simultaneous improvement in multiple traits in hybrid striped bass may require evaluation of large numbers of candidate breeders. The effect of sex on body weight and all non‐standardized carcass‐quality traits was significant and appeared to be due to faster growth in females. These results indicate that selection for faster growth of hybrid striped bass would lead to a correlated increase in fillet weight and viscera weight but not necessarily to an increase in the proportion of fillet and waste product generated. The significant dam, sire and dam × sire interaction effects on viscera percentage and the negative genetic correlations between body weight and viscera percentage indicate that selection for reduced proportion of viscera relative to body weight might be feasible.     

Genetic parameters for loin eye area and other body traits of an important Neotropical aquaculture species,Colossoma macropomum (Cuvier, 1818)

Estimating components of variance and genetic parameters of economically relevant traits is the first step towards planning a breeding program for aquaculture species. This study estimated the (co)variance components for growth rate and other body traits and then determined a multiple regression equation to assess the loin eye area (LEA) from morphometric traits of the Neotropical aquaculture species Colossoma macropomum. Estimation of variance components was performed using derivative‐free restricted maximum likelihood estimation using the MTDFREML package. Six predictive variables were tested to estimate the coefficient of regression equation and to select the most suitable model for predicting LEA. The estimated genetic parameter for body weight showed moderate‐to‐high heritability estimates of 0.26 (0.01) and 0.49 (0.01) at 221 and 623 days respectively. The genetic correlation (r_g) estimates between body size measurements were positive and ranged from low to high at both ages. The heritability for LEA in this assessment was 0.39 (0.03). The genetic and phenotypic correlations between LEA and the other body measurements ranged from 0.16 to 0.94 and 0.75 and 0.90 respectively. The outcomes of this study can contribute to the development of a genetics‐based breeding program that will improve (tambaqui) productivity and carcass quality.     

Effects of light and artificial fish shelter (PVC pipe) on some phenotypic traits of stinging catfish (Heteropneustes fossilis Bloch, 1794)

Light and shelter are very important ecological factors that can affect many traits of fish. Therefore, a study was conducted to explore the effect of light and shelter on some phenotypic traits of stinging catfish (Heteropneustes fossilis Bloch, 1794). During experiment, equal‐sized juveniles (mean ± SE: 9.04 ± 0.09 cm) were collected and reared in aquariums dividing into four treatment groups, such as T₁ (0L:24D without pipe), T₂ (0L:24D with pipe), T₃ (12L:12D without pipe) and T₄ (12L:12D with pipe). Each treatment had 36 fish, which were randomly distributed into three replications. The fish were kept up to 120 days, and then, the growth performance and skin colour were analysed. The results showed that both lighting and shelter conditions as well as their interactions had significant effects on some traits expression. The analyses revealed that lighting condition significantly influenced body area, head width and skin coloration, while shelter condition significantly affected total and standard length, body area, and their interaction showed significant effects on body area, head width and anal fin length. Thus, this study indicates that stinging catfish show better growth performance and colour patterns especially in dark and sheltered conditions which could be recommended for the successive production of this highly priced fish species.     

Effects of the diet on seahorse (Hippocampus hippocampus) growth,body colour and biochemical composition

The short‐snouted seahorse (Hippocampus hippocampus) is a benthic fish that bases its survival on camouflage with the environment; therefore, both in wild and in captivity specimens, differences in coloration have been observed. This study was conducted to study the effect of five different diets, based on Artemia and frozen mysis, on fish survival, growth, skin colour parameters and biochemical composition. After 102 days of feeding different diets, no effect was observed on fish survival, growth, protein, ash or humidity content, except for colour changes on yellow and red fish. Differences on seahorse lipid and total carotenoids content were obtained in the experiment because of experimental diets. Fish eating Artemia showed the highest colour pattern response during the trial, with a maximum yellowness attained of 21. Additionally, a plateau of the skin colour expression for Artemia‐feeding fish was reached on day 180. A reversion of the yellowish skin colour was determined after a change of diet.     

Evidence for genetic distinction among sympatric ecotypes of Arctic char (Salvelinus alpinus) in south‐western Alaskan lakes

Resource polymorphism may play an important role in the process of speciation. The Arctic char (Salvelinus alpinus) exhibits great phenotypic and genetic diversity across its range, making it an ideal species for studies of resource polymorphism and divergence. Here, we investigated genetic variation at 11 microsatellite loci among 287 Arctic char from five isolated yet proximate postglacial lakes in south‐western Alaska that were previously examined for resource polymorphism. Significant differences in pairwise F_ST were detected among all lakes (range from 0.05 to 0.28, all P < 0.02). In one lake (Lower Tazimina Lake), we found evidence for two genetic groups of char and for significant differences in the distribution of microsatellite variability among at least two of the three previously described body size morphotypes (‘large’‐, ‘medium’‐, and ‘small’‐bodied char; maximum F_ST = 0.09; differences in admixture proportions). We also found a significant association between genetic admixture proportions and gill raker counts among body size morphs (r = ?0.73, P < 0.001). Our data represent the first record of genetically distinct sympatric morphs of Arctic char in Alaska and provide further evidence that differences in morphology associated with feeding (gill rakers) and growth trajectories reflect niche diversification and promote genetic divergence in Holarctic populations of Arctic char.     

