Interaction of direct and social genetic effects with feeding regime in growing rabbits

Genetic analysis of feed efficiency and novel feeding behavior traits measured in group-housed broilers using electronic feeders

This study aimed to estimate genetic parameters for feeding behavior (FB) traits and to assess their genetic relationship with performance traits in group-housed broilers. In total, 99,472,151 visits were recorded for 95,711 birds between 2017 and 2022 using electronic feeders. The visits were first clustered into 2,667,617 daily observations for ten FB traits: daily feed intake (DFI), daily number of visits (NVIS), time spent at the feeders (TSF), number of visited feeders (NVF), visiting activity interval (VAI), feeding rate (FR), daily number of meals (NMEAL), average intake per meal (INTMEAL), number of visits per meal (VISMEAL) and interval between meals (MEALIVL). All FB traits were then considered as the average per bird across the feeding test period. Three growth traits (body weight at the start - SBW and at the end of the feeding test - FBW, and weight gain over the test period - BWG), and 2 feed efficiency (FE) traits (Feed Conversion Rate - FCR and Residual Feed Intake - RFI) were also recorded. The (co)variance components were estimated using multitrait animal mixed models. For growth and FE, the heritability (h2) estimates were moderate, ranging from 0.20 ± 0.01 (BWG) to 0.32 ± 0.02 (RFI). Overall, the h2 estimates for FB traits were higher than for productive traits, ranging from 0.31 ± 0.01 (DFI) to 0.56 ± 0.02 (TSF). DFI presented high genetic correlations (0.53-0.86) with all performance traits. Conversely, the remaining FB traits presented null to moderate genetic correlations with these traits, ranging from -0.38 to 0.42 for growth traits and between -0.14 and 0.25 for FE traits. Genetic selection for favorable feeding behavior is expected to exhibit a fast genetic response. The results suggest that it is possible to consider different feeding strategies without compromising the genetic progress of FE. Conversely, breeding strategies prioritizing a higher bird activity might result in lighter broiler lines in the long term, given the negative genetic correlations between visit-related traits (NV, NVF, and NMEAL) and growth traits (SBW and FBW).

Conditional indirect genetic effects of caregivers on brood in the clonal raider ant

Caregivers shape the rearing environment of their young. Consequently, offspring traits are influenced by the genes of their caregivers via indirect genetic effects (IGEs). However, the extent to which IGEs are modulated by environmental factors, other than the genotype of social partners (i.e., intergenomic epistasis), remains an open question. Here we investigate how brood are influenced by the genotype of their caregivers in the clonal raider ant, Ooceraea biroi, a species in which the genotype, age and number of both caregivers and brood can be experimentally controlled. First, we used four clonal lines to establish colonies that differed only in the genotype of caregivers and measured effects on foraging activity, as well as IGEs on brood phenotypes. In a second experiment, we tested whether these IGEs are conditional on the age and number of caregivers. We found that caregiver genotype affected the feeding and foraging activity of colonies, and influenced the rate of development, survival, body size, and caste fate of brood. Caregiver genotype interacted with other factors to influence the rate of development and survival of brood, demonstrating that IGEs can be conditional. Thus, we provide an empirical example of phenotypes being influenced by IGE-by-environment interactions beyond intergenomic epistasis, highlighting that IGEs of caregivers/parents are alterable by factors other than their brood's/offspring's genotype.

Genotype by heat conditions interaction effects on growth and litter traits in rabbits

Heat stress has severe impacts on rabbit performance because they have difficulty getting rid of excess heat. The interaction between genetic and environmental factors plays a vital role in the adaptation process. The current study aimed to evaluate the effects of interaction between the genotype and heat conditions (G×H) on litter size and growth traits. Two rabbit lines were used in the current study, Egyptian maternal line (APRI) and New Zealand White (NZW). The rabbits were raised under normal (22°C) or heat stress (35°C) conditions. The does were raised in individual cages, and their kits were reared under the same conditions. Negative effects of heat conditions were noted for litter traits, as heat stress had significantly reduced the number of born alive, total born, and marketed number rabbits by about 16, 11, and 25%, respectively. Moreover, growth traits were reduced under heat stress conditions compared to normal temperature conditions. Significant differences between genotypes were observed, APRI rabbits were higher than NWZ rabbits in the total born, number of born alive, number weaned, and the number of marketed rabbits by 10, 8, 11, and 10%, respectively. Genotype by heat conditions interaction effects were observed, APRI litters under normal conditions showed significantly higher litter traits than NWZ litters, whereas relevant reductions in litter traits of APRI line than NZW litters when reared in heat conditions. For growth traits, the differences between the two lines under normal conditions were reduced when animals of the two lines were raised under heat stress, for BW28, BW42, BW63, ADG28-42, and DF28-42 while these differences were increased for ADG42-63, DF28-42 and feed conversion during the whole fattening period. Based on the observed G × H interactions, it is important to select the animals under the same production conditions to raise rabbits that can cope with the expected global warming conditions.

