Broodstock nutritional programming differentially affects the hepatic transcriptome and genome-wide DNA methylome of farmed gilthead sea bream (Sparus aurata) depending on genetic background

BACKGROUND

Broodstock nutritional programming improves the offspring utilization of plant-based diets in gilthead sea bream through changes in hepatic metabolism. Attention was initially focused on fatty acid desaturases, but it can involve a wide range of processes that remain largely unexplored. How all this can be driven by a different genetic background is hardly underlined, and the present study aimed to assess how broodstock nutrition affects differentially the transcriptome and genome-wide DNA methylome of reference and genetically selected fish within the PROGENSA® selection program.

RESULTS

After the stimulus phase with a low fish oil diet, two offspring subsets of each genetic background received a control or a FUTURE-based diet. This highlighted a different hepatic transcriptome (RNA-seq) and genome-wide DNA methylation (MBD-seq) pattern depending on the genetic background. The number of differentially expressed transcripts following the challenge phase varied from 323 in reference fish to 2,009 in genetically selected fish. The number of discriminant transcripts, and associated enriched functions, were also markedly higher in selected fish. Moreover, correlation analysis depicted a hyper-methylated and down-regulated gene expression state in selected fish with the FUTURE diet, whereas the opposite pattern appeared in reference fish. After filtering for highly represented functions in selected fish, 115 epigenetic markers were retrieved in this group. Among them, lipid metabolism genes (23) were the most reactive following ordering by fold-change in expression, rendering a final list of 10 top markers with a key role on hepatic lipogenesis and fatty acid metabolism (cd36, pitpna, cidea, fasn, g6pd, lipt1, scd1a, acsbg2, acsl14, acsbg2).

CONCLUSIONS

Gene expression profiles and methylation signatures were dependent on genetic background in our experimental model. Such assumption affected the magnitude, but also the type and direction of change. Thus, the resulting epigenetic clock of reference fish might depict an older phenotype with a lower methylation for the epigenetically responsive genes with a negative methylation-expression pattern. Therefore, epigenetic markers will be specific of each genetic lineage, serving the broodstock programming in our selected fish to prevent and mitigate later in life the risk of hepatic steatosis through changes in hepatic lipogenesis and fatty acid metabolism.

Modulation of Energy Metabolism and Epigenetic Landscape in Rainbow Trout Fry by a Parental Low Protein/High Carbohydrate Diet

Simple Summary

While the effects of parental diets on their progeny have been highly described in mammals, such studies are lacking in fish. To explore such a question in a high trophic level teleost fish, two-year old male and female rainbow trout were fed either a control diet (0% carbohydrate and 63.89% protein) or a high-carbohydrate diet (35% carbohydrate and 42.96% protein), for a complete reproductive cycle for females and for a period of 5 months for males. Neither the maternal nor the paternal high-carbohydrate diet alone had induced significant effects on their progeny. Nevertheless, when both parents were fed the high-carbohydrate diet, the energy metabolism and mitochondrial dynamics of their progeny were altered. Moreover, the epigenetic landscape was also highly affected. Even though, offspring growth was only slightly affected at the early stage of life; the effect of parental high-carbohydrate diet should be explored over the long term.

Abstract

It is now recognized that parental diets could highly affect offspring metabolism and growth. Studies in fish are, however, lacking. In particular, the effect of a parental diet high in carbohydrate (HC) and low in protein (LP) on progeny has never been examined in higher trophic level teleost fish. Thus, two-year old male and female rainbow trout (Oncorhynchus mykiss) were fed either a control diet (0% carbohydrate and 63.89% protein) or a diet containing 35% carbohydrate and 42.96% protein (HC/LP) for a complete reproductive cycle for females and over a 5-month period for males. Cross-fertilizations were then carried out. To evaluate the effect of the parental diet on their offspring, different phenotypic and metabolic traits were recorded for offspring before their first feeding and again three weeks later. When considering the paternal and maternal HC/LP nutrition independently, fry phenotypes and transcriptomes were only slightly affected. The combination of the maternal and paternal HC/LP diets altered the energy metabolism and mitochondrial dynamics of their progeny, demonstrating the existence of a synergistic effect. The global DNA methylation of whole fry was also highly affected by the HC/LP parental diet, indicating that it could be one of the fundamental mechanisms responsible for the effects of nutritional programming.

