The genetic correlation between feed conversion ratio and growth rate affects the design of a breeding program for more sustainable fish production

Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera

BACKGROUND

In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes.

RESULTS

We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene.

CONCLUSIONS

Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.

Defining desired genetic gains for Pacific white shrimp (Litopenaeus vannamei) breeding objective using participatory approaches

The objective of this study was to define desired genetic gains from economically important traits of Pacific white shrimp (Litopenaeus vannamei) using participatory approaches. Two questionnaires were sent out to 100 Pacific white shrimp farmers in all five Iranian shrimp farming provinces. Questionnaire A (Q-A) includes management factors and farming environments. Moreover, in this questionnaire, farmers were asked to rank the fourth most important traits in shrimp among 10 economic traits in the list for genetic improvement. In questionnaire B (Q-B), priorities of the four traits with the highest value were obtained using pairwise comparison. The results showed that the four most important traits were white spot syndrome virus resistance (WSSV), growth rate before 4 months (GR), acute hepatopancreatic necrosis disease resistance (AHPND), and female total weight at ablation (FTW). Medians of the best individual preference values were WSSV (0.222), GR (0.173), AHPND (0.157), and FTW (0.053). Most disagreements were found between the social group preference values in the commercial products and water salinity categories. Desired genetic gains were 1.71%, 1.57%, 0.53% and 0.31% for GR, AHPND, WSSV and FTW, respectively. This study highlighted that despite environmental and management differences, participatory approaches can achieve desired genetic results for Pacific white shrimp breeding programme.

Morphology and metabolic traits related to swimming performance in Australasian snapper (Chrysophrys auratus) selected for fast growth

Changes in body shape are linked to swimming performance and become relevant for selective breeding programmes in cultured finfish. We studied how the selection for fast growth could affect phenotypes by investigating the relationship between swimming performance and body shape. We also investigated how swimming might affect plasma metabolite concentrations. Critical swimming speed (UCrit), body traits (e.g., BW, body weight; BL, body length; K, condition factor), and plasma lactate and glucose concentrations were evaluated in two cohorts of Australasian snapper (Chrysophrys auratus): one derived from wild broodstock (F1), and the other selected for fast growth (F4). UCrit tests (n = 8) were applied in groups of 10 snapper of similar BW (71.7 g) and BL (14.6 cm). The absolute or relative UCrit values of both cohorts were similar (0.702 m⋅s-1 and 4.795 BL⋅s-1, respectively), despite the F4 cohort displaying a higher K. A positive correlation between K and absolute UCrit (Pearson's r = 0.414) was detected in the F4 cohort, but not in the F1 cohort, which may be linked to differences in body shape. A negative correlation between relative UCrit and body size (Pearson's r between -0.682 and -0.501), but no correlation between absolute UCrit and body size, was displayed in both cohorts. Plasma lactate and glucose concentrations were higher in the F4 cohort at UCrit. Whether a longer selective breeding programme could result in more changes in body shape, potentially affecting swimming performance, should be explored, along with the potential outcomes of the differences in metabolic traits detected.

Effect of Biofloc Technology Enriches the Growth of Litopenaeus vannamei (Boone, 1931)

The use of probiotics in shrimp farms has expanded as an alternative to antibiotics, improving shrimp health, growth, disease control and water quality. However, the efficacy of probiotics in intensive systems using biofloc remains uncertain. This study investigated bioremediation and biocontrol of commercial probiotics using biofloc, analysing water quality and bacterial groups influencing shrimp performance. Thirteen microbial colonies were observed in the biofloc samples, and their evolutionary history was inferred using the neighbour-joining method. Analysis using MEGA6 software revealed 99.6% similarity between colony 1P1 and Virgibacillus sp. and 99.8% similarity between colony 2P2 and Bacillus kochii. The study analysed the biochemical and amino acid content of shrimp cultured using biofloc technology for 85 days. The study found that biofloc-cultured L. Vannamei flesh had higher levels of moisture (31%), ash (15.2%), protein (34%) and lipid (12.6%). No seasonal variations were observed between biofloc samples in winter and summer seasons. Protein levels were found to be appropriate for shrimp growth in both ex situ and in situ biofloc systems. The average growth rate (kg/m2) of biofloc-cultured shrimp was significantly greater than in normal pond shrimp in both samples. The feed conversion ratio in the biofloc tank was lower than in the usual pond-cultured shrimp, possibly due to lower growth rate, lower feeding frequency (2 times per day) and higher density. The growth of L. vannamei shrimp is influenced by stocking density, with higher stocking density affecting the average weight. The study also examined the growth biochemical and amino acid content of shrimp cultured using biofloc technology.