Genotype by feeding regimen interactions for slaughter traits in rabbit and expected responses under restricted and full feeding

The interaction between the genotype and feeding regimen (G×FR) for slaughter traits was estimated from data corresponding to 2557 animals under full (FF) and 2424 with restricted feeding (RF). Expected responses to selection under different scenario regarding feeding regimen were also calculated. Body weight at slaughter (SW), carcass weight (CW) and dressing out percentage (DoP) were analysed by using linear animal models in which records obtained under different feeding regimes were treated as different traits. Animals belonged to Caldes line, selected for average daily gain (G) under ad libitum feeding. The selection process information was included in the analyses. Marginal posterior mean of heritabilities were 0.102 for G, and 0.364, 0.257 and 0.167 for SW, CW and DoP under FF feeding. The corresponding values for animals fed on RF were 0.243, 0.203 and 0.379 for SW, CW and DoP, respectively. Genetic correlations between G and CW were positive and moderate, and those between G and DoP were low. The estimated genetic correlation between SW, CW and DoP under different feeding regimens were: 0.73, 0.69 and 0.87, respectively. These correlations cannot be said to be far enough from one to generate relevant G×FR interaction variance, which were estimated to be only 11.1%, 8.6% and 5.3% of the mean of the phenotypic variance for SW, CW and DoP, respectively. This lack of G×FR interaction variance, jointly with the higher heritability of DoP under RF, explains that the genetic improvement of DoP can be done more efficiently recording traits on animals under RF, even if the interest is on the performances under FF, i.e. by indirect selection.

Anticipated effects of abiotic environmental change on intraspecific social interactions

Social interactions are ubiquitous across the animal kingdom. A variety of ecological and evolutionary processes are dependent on social interactions, such as movement, disease spread, information transmission, and density-dependent reproduction and survival. Social interactions, like any behaviour, are context dependent, varying with environmental conditions. Currently, environments are changing rapidly across multiple dimensions, becoming warmer and more variable, while habitats are increasingly fragmented and contaminated with pollutants. Social interactions are expected to change in response to these stressors and to continue to change into the future. However, a comprehensive understanding of the form and magnitude of the effects of these environmental changes on social interactions is currently lacking. Focusing on four major forms of rapid environmental change currently occurring, we review how these changing environmental gradients are expected to have immediate effects on social interactions such as communication, agonistic behaviours, and group formation, which will thereby induce changes in social organisation including mating systems, dominance hierarchies, and collective behaviour. Our review covers intraspecific variation in social interactions across environments, including studies in both the wild and in laboratory settings, and across a range of taxa. The expected responses of social behaviour to environmental change are diverse, but we identify several general themes. First, very dry, variable, fragmented, or polluted environments are likely to destabilise existing social systems. This occurs as these conditions limit the energy available for complex social interactions and affect dissimilar phenotypes differently. Second, a given environmental change can lead to opposite responses in social behaviour, and the direction of the response often hinges on the natural history of the organism in question. Third, our review highlights the fact that changes in environmental factors are not occurring in isolation: multiple factors are changing simultaneously, which may have antagonistic or synergistic effects, and more work should be done to understand these combined effects. We close by identifying methodological and analytical techniques that might help to study the response of social interactions to changing environments, highlight consistent patterns among taxa, and predict subsequent evolutionary change. We expect that the changes in social interactions that we document here will have consequences for individuals, groups, and for the ecology and evolution of populations, and therefore warrant a central place in the study of animal populations, particularly in an era of rapid environmental change.