Heritabilities and correlations of deformities and growth‐related traits in the European sea bass (Dicentrarchus labrax,L) in four different sites

Skeletal deformities are important traits for aquaculture as they induce slow growing and low market value. We studied their genetic determinism and their interactions with the environment at the ongrowing stage in 5839 European sea bass from a partial factorial mating of 33 sires and 23 dams, reared in four sites. All families were mixed, and fish were first reared in one site (site B) until 35 g mean weight, then distributed to the four sites. A posteriori reconstruction of pedigree with microsatellites was used. Deformities were scored internally at slaughtering, and externally from photographs. Site B, where all fish were initially stocked until 35 g and exposed to forced swimming because of fast water current showed the highest rate of deformities with 83% and 65% from internal and external scoring respectively. Heritability on the underlying scale was h² = 0.25 ± 0.03 across all sites, and varied little between sites, while genetic correlations of deformities between sites were always high (>0.85). Genetic correlations between deformities and daily growth coefficient were variable between sites(r_A = 0.50 ± 0.09, 0.43 ± 0.10, 0.32 ± 0.10, 0.18 ± 0.10 for sites A, B, C, D respectively) and were positively linked with the average growth rate in each site. These results pointed out that there could be a relation between growth rate and the evolution of deformities at the grow‐out stage.     

Maslinic acid,a natural triterpene,and ration size increased growth and protein turnover of white muscle in gilthead sea bream (Sparus aurata)

Maslinic acid (MA) is a pentacyclic triterpene used, at experimental level, as an additive to stimulate growth, protein‐turnover rates and hyperplasia in fish. In this experiment we have studied the effects of feeding with MA at daily fixed ration of 10 g kg^?1 of body mass, on growth, protein‐turnover rates and nucleic acid concentration in white muscle of gilthead sea bream grown in a local fish farm. The experimental groups contained 0 (control), 50 (MA₅₀) and 100 (MA₁₀₀) mg MA per kg of diet. Two groups were provided feed ad libitum (control AL and MA₁₀₀AL), while three were given a fixed ration (control R, MA₅₀R, and MA₁₀₀R). We have determined the following: growth rate; nucleic acid and protein levels; relative and absolute protein‐accumulation (K_G, A_G), synthesis (K_S, A_S) and degradation (K_D, A_D) rate, protein‐synthesis capacity (C_S), protein‐synthesis efficiency (K_RNA), protein‐synthesis rate per DNA (K_DNA) and protein‐retention efficiency. At the end of the experiment, higher body weights and muscle growth rates were found in both groups of fish fed with 100 mg MA per kg of diet. Feed‐efficiency rate, protein‐efficiency ratio and protein productive value, were higher in the MA₁₀₀AL group than in control AL. Fractional and absolute protein‐synthesis and degradation rates in white muscle of MA₁₀₀AL and MA₁₀₀R fish were higher than in the control, resulting in a higher protein‐accumulation rate and tissue growth. Total DNA content, indicated cell hyperplasia, was higher in MA₁₀₀AL and MA₁₀₀R than its respective controls. Studies of optical and electronic microscopy corroborated these results. These findings indicate that MA added to the diet can stimulate the growth, white‐muscle protein‐turnover rates and tissue hyperplasia in gilthead sea bream.     

A preliminary identification of genomic loci for body colour variation in the sea cucumber Apostichopus japonicus

The sea cucumber Apostichopus japonicus is one of the most economically important aquaculture species in China, which shows a distinct characteristic of body colour variation. A number of purple variants were obtained in the coast of China, which shows great potential to develop a niche market. In the present study, to understand the genetic basis of green‐purple colour variation, a genome‐wide association study based on the 2b‐RAD sequencing was conducted. As a result, 8,795 genome‐wide single nucleotide polymorphism (SNP) markers were obtained and then applied to the association analysis. Ten most associated SNP loci with p‐value <1.0 × 10^–8 were obtained, and they were assigned to 4 chromosomes (chr17, chr21, chr15 and chr05). In genomic regions neighbouring to those SNPs, 33 candidate genes with annotation were obtained and the endothelin‐converting enzyme‐1, which was reported to be involved in pigmentation variation, was identified. To our knowledge, this is the first report of the genetic locus for body colour variation in this species. These findings will be useful for the fine mapping of the determining gene for body colour variation of A. japonicus.     