Transcriptome analysis of the muscle of fast- and slow-growing phoenix barb (Spinibarbus denticulatus denticulatus)

Growth rate is a commercial trait in aquaculture that is influenced by multiple factors, among which genetic composition plays a fundamental role in the growth rate of species. The phoenix barb (Spinibarbus denticulatus denticulatus) is a widely distributed freshwater fish species in South China. Although S. d. denticulatus is reared in South China, the molecular mechanisms underlying the growth rate of the species remain unclear. Here, the authors performed transcriptome analysis of muscle tissues from fast-growing (FG) and slow-growing (SG) S. d. denticulatus at 90, 150, and 300 days after hatch (DAH) to elucidate its growth mechanism. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed genes (DEGs) between the two groups were enriched in pathways related to muscle growth, glycolysis, and energy and lipid metabolism. Nonetheless, a higher number of DEGs were identified in the FG vs. SG groups at 90 and 300 DAH compared with 150 DAH. DEGs identified at 90 DAH were mainly enriched in the GH/IGF axis, PI3K-Akt signalling pathway, AMPK signalling pathway and lipid metabolism highly expressed in FG individuals. DEGs identified at 300 DAH were mainly enriched in PI3K-Akt signalling pathway, glycolysis/gluconeogenesis, gene translation and lipid metabolism. In addition, some genes were expressed during the early growth stage in FG individuals but expressed during the late stage in SG individuals, indicating considerable variations in the expression profiles of growth-related genes at different developmental stages. Overall, these findings contribute to the understanding of the growth mechanism of S. d. denticulatus, which would be useful for the propagation of fast-growing breeds.

Improvement of Fish Growth and Metabolism by Oligosaccharide Prebiotic Supplement

Finfish aquaculture is expected to continue to benefit from significantly improved fish diets, which are the source of energy to support the growth and health of fish. Strategies to enhance the transformation rate of dietary energy and protein to fish growth are greatly desired by fish culturists. Prebiotic compounds can be used as supplements to human, animal, and fish diets to populate beneficial bacteria in the gut. The goal of the present study is to identify low-cost prebiotic compounds with high efficacy in increasing the absorption of food nutrients by fish. Several oligosaccharides were evaluated as prebiotics in Nile tilapia (Oreochromis niloticus), one of the most widely cultured species in the world. Several parameters of the fish on different diets were evaluated, including feed conversion ratios (FCRs), enzymatic activities, expression of growth-related genes, and the gut microbiome. Two age groups of fish (30 days old and 90 days old) were used in this study. The results indicated that the addition of xylooligosaccharide (XOS), galactooligosaccharide (GOS), or XOS and GOS combination to the basic fish diet significantly decreased the feed conversion ratio (FCR) of the fish in both age groups. Both XOS and GOS decreased the FCR of 30-day-old fish by 34.4% compared to the fish on the control diet. In the 90-day-old fish group, XOS and GOS decreased the FCR by 11.9%, while the combination of the two prebiotics led to a 20.2% decrease in FCR compared to the control group. The application of XOS and GOS also elevated the production of glutathione-related enzymes and the enzymatic activity of glutathione peroxidase (GPX), indicating the enhancement of antioxidation processes in fish. These improvements were associated with significant changes in the fish gut microbiota. The abundance of Clostridium ruminantium, Brevinema andersonii, Shewanella amazonensis, Reyranella massiliensis, and Chitinilyticum aquatile were upregulated by XOS and GOS supplements. The findings of the present study suggested that the prebiotics would be more effective when they were applied to the younger fish, and the application of multiple oligosaccharide prebiotic compounds could result in a greater growth enhancement. The identified bacteria can be potentially used as probiotic supplements in the future to improve fish growth and feeding efficiency and ultimately reduce the cost of tilapia aquaculture.