Networks of inbreeding coefficients in a selected population of rabbits

The correlation between pedigree and genomic-based inbreeding coefficients is usually discussed in the literature. However, some of these correlations could be spurious. Using partial correlations and information theory, it is possible to distinguish a significant association between two variables which is independent from associations with a third variable. The objective of this study is to implement partial correlations and information theory to assess the relationship between different inbreeding coefficients using a selected population of rabbits. Data from pedigree and genomic information from a 200K SNP chip were available. After applying filtering criteria, the data set comprised 437 animals genotyped for 114,604 autosomal SNP. Fifteen pedigree- and genome-based inbreeding coefficients were estimated and used to build a network. Recent inbreeding coefficient based on runs of homozygosity had 9 edges linking it with different inbreeding coefficients. Partial correlations and information theory approach allowed to infer meaningful associations between inbreeding coefficients and highlighted the importance of the recent inbreeding based on runs of homozygosity, but a good proxy of it could be those pedigree-based definitions reflecting recent inbreeding.

Rederivation by Cryopreservation of a Paternal Line of Rabbits Suggests Exhaustion of Selection for Post-Weaning Daily Weight Gain after 37 Generations

Rabbit selection programmes have mainly been evaluated using unselected or divergently selected populations, or populations rederived from cryopreserved embryos after a reduced number of generations. Nevertheless, unselected and divergent populations do not avoid genetic drift, while rederived animals seem to influence phenotypic traits such as birth and adult weights or prolificacy. The study aimed to evaluate the effect of a long-term selection for post-weaning average daily weight gain (ADG) over 37 generations with two rederived populations. Specifically, two coetaneous populations were derived from vitrified embryos with 18 generational intervals (R19 and R37), reducing or avoiding genetic drift and environmental and cryopreservation effects. After two generations of both rederived populations (R21 vs. R39 generations), all evaluated traits showed some progress as a result of the selection, the response being 0.113 g/day by generation. This response does not seem to affect the estimated Gompertz growth curve parameters in terms of the day, the weight at the inflexion point or the adult weight. Moreover, a sexual dimorphism favouring females was observed in this paternal line. Results demonstrated that the selection programme had improved ADG without variations in adult body weight but, after 37 generations of selection, this trait seems exhausted. Given the reduction in the cumulative reproductive performance and as a consequence in the selection pressure, or possibly/perhaps due to an unexpected effect, rederivation could be the cause of this weak selection response observed from generation 18 onwards.

Genome-wide association study for feed efficiency in collective cage-raised rabbits under full and restricted feeding

Feed efficiency (FE) is one of the most economically and environmentally relevant traits in the animal production sector. The objective of this study was to gain knowledge about the genetic control of FE in rabbits. To this end, GWASs were conducted for individual growth under two feeding regimes (full feeding and restricted) and FE traits collected from cage groups, using 114 604 autosome SNPs segregating in 438 rabbits. Two different models were implemented: (1) an animal model with a linear regression on each SNP allele for growth trait; and (2) a two‐trait animal model, jointly fitting the performance trait and each SNP allele content, for FE traits. This last modeling strategy is a new tool applied to GWAS and allows information to be considered from non‐genotyped individuals whose contribution is relevant in the group average traits. A total of 189 SNPs in 17 chromosomal regions were declared to be significantly associated with any of the five analyzed traits at a chromosome‐wide level. In 12 of these regions, 20 candidate genes were proposed to explain the variation of the analyzed traits, including genes such as FTO, NDUFAF6 and CEBPA previously associated with growth and FE traits in monogastric species. Candidate genes associated with behavioral patterns were also identified. Overall, our results can be considered as the foundation for future functional research to unravel the actual causal mutations regulating growth and FE in rabbits.

Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG)

Background

The mammalian intestinal tract harbors diverse and dynamic microbial communities that play pivotal roles in host health, metabolism, immunity, and development. Average daily gain (ADG) is an important growth trait in meat rabbit industry. The effects of gut microbiota on ADG in meat rabbits are still unknown.