Possible Dietary Effects of Insect-Based Diets across Zebrafish (Danio rerio) Generations: A Multidisciplinary Study on the Larval Phase

Insects represent a valuable and sustainable alternative ingredient for aquafeed formulation. However, insect-based diets have often highlighted controversial results in different fish species, especially when high inclusion levels were used. Several studies have demonstrated that nutritional programming through parental feeding may allow the production of fish better adapted to use sub-optimal aquafeed ingredients. To date, this approach has never been explored on insect-based diets. In the present study, five experimental diets characterized by increasing fish meal substitution levels with full-fat Black Soldier Fly (Hermetia illucens; BSF) prepupae meal (0%, 25%, 50%, 75% and 100%) were used to investigate the effects of programming via broodstock nutrition on F1 zebrafish larvae development. The responses of offspring were assayed through biometric, gas chromatographic, histological, and molecular analyses. The results evidenced that the same BSF-based diets provided to adults were able to affect F1 zebrafish larvae fatty acid composition without impairing growth performances, hepatic lipid accumulation and gut health. Groups challenged with higher BSF inclusion with respect to fish meal (50%, 75% and 100%) showed a significant downregulation of stress response markers and a positive modulation of inflammatory cytokines gene expression. The present study evidences that nutritional programming through parental feeding may make it possible to extend the fish meal substitution level with BSF prepupae meal in the diet up to almost 100% without incurring the well-known negative side effects of BSF-based diets.

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.

Zinc supplementation improves growth performance in small ruminants: a systematic review and meta-regression analysis

Appropriate supplementation of trace minerals is fundamental to enhance the metabolic status of growing animals and promote an adequate expression of genetic potential. Zinc (Zn) is an essential mineral fundamental in many biological processes that are related to growth, energy balance and immunity. The aim of the present study was to analyse the effect of Zn supplementation on growth parameters in small ruminants by using a meta-analytic approach. Sources of heterogeneity were explored using a meta-regression analysis. The final database was integrated from a total of 53 trials. Only indexed articles that provided an effect size measure, variability measure, sample size and randomisation of the procedure were considered. The dependent variables considered for the study were average daily gain (ADG), dry-matter intake (DMI), feed conversion ratio (FCR), final bodyweight, and glucose blood concentration. The exploratory variables included species (sheep and goat), breed, production level, Zn source and dosage. The ‘meta’ package in R statistical software was used to conduct the meta-analyses. For response variables that showed substantial heterogeneity (I2 > 50%), mixed-effect models (meta-regression analysis) were constructed to explore the sources of heterogeneity using the ‘Metafor’ package. DMI was higher in animals supplemented with Zn (>21.08 g/day, P = 0.0001). Breed, species, production level, and dosage reduced heterogeneity of DMI response from I2 = 84.8 to I2 = 48.1%. Zn-supplemented animals showed higher ADG (17.39 g/day, P = 0.001), which was affected by species, breed dosage and Zn-source. Zn supplementation improved feed efficiency, with lower values of FCR (–1.56 g/g, P < 0.0001). There was a positive relationship between the dosage and effect size in all outcome variables (P < 0.05). Zn-proteinate showed the best response in both species to ADG, FCR and final body weight. Our findings of the systematic review concluded that dietary Zn supplementation improves growth performance in small ruminants and their level of response is influenced mainly by species, production level, and Zn-source and dosage.

Parental LC-PUFA biosynthesis capacity and nutritional intervention with alpha-linolenic acid affect performance of Sparus aurata progeny

Environmental factors such as nutritional interventions during early developmental stages affect and establish long-term metabolic changes in all animals. Diet during the spawning period has a nutritional programming effect in offspring of gilthead seabream and affects long-term metabolism. Studies showed modulation of genes such as fads2, which is considered to be a rate-limiting step in the synthesis of n-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA). However, it is still unknown whether this adaptation is related to the presence of precursors or to limitations in the pre-formed products, n-3 LC-PUFA, contained in the diets used during nutritional programming. This study investigated the combined effects of nutritional programming on Sparus aurata through broodstock diets during the spawning period and in broodfish showing higher or lower fads2 expression levels in the blood after 1 month of feeding with a diet containing high levels of plant protein sources and vegetable oils (VM/VO). Broodfish showing high fads2 expression had a noticeable improvement in spawning quality parameters as well as in the growth of 6 month old offspring when challenged with a high VM/VO diet. Further, nutritional conditioning with 18:3n-3-rich diets had an adverse effect in comparison to progeny obtained from fish fed high fish meal and fish oil (FM/FO) diets, with a reduction in growth of juveniles. Improved growth of progeny from the high fads2 broodstock combined with similar muscle fatty acid profiles is also an excellent option for tailoring and increasing the flesh n-3 LC-PUFA levels to meet the recommended dietary allowances for human consumption.