Partially replacing dietary fish meal by Saccharomyces cerevisiae culture improve growth performance, immunity, disease resistance, composition and function of intestinal microbiota in channel catfish (Ictalurus punctatus)

The aim of the present study was to investigate the partial replacement of fish meal by Saccharomyces cerevisiae culture on growth performance, immunity, composition and function of intestinal microbiota and disease resistance in channel catfish (Ictalurus punctatus). Two equal nitrogen and energy diets were prepared including a basal diet (containing 10% fish meal, Control) and an experimental diet (replacing 20% of the fish meal of the basal diet with yeast culture, RFM). Channel catfish were fed with the diets for 12 weeks. The results showed that weight gain and condition factor were significantly increased, and FCR was significantly decreased in RFM group (P < 0.05). The gene expression of intestinal HIF1α was significantly increased in RFM group (P < 0.05), while the expressions of NF-κB in the intestine and liver were significantly decreased (P < 0.05). The relative abundance of Firmicutes tended to increase, and the Turicibacter had an upward trend (0.05 < P < 0.2). In addition, the survival rate of channel catfish was significantly increased in RFM group after challenged with Aeromonas veronii Hm091 and Aeromonas hydrophila NJ-1 (P < 0.05). Compared with intestinal microbiota of channel catfish of control group, intestinal microbiota of channel catfish of RFM group significantly increased the expression of HIF1α, and decreased the expression of IL-1β and TNF-α (P < 0.05) in germ-free zebrafish. Intestinal microbiota induced by RFM diet also significantly increased disease resistance to Aeromonas veronii Hm091 and Aeromonas hydrophila NJ-1. In conclusion, replacement of fish meal by the yeast culture improved the growth, immunity and disease resistance of channel catfish, and intestinal microbiota of channel catfish induced by the yeast culture played a critical role in these effects.

Genetic parameter estimates for three antioxidant factors in cultured Takifugu rubripes

Genetic parameters of three antioxidant factors, including superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX), were evaluated in liver samples from 840 Takifugu rubripes individuals from 28 full-sib families. Heritability values of SOD, CAT, and GPX were 0.17, 0.18, and 0.14, respectively, and the full-sib family effect values for these antioxidant factors were 0.46, 0.47, and 0.49, respectively. The ranges of phenotypic and genetic correlations among the three immune factors were 0.748-0.848 and 0.726-0.806, respectively. Considering the low heritability and high full-sib family effect of the three antioxidant indexes, the use of both genome-wide selection and clustered regularly interspaced short palindromic repeats (CRISPR) is promising for genetically improving the three antioxidant indexes in cultured fish. In addition, given positive phenotypic and genetic correlations among the three antioxidant enzymes SOD, CAT and GPX, the antioxidant competence of Takifugu rubripes can be improved by genetically improving these three antioxidant traits via multi-trait integrated breeding technology or indirect selection.

Sustained swimming exercise training decreases the individual variation in the metabolic phenotype of gilthead sea bream (Sparus aurata)

Cultured fish can be induced to swim, although the suitability and benefits remain to be tested. Sustained swimming exercise (SSE) training and detraining (DET) were applied in juvenile gilthead sea bream (Sparus aurata) and the metabolic rates were investigated. Fish with a total body mass of 80.5 ± 1.5 g and total length 17.2 ± 0.1 cm were maintained untrained (spontaneously swimming activity, UNT), swim-trained (induced sustained swimming activity, SSE) at 1 BL s^-1 for 28 days, or detrained (28 days of swimming followed by 10 days of untraining, DET). Standard metabolic rate (SMR), maximum metabolic rate (MMR), and excess post-exercise oxygen consumption (EPOC) were assessed (n = 10). In addition, the effects of SSE training (51 days) on blood and plasma parameters were investigated before and immediately after applying a high-intensity swimming (HIS) protocol. SMR, MMR, and EPOC values were not different between SSE, UNT, or DET fish (143.2, 465.5 mg O₂ kg^-1 h^-1, and 459.1 mg O₂ kg^-1, respectively). Spite the lack of differences between treatments, the dispersion in the residuals for SMR, MMR, and absolute aerobic scope (AAS) values followed the order UNT > DET > SSE, indicating that swim training decreases the individual variation of these metabolic parameters. Haematological parameters, plasma glucose, lactate, and cortisol levels were similar between SSE and UNT groups before HIS. Plasma glucose and lactate levels increased in both groups after HIS, being higher in the SSE group. Plasma cortisol levels were similar between both groups after HIS. Results suggest that SSE training improves energy use and reduces individual variation in SMR and MMR, an effect that declines with detraining.