Results

In this study, we investigated the dynamic distribution of gut microbiota in commercial Ira rabbits from weaning to finishing and uncover the relationship between the microbiota and average daily gain (ADG) via 16S rRNA gene sequencing. The results indicated that the richness and diversity of gut microbiota significantly increased with age. Gut microbial structure was less variable among finishing rabbits than among weaning rabbits. The relative abundances of the dominant phyla Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria, and the 15 predominant genera significantly varied with age. Metagenomic prediction analysis showed that both KOs and KEGG pathways related to the metabolism of monosaccharides and vitamins were enriched in the weaning rabbits, while those related to the metabolism of amino acids and polysaccharides were more abundant in the finishing rabbits. We identified 34 OTUs, 125 KOs, and 25 KEGG pathways that were significantly associated with ADG. OTUs annotation suggested that butyrate producing bacteria belong to the family Ruminococcaceae and Bacteroidales_S24-7_group were positively associated with ADG. Conversely, Eubacterium_coprostanoligenes_group, Christensenellaceae_R-7_group, and opportunistic pathogens were negatively associated with ADG. Both KOs and KEGG pathways correlated with the metabolism of vitamins, basic amino acids, and short chain fatty acids (SCFAs) showed positive correlations with ADG, while those correlated with aromatic amino acids metabolism and immune response exhibited negative correlations with ADG. In addition, our results suggested that 10.42% of the variation in weaning weight could be explained by the gut microbiome.

Conclusions

Our findings give a glimpse into the dynamic shifts in gut microbiota of meat rabbits and provide a theoretical basis for gut microbiota modulation to improve ADG in the meat rabbit industry.

Use of group records of feed intake to select for feed efficiency in rabbit

Models for genetic evaluation of feed efficiency (FE) for animals housed in groups when they are either fed ad libitum (F) or on restricted (R) feeding were implemented. Definitions of FE on F included group records of feed intake ( FI ¯ F ) and individual records of growth rate (G_F ) and metabolic weight (M_F ). Growth rate (G_R ) as FE measurement on R was used. Data corresponded to 5,336 kits from a rabbit sire line, from 1,255 litters in 14 batches and 667 cages. A five-trait mixed model (also with metabolic weight on R, M_R ) was implemented including, for each trait, the systematic effects of batch, body weight at weaning, parity order and litter size; and the random effects of litter, additive genetic and individual. A Bayesian analysis was performed. Conditional traits such as FI ¯ F | M F , G F and G F | M F , FI ¯ F were obtained from elements of additive genetics ( FI ¯ F | M F , G F g and G F | M F , FI ¯ F g ) or phenotypic ( FI ¯ F | M F , G F p and G F | M F , FI ¯ F p ) (co)variance matrices. In the first case, heritabilities were low (0.07 and 0.06 for FI ¯ F | M F , G F g and G F | M F , FI ¯ F g , respectively) but null genetic correlation between the conditional and conditioning traits is guaranteed. In the second case, heritabilities were higher (0.22 and 0.16 for FI ¯ F | M F , G F p and G F | M F , FI ¯ F p , respectively) but the genetic correlation between FI ¯ F | M F , G F p and G F was moderate (0.58). Heritability of G_R was low (0.08). This trait was negatively correlated with G F | M F , FI ¯ F p and G F | M F , FI ¯ F g of animals on F, which indicate a different genetic background. The correlation between G_R and G_F was also low to moderate (0.48) and the additive variance of G_F was almost four times that of G_R , suggesting the presence of a substantial genotype by feeding regimen interaction.

Estimating direct genetic and maternal effects affecting rabbit growth and feed efficiency with a factorial design

The aim of this experiment was to evaluate the significance of neonatal environment on feed efficiency. For that purpose, rabbits from a line selected for residual feed intake (RFI) during 10 generations (G10 kits) were cross-fostered with non-selected control does (i.e., G0 line), and reciprocally. In parallel, sibs were fostered by mothers from their original line. Nine hundred animals were raised in individual (N = 456) or collective (N = 320) cages. Traits analysed in this study were body weight at 32 days and at 63 days, average daily gain (ADG), feed intake between weaning and 63 days (FI), feed conversion ratio (FCR) and RFI. The maternal environment offered by does from the line selected for RFI deteriorated the FCR of the kits, independently of their line of origin, during fattening (+0.08 ± 0.02) compared to FCR of kits nursed by G0 does. The line, the type of housing and the batch were significant effects for all the measured traits: G10 kits were lighter than their G0 counterparts at 32 days (-82.9 ± 9 g, p < 0.0001) and at 63 days (-161 ± 16 g, p < 0.0001). They also had a lower ADG (-2.36 ± 0.36 g/day, p < 0.0001), RFI (-521 ± 24 g/day, p < 0.0001) and a lower FI (-855 ± 31 g, p < 0.0001), resulting in a more desirable feed efficiency (FCR: -0.35 ± 0.02). There was no significant difference in the contrast of G10 and G0 performances between collective and individual/digestive cages (p > 0.22): -2.35 g/day versus 2.94 g/day for ADG, -0.39 versus -0.40 for FCR, -577 g versus -565 g for RFI and -879 g versus -859 g for FI, respectively). Thus, no genotype-by-environment (housing) interaction is expected at the commercial level, that is, no re-ranking of the animals due to collective housing.