Microsatellites markers to depict the reproductive and genetic patterns of farmed gilthead seabream (Sparus aurata): illustration by a case study on mass spawning

In the absence of breeding strategy, natural spawning constitutes the breeding ground for fish farmers to empirically manage their commercial broodstock. In this context, we used six microsatellite markers to characterize the genetic pattern of six commercial seabream broodfish tanks having a common history spanning four generations. The progeny of one tank single‐day mass‐spawning event, reared in two different environments, was used to estimate the genetic parameters for body weight. Limited genetic differentiation was observed among broodfish groups. A panel of nine loci allowed us to unambiguously assign 95.4% of the offspring (1692) and identify 37 parents (65% of the total broodfish). The limited effective population size (N_e = 15.3) was due to the elevated variance of parental contributions and to broodfish failing to contribute to the progeny. The fluctuation of the allele frequency highlighted the risks of genetic drift and reduction in the heterozygosity in the next generations. Heritability for body weight was moderate at commercial size (0.40 ± 0.10) and the high genetic correlation at later stages laid the groundwork for precocious selection criteria for growth. The discussion opens on the opportunity to use mass spawning for selective breeding.     

A first insight into genotype × diet interactions in European sea bass (Dicentrarchus labrax L. 1756) in the context of plant‐based diet use

This preliminary study assessed genotype × diet interaction in late growth of European sea bass (Dicentrarchus labrax) fed with either a fish meal (FM)‐ or a fish oil (FO)‐based diet (M) or an all‐plant‐based (PB) diet. A total of 550 fish from 224 families were reared together and tagged. DNA was sampled and microsatellites were used to assign parentage. When fish weight was 192 ± 54 g, two tanks were fed with M (FM: 100%; FO: 100%) and two others with PB (FM: 0% and FO: 0%). Body weight (BW), fork length (FL) and fillet lipid content (CorrFat) were analysed with a linear model and with REML methodology. We observed no significant differences between groups, but a slightly lower (P=0.03) daily growth coefficient in sea bass fed PB than in those fed M. Heritability estimates of BW differed significantly from zero (PB: 0.37 ± 0.18; M: 0.47 ± 0.24). Sire × diet interactions were significant and genetic correlations ranged between 0.51 and 0.87, showing genotype × diet interaction for BW and CorrFat. For the first time, genetic parameters in the context of total replacement of marine fishery by‐products were estimated in European sea bass, showing re‐ranking of family performances with extremely contrasted diets.     

Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.     

Influence of high content of dietary soybean oil on quality of large fresh,smoked and frozen Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis>)

Atlantic salmon (Salmo salar) was grown in sea cages from 700 g to a market size of 3.2 kg on diets containing either 29% Peruvian high polyunsaturated fatty acids (PUFA) fish oil (FO) or 29% soybean oil (SO) as oil source. Chemical analyses and a triangular consumer test were performed on fresh muscle, while colour, texture and liquid holding capacity (LHC) analyses were performed on both fresh muscle, frozen muscle (stored for 3 months) and smoked salmon. The growth and chemical composition of flesh was not affected by the dietary treatment. The muscle fatty acid (FA) profile was reflected by the dietary oil source, and the amount of malondialdehyde (MDA) was threefold higher in the salmon fed FO than SO. Muscle pigment concentration was significantly different (p < 0.01) with 7.9 mg kg^–1 for FO and 5.6 mg kg^–1 for SO fed salmon, respectively. This result was also significantly (p < 0.05) reflected in the difference between the instrumentally measured colour of fresh, frozen and smoked muscle, and visual impressions of fresh and frozen muscle. Gaping, texture and liquid holding capacity was not affected by the dietary treatment, and the consumer panel did not detect any differences between the dietary groups. SO can be used as a dietary oil source in the grow-out phase of salmon production without sacrificing product quality in terms of texture, liquid holding capacity and consumer preference. However, a total substitution of high PUFA fish oil by SO in diets for salmon grown to market size, affects muscle colour and the FA profile significantly. (p < 0.05).     

Estimates of Heritabilities and Genetic Correlations for Growth and Gonad Traits in Blunt Snout Bream,Megalobrama amblycephala

Blunt snout bream, Megalobrama amblycephala, is an herbivorous freshwater fish and has been recognized as a main aquaculture species in the Chinese freshwater polyculture system. The objective of the study is to estimate the genetic parameters for growth, body shape, and gonad traits for M. amblycephala at 1 yr of age. The phenotypic analysis showed that coefficients of variation for gonad traits had large variation relative to the other traits analyzed, and there was no sexual dimorphism by comparing growth and body shape in M. amblycephala. Based on restricted maximum likelihood and Markov chain Monte Carlo Bayesian methods using the animal model, the heritabilities of body weight (0.423–0.504), body length (0.309–0.678), body height (0.408–0.599), and dressed weight (0.359–0.643) were moderate and high, while the other traits, including conditional factor (0.029–0.199), body shape coefficient (0.095–0.405), edible ratio (0.073–0.207), gonad weight (0.018–0.170), and gonadosomatic index (0.050–0.222), had moderate or low heritabilities. High genetic and phenotypic correlations were found among growth traits, but not between growth traits and body shape or gonad traits except dressed weight. Based on our results, it could be efficient to combine the selection on body weight for fast growth and nonearly sexual maturity varieties of M. amblycephala breeding.