A tool for functional selection of leisure camels: Behaviour breeding criteria may ensure long-term sustainability of a European unique breed

Livestock selection for desirable temperament traits still remains disregarded for minor productive species, such as camels. Despite dromedary camels from Canary Islands were at once polyvalent, current major functionality for this unique European recognised breed is limited to tourism-oriented interactive experiences. The conservation of this endemic breed implies the immediate enforcement of selective breeding programmes by including behavioural functional traits as genetic selection criteria. With this purpose, we evaluated the suitability of a practical proposal to qualitatively and quantitatively evaluate camel behaviour performance to be applied in breeding programmes for the improvement of camel personality dimensions. One-hundred thirty-one respondents enjoying a camelback leisure riding during high season in Southern Spain were asked to voluntarily fulfill an on-site questionnaire just after the tourist ride concluded. Eleven behaviour criteria were rated on a 5-point Likert-type scale by each respondent for the camel they had ridden on. Generalized Procrustes Analysis revealed that a general consensus between participants for dromedary behavioural features were reached, more substantial for those expressions reflecting agitation and/or indifference towards interaction with human. Moreover, the variability in animal behaviour patterns could be attributed to camel sex- and age-related differences. Mid- to long-term sustainability of Canarian camels may rely on the ability of involved stakeholders to adapt leisure opportunities to customer demands and expectations. Hence, those camel behavioural features with a conditioning potential of overall participants satisfaction, may become potential objective selection criteria candidates. Consequently, camel functional selective breeding may ensure camel breed preservation and sustainable protection based on leisure activities.

Economic and environmental assessments of combined genetics and nutrition optimization strategies to improve the efficiency of sustainable pork production

We evaluated the economic and environmental impacts of strategies that incorporated selection for pig feed efficiency and dietary optimization based on a single or multiple objectives tailored to meet the population nutritional requirements, with the goal to optimize sustainable farm feed efficiency. The economic and environmental features of the strategy were evaluated using life cycle assessment (LCA) and bio-economic models. An individual trait-based LCA model was applied to evaluate global warming potential, terrestrial acidification potential, freshwater eutrophication potential (EP), and land occupation of the combined genetics and nutrition optimization to produce 1 kg of live pig weighing 120 kg at the farm gate. A parametric individual trait-based bio-economic model was developed and applied to determine the cost breakdown, revenue, and profit to be gained from a 120-kg live pig at the farm gate. Data from two genetic lines with contrasted levels of feed efficiency were used to apply the combined genetics and nutrition optimization: accounting for the average nutritional requirements for each line, the individual pig responses to diets formulated for least cost, least environmental impacts, or minimum combination of costs and environmental impacts objectives were predicted with INRAPorc. Significant differences in the environmental impacts (P < 0.0001) and profit (P < 0.05) between lines predicted with the same reference diet showed that selection for feed efficiency (residual feed intake) in pigs improves pig production sustainability. When pig responses were simulated with their line-optimized diets, except for EP, all the line environmental impacts were lower (P < 0.05) than with the reference diet. The high correlations of feed conversion ratio with the environmental impacts (> 0.82) and the profit (< −0.88) in both lines underlined the importance of feed efficiency as a lever for the sustainability of pig production systems. Implementing combined genetics and nutrition optimization, the inherent profit and environmental differences between the genetic lines were predicted to be reduced from 23.4% with the reference diet to 7.6% with the diet optimized jointly for economic and environmental objectives (joint diet). Consequently, for increased pig sustainability, diet optimization for sustainability objectives should be applied to cover the specific nutritional requirements arising in the herd from the pigs genetic level.