Indirect genetic effect model using feeding behaviour traits to define the degree of interaction between mates: an implementation in pigs growth rate

An alternative implementation of the animal model including indirect genetic effect (IGE) is presented considering pair-mate-specific interaction degrees to improve the performance of the model. Data consisted of average daily gain (ADG) records from 663 pigs kept in groups of 10 to 14 mates during the fattening period. Three types of models were used to fit ADG data: (i) animal model (AM); (ii) AM with classical IGE (AM-IGE); and (iii) AM fitting IGE with a specific degree of interaction between each pair of mates (AM-IGE_i). Several feeding behavior phenotypes were used to define the pair-mate-specific degree of interaction in AM-IGE_i: feeding rate (g/min), feeding frequency (min/day), the time between consecutive visits to the feeder (min/day), occupation time (min/day) and an index considering all these variables. All models included systematic effects batch, initial age (covariate), final age (covariate), number of pigs per pen (covariate), plus the random effect of the pen. Estimated posterior mean (posterior SD) of heritability was 0.47 (0.15) using AM. Including social genetic effects in the model, total heritable variance expressed as a proportion of total phenotypic variance (T²) was 0.54 (0.29) using AM-IGE, whereas it ranged from 0.51 to 0.55 (0.12 to 0.14) with AM-IGE_i, depending on the behavior trait used to define social interactions. These results confirm the contribution of IGEs to the total heritable variation of ADG. Moreover, important differences between models were observed in EBV rankings. The percentage of coincidence of top 10% animals between AM and AM-IGE_i ranged from 0.44 to 0.89 and from 0.41to 0.68 between AM-IGE and AM-IGE_i. Based on the goodness of fit and predictive ability, social models are preferred for the genetic evaluation of ADG. Among models including IGEs, when the pair-specific degree of interaction was defined using feeding behavior phenotypes we obtained an increase in the accuracy of genetic parameters estimates, the better goodness of fit and higher predictive ability. We conclude that feeding behavior variables can be used to measure the interaction between pen mates and to improve the performance of models including IGEs.

Longitudinal analysis of direct and indirect effects on average daily gain in rabbits using a structured antedependence model

BACKGROUND

Indirect genetic effects (IGE) are important components of various traits in several species. Although the intensity of social interactions between partners likely vary over time, very few genetic studies have investigated how IGE vary over time for traits under selection in livestock species. To overcome this issue, our aim was: (1) to analyze longitudinal records of average daily gain (ADG) in rabbits subjected to a 5-week period of feed restriction using a structured antedependence (SAD) model that includes IGE and (2) to evaluate, by simulation, the response to selection when IGE are present and genetic evaluation is based on a SAD model that includes IGE or not.

RESULTS

The direct genetic variance for ADG (g/d) increased from week 1 to 3 [from 8.03 to 13.47 (g/d)²] and then decreased [6.20 (g/d)² at week 5], while the indirect genetic variance decreased from week 1 to 4 [from 0.43 to 0.22 (g/d)²]. The correlation between the direct genetic effects of different weeks was moderate to high (ranging from 0.46 to 0.86) and tended to decrease with time interval between measurements. The same trend was observed for IGE for weeks 2 to 5 (correlations ranging from 0.62 to 0.91). Estimates of the correlation between IGE of week 1 and IGE of the other weeks did not follow the same pattern and correlations were lower. Estimates of correlations between direct and indirect effects were negative at all times. After seven generations of simulated selection, the increase in ADG from selection on EBV from a SAD model that included IGE was higher (~ 30%) than when those effects were omitted.

CONCLUSIONS

Indirect genetic effects are larger just after mixing animals at weaning than later in the fattening period, probably because of the establishment of social hierarchy that is generally observed at that time. Accounting for IGE in the selection criterion maximizes genetic progress.