Abstract
To provide food for the earth's human population, sustainable growth in food production is simultaneously a necessity and a challenge. Several approaches have been suggested to improve aquaculture sustainability including selective breeding and nutritional methods. Improving feed utilization efficiency which is a beneficial approach towards sustainability is a challenge in aquaculture. Therefore, we developed an indirect benchmark to use in selecting trout for improved efficiency of feed utilization on plant protein (soy)-based diets, with the long-term goal of reducing the cost of commercial trout production. This benchmark is consisted of a four-part integrative approach to identify feed-efficient individuals among 1595 fish coming from 12 genetically selected families by establishing the phenotypic relationship between feed conversion ratio (FCR) and body weight variations during consecutive periods of feed deprivation (FD) and re-feeding (RF). Additionally, we examined the nutritional composition of fish filet, the expression level of some hepatic and muscular genes involved in growth, energy metabolism, and protein turn over as well as fish gut microbiome to create a big-picture understanding of events for each efficiency phenotype during the compensatory regimen. The current study showed that the fish with the lowest weight loss during a feed deprivation period and the highest weight gain during the refeeding period (FD-/RF+) demonstrated the lowest FCR (FCR=0.99) and consisted of individuals from several families. FCR in the other three groups, FD+/RF+, FD-/RF-, and FD+/RF- FCR equal to 1.26, 1.41, and 1.40 respectively. With repetition of the indirect criteria, we have shown that some fish demonstrated consistent behavior throughout time and life stages. The selection of such fish can guarantee the improvement of feed utilization efficiency in a breeding plan. This finding confirms the possibility of improving feed efficiency in mixed lines. Although the feeding period has an effect on the nutritional composition of fillets, such selection criteria did not show an effect on groups. Long periods of feed deprivation did not have a different effect on the four groups in terms of muscle lipid and protein contents. Therefore, while genetic selection based on such criteria will improve feed efficiency and growth performance, it will not change muscle quality.During the second phase of the study, we investigated the expression level of several genes involved in three cellular functions (growth, energy metabolism, and protein turnover) in the four groups of selected rainbow trout (FD-/RF+, FD-/RF-, FD+/RF+, FD+/RF-) as they went through two successive periods of FD and RF (second feeding challenge). We observed that while hepatic expression of IGF1 was similar among groups at the end of each feed deprivation it was significantly higher in FD-/RF+ (most efficient group) at the end of both re-feeding periods. Among the studied genes involved in energy metabolism, only COX1 was observed not to be significantly affected by the FD and RF periods in the liver and muscle. While NDH1 and ATP6 in the liver were upregulated during RF when energy sources are abundant and downregulated at the end of FD, the opposite pattern was observed in the muscle which can be explained due to the tissue specificity of these genes. Whilst the genes involved in muscle atrophy are expected to upregulate when external energy sources are limited, we did not observe that pattern during the first half of the feeding challenge which might be due to epigenetic cell memory as these fish have been exposed to consecutive prolonged FD and RF periods twice before the gene expression study. During the 2nd FD and 2nd RF as the fish got closer to their reproduction season and cell priorities changed towards fecundity muscle atrophy genes were upregulated to conserve as much lipid as possible for reproduction during FD.
Besides the gene expression patterns, this study also focused on the gut microbial community of the most efficient (FD-/RF+), least efficient (FD+/RF-), and control (continuously fed fish) groups As they went through the FD and RF periods during the second phase of the experiment. Interestingly, the gut microbiome of rainbow trout varied significantly over time, regardless of changes in feed intake. Even continuously fed fish had similar bacterial profiles to those exposed to different feeding regimes. Fluctuations in the water bacterial community may have contributed significantly to microbiome variations in the fish gut.
Moving towards the sustainability goal, this dissertation also pursued a nutrition-based approach to test the effect of a variety of alternative oils sources (linseed (LO), soy (SO), canola (CO), coriander (CNO) and algae (AO)), all of which include various levels of α-linolenic acid, linoleic acid, oleic acid, and DHA fatty acids (FA) in the diet of vegetarian rainbow trout, on growth, muscle tissue FA composition, and lipid-related hepatic gene expression. The growth of rainbow trout was observed to improve with the consumption of dietary algae oil and linseed oil, without any negative impact on feed efficiency. The upregulation of genes responsible for elongating α-linolenic acid to long-chain polyunsaturated fatty acids was found in fish fed with algae oil, and these fish also had higher levels of docosahexaenoic acid. These findings suggest that the nutritional value of the fish fillet in terms of health-promoting fatty acids may be altered not only due to the direct effect of the diet but also through de novo biosynthesis of eicosapentaenoic acid and docosahexaenoic acid. In addition, the expression of Catalase and glutathione S-transferase genes was affected by the dietary oils, indicating that alternative oils may improve the antioxidant status of rainbow trout and protect them from oxidative stress.
The outcomes of this dissertation improved the feed efficiency in rainbow trout which can have a broad application in commercial fish selective breeding programs, leading to increased profitability for global fish farmers for sustainable aquaculture.