The Effects of Feed Restriction and Isolated or Group Rearing on the Measurement of Individual Feed Intake and Estimation of Feed Conversion Ratio in Juvenile Nile Tilapia (Oreochromis niloticus) for Selective Breeding Purposes

Accurately measuring the phenotype at the individual level is critical to the success of selective breeding programs. Feed efficiency is a key sustainability trait and is typically approached through feed conversion ratio (FCR). This requires measurements of body weight gain (BWG) and feed intake (FI), the latter being technically challenging in fish. We assessed two of the principal methods for measuring feed intake in fish over consecutive days: (1) group rearing 10 fish per group and video recording the meals and (2) rearing fish individually on a restricted ration. Juvenile Nile tilapia (Oreochromis niloticus) from the Genetically Improved Farmed Tilapia (GIFT) strain and the Cirad strain were entered into the study (128 GIFT and 109 Cirad). The GIFT strain were reared over three consecutive periods of 7 days each under different feeding, recording, and rearing scenarios (i) in groups fed an optimal ration (g100) or (ii) fed a 50% restricted ration (g50) both with video records of all meals and (iii) reared in isolation and fed a 50% restrictive ration. The Cirad strain were tested similarly but only for scenarios (i) and (iii). All fish were fed twice daily with a calculated ration. Correlations showed the same trends for the GIFT and the Cirad strains. For the GIFT strain, correlations were positive and significant for BWG and FI measured in scenarios (i) and (ii), 0.49 and 0.63, respectively, and FI measured in scenarios (i) and (iii) (0.50) but not for BWG measured in scenarios (i) and (iii) (0.29, NS). The phenotypic correlation estimated for FCR between scenarios (i) and (ii) with fish fed an optimal or a 50% restricted ration was low and not significant (0.22). Feed Conversion Ratio for GIFT fish reared in groups or in isolation and fed with a restricted ration [scenarios (ii) and (iii)] were not significantly correlated either. Social interactions between fish, potentially impacting their efficiency, may explain the results. Therefore, selective breeding programs seeking to improve feed efficiency will need to carefully plan the feeding rate and the rearing system used to estimate FCR in order to optimize selection for the targeted production system.

Evaluating environmental impacts of selection for residual feed intake in pigs

To identify a proper strategy for future feed-efficient pig farming, it is required to evaluate the ongoing selection scenarios. Tools are lacking for the evaluation of pig selection scenarios in terms of environmental impacts to provide selection guidelines for a more sustainable pig production. Selection on residual feed intake (RFI) has been proposed to improve feed efficiency and potentially reduce the associated environmental impacts. The aim of this study was thus to develop a model to account for individual animal performance in life cycle assessment (LCA) methods to quantify the responses to selection. Experimental data were collected from the fifth generation of pig lines divergently selected for RFI (low line, more efficient pigs, LRFI; high line, less efficient pigs, HRFI). The average feed conversion ratio (FCR) and daily feed intake of LRFI pigs were 7% lower than the average of HRFI pigs (P < 0.0001). A parametric model was developed for LCA based on the dietary net energy fluxes in a pig system. A nutritional pig growth tool, InraPorc®, was included as a module in the model to embed flexibility for changes in feed composition, animal performance traits and housing conditions and to simulate individual pig performance. The comparative individual-based LCA showed that LRFI had an average of 7% lower environmental impacts per kilogram live pig at farm gate compared to HRFI (P < 0.0001) on climate change, acidification potential, freshwater eutrophication potential, land occupation and water depletion. High correlations between FCR and all environmental impact categories (>0.95) confirmed the importance of improvement in feed efficiency to reduce environmental impacts. Significant line differences in all impact categories and moderate correlations with impacts (>0.51) revealed that RFI is an effective measure to select for improved environmental impacts, despite lower correlations compared to FCR. Altogether more optimal criteria for efficient environment-friendly selection can then be expected through restructuring the selection indexes from an environmental point of view.