Milk replacer restriction during early life impairs the live body weight and progesterone patterns of ewe lambs during the replacement period

Nutritional programming caused by feed restriction during the early life may counteract the profitability of the dairy sheep farm. However, most studies have been focused exclusively on the prenatal period, and scarce information regarding the effect of milk replacer (MR) restriction on feed efficiency [residual feed intake (RFI)] and progesterone patterns of replacement ewe lambs is available. Therefore, in the present study 40 Assaf female newborn lambs were penned individually and assigned randomly to 1 of 2 treatment groups (n = 20 per treatment). The first group of lambs was fed MR ad libitum (ADLB), whereas the second one (restricted, RES) only received approximately 62.5% of the MR intake measured in the ADLB group. All the lambs were weighed twice a week until they were 35 d old. Then 8 lambs from each group were killed and a morphological study of the gut was performed. Moreover, a piece of liver was cut to measure fat content and oxidative status. The rest of the ewe lambs (24) were weaned and offered a total mixed ration ad libitum to calculate the RFI during the replacement phase. Plasma samples were collected when ewe lambs were 8 mo old to perform a nontargeted metabolomic analysis on a hybrid quadrupole-time-of-flight mass spectrometer coupled to an ultra-high-performance liquid chromatographic system. Progesterone was also measured weekly on serum samples by sequential competitive immunoassay until the end of the experiment (9.5 mo old). The results observed indicate that moderated MR restriction promoted differences in the morphology of the gut of the 35-d-old lambs, but not in the apparent digestibility or feed efficiency traits (RFI) during the replacement phase. However, there was a trend toward reduced live body weight of the RES ewe lambs when they were 9.5 mo old. Moreover, progesterone patterns revealed that only 1 RES versus 4 ADLB ewe lambs had ovulated for the first time at the end of the experiment. This evidence suggests the existence of long-term effects caused by early feed restriction with negative consequences on live body weight and reproductive traits of replacement ewe lambs.

Parental nutritional programming and a reminder during juvenile stage affect growth, lipid metabolism and utilisation in later developmental stages of a marine teleost, the gilthead sea bream (Sparus aurata)

Nutrition during periconception and early development can modulate metabolic routes to prepare the offspring for adverse conditions through a process known as nutritional programming. In gilthead sea bream, replacement of fish oil (FO) with linseed oil (LO) in broodstock diets improves growth in the 4-month-old offspring challenged with low-FO and low-fishmeal (FM) diets for 1 month. The present study further investigated the effects of broodstock feeding on the same offspring when they were 16 months old and were challenged for a second time with the low-FM and low-FO diet for 2 months. The results showed that replacement of parental moderate-FO feeding with LO, combined with juvenile feeding at 4 months old with low-FM and low-FO diets, significantly (P<0·05) improved offspring growth and feed utilisation of low-FM/FO diets even when they were 16 months old: that is, when they were on the verge of their first reproductive season. Liver fatty acid composition was significantly affected by broodstock or reminder diets as well as by their interaction. Moreover, the reduction of long-chain PUFA and increase in α-linolenic acid and linoleic acid in broodstock diets lead to a significant down-regulation of hepatic lipoprotein lipase (P<0·001) and elongation of very long-chain fatty acids protein 6 (P<0·01). Besides, fatty acid desaturase 2 values were positively correlated to hepatic levels of 18 : 4n-3, 18 : 3n-6, 20 : 5n-3, 22 : 6n-3 and 22 : 5n-6. Thus, this study demonstrated the long-term nutritional programming of gilthead sea bream through broodstock feeding, the effect of feeding a ‘reminder’ diet during juvenile stages to improve utilisation of low-FM/FO diets and fish growth as well as the regulation of gene expression along the fish’s life-cycle.