Correlated response to selection for litter size environmental variability in rabbits' resilience

Sequence variants associated with resilient responses in growing pigs

The current work aimed to identify genomic regions and candidate genes associated with resilience in pigs. In previous work, we proposed the body weight deviation from the expected growth curve (ΔBW) and the increase of the positive acute-phase protein haptoglobin (ΔHP) after a vaccine challenge as resilience indicators which may be improved through selective breeding in pigs. Individuals with steady growth rate and minor activation of haptoglobin (high ΔBW and low ΔHP values) were considered resilient. In contrast, pigs with perturbed growth rate and high activation of haptoglobin (low ΔBW and high ΔHP values) were considered susceptible. Both ∆BW and ∆HP were simultaneously considered to select the most resilient (N = 40) and susceptible (N = 40) pigs. A genome-wide association study was carried out for the pigs' response classification to the challenge test using whole-genome sequence data (7,760,720 variants). Eleven associated genomic regions were identified, harbouring relevant candidate genes related to the immune response (such as pro- and anti-inflammatory responses) and growth pathways. These associated genomic regions harboured 41 potential functional mutations (frameshift, splice donor, splice acceptor, start loss and stop loss/gain) in candidate genes. Overall, this study advances our knowledge about the genetic determinism of resilience, highlighting its polygenic nature and strong relationship with immunity and growth.

Quantifying resistance to myxomatosis in wild rabbits produces novel evolutionary insights

Wild rabbits in Australia developed genetic resistance to the myxoma virus, which was introduced as a biological control agent. However, little is known about the rate at which this evolutionary change occurred. We collated data from challenge trials that estimated rabbit resistance to myxomatosis in Australia and expressed resistance on a continuous scale, enabling trends in its development to be assessed over 45 years up to 1995. Resistance initially increased rapidly, followed by a plateau lasting ten years, before a second rapid increase occurred associated with the introduction of European rabbit fleas as myxoma virus vectors. By contrast, in the United Kingdom, where rabbit flea vectors were already present when the myxoma virus initially spread, resistance developed more slowly. No estimates of rabbit resistance to myxomatosis have been made for almost 30 years, despite other highly lethal rabbit pathogens becoming established worldwide. Continued testing of wild-caught rabbits in Australia to determine current levels of resistance to myxomatosis is recommended to assess its current effectiveness for managing pest rabbits. Given the economic and environmental significance of invasive rabbits, it would be remiss to manage such biological resources and ecosystem services poorly.

Selection for environmental variance shifted the gut microbiome composition driving animal resilience

BACKGROUND

Understanding how the host's microbiome shapes phenotypes and participates in the host response to selection is fundamental for evolutionists and animal and plant breeders. Currently, selection for resilience is considered a critical step in improving the sustainability of livestock systems. Environmental variance (V _E), the within-individual variance of a trait, has been successfully used as a proxy for animal resilience. Selection for reduced V _E could effectively shift gut microbiome composition; reshape the inflammatory response, triglyceride, and cholesterol levels; and drive animal resilience. This study aimed to determine the gut microbiome composition underlying the V _E of litter size (LS), for which we performed a metagenomic analysis in two rabbit populations divergently selected for low (n = 36) and high (n = 34) V _E of LS. Partial least square-discriminant analysis and alpha- and beta-diversity were computed to determine the differences in gut microbiome composition among the rabbit populations.

RESULTS

We identified 116 KEGG IDs, 164 COG IDs, and 32 species with differences in abundance between the two rabbit populations studied. These variables achieved a classification performance of the V _E rabbit populations of over than 80%. Compared to the high V _E population, the low V _E (resilient) population was characterized by an underrepresentation of Megasphaera sp., Acetatifactor muris, Bacteroidetes rodentium, Ruminococcus bromii, Bacteroidetes togonis, and Eggerthella sp. and greater abundances of Alistipes shahii, Alistipes putredinis, Odoribacter splanchnicus, Limosilactobacillus fermentum, and Sutterella, among others. Differences in abundance were also found in pathways related to biofilm formation, quorum sensing, glutamate, and amino acid aromatic metabolism. All these results suggest differences in gut immunity modulation, closely related to resilience.

CONCLUSIONS

This is the first study to show that selection for V _E of LS can shift the gut microbiome composition. The results revealed differences in microbiome composition related to gut immunity modulation, which could contribute to the differences in resilience among rabbit populations. The selection-driven shifts in gut microbiome composition should make a substantial contribution to the remarkable genetic response observed in the V _E rabbit populations. Video Abstract.

Effect of environmental variance-based resilience selection on the gut metabolome of rabbits

BACKGROUND

Gut metabolites are key actors in host-microbiota crosstalk with effect on health. The study of the gut metabolome is an emerging topic in livestock, which can help understand its effect on key traits such as animal resilience and welfare. Animal resilience has now become a major trait of interest because of the high demand for more sustainable production. Composition of the gut microbiome can reveal mechanisms that underlie animal resilience because of its influence on host immunity. Environmental variance (V_E), specifically the residual variance, is one measure of resilience. The aim of this study was to identify gut metabolites that underlie differences in the resilience potential of animals originating from a divergent selection for V_E of litter size (LS). We performed an untargeted gut metabolome analysis in two divergent rabbit populations for low (n = 13) and high (n = 13) V_E of LS. Partial least square-discriminant analysis was undertaken, and Bayesian statistics were computed to determine dissimilarities in the gut metabolites between these two rabbit populations.

RESULTS

We identified 15 metabolites that discriminate rabbits from the divergent populations with a prediction performance of 99.2% and 90.4% for the resilient and non-resilient populations, respectively. These metabolites were suggested to be biomarkers of animal resilience as they were the most reliable. Among these, five that derived from the microbiota metabolism (3-(4-hydroxyphenyl)lactate, 5-aminovalerate, and equol, N6-acetyllysine, and serine), were suggested to be indicators of dissimilarities in the microbiome composition between the rabbit populations. The abundances of acylcarnitines and metabolites derived from the phenylalanine, tyrosine, and tryptophan metabolism were low in the resilient population and these pathways can, therefore impact the inflammatory response and health status of animals.

CONCLUSIONS

This is the first study to identify gut metabolites that could act as potential resilience biomarkers. The results support differences in resilience between the two studied rabbit populations that were generated by selection for V_E of LS. Furthermore, selection for V_E of LS modified the gut metabolome, which could be another factor that modulates animal resilience. Further studies are needed to determine the causal role of these metabolites in health and disease.

A genome-wide screen for resilient responses in growing pigs

Background

There is a growing interest to decipher the genetic background of resilience and its possible improvement through selective breeding. The objective of the present study was to provide new insights into the genetic make-up of resilience in growing pigs by identifying genomic regions and candidate genes associated with resilience indicators. Commercial Duroc pigs were challenged with an attenuated Aujeszky vaccine at 12 weeks of age. Two resilience indicators were used: deviation from the expected body weight at 16 weeks of age given the growth curve of non-vaccinated pigs (∆BW) and the increase in acute-phase protein haptoglobin at four days post-vaccination (∆HP). Genome-wide association analyses were carried out on 445 pigs, using genotypes at 41,165 single nucleotide polymorphisms (SNPs) and single-marker and Bayesian multiple-marker regression approaches.

Results

Genomic regions on pig chromosomes 2, 8, 9, 11 (∆BW) and 8, 9, 13 (∆HP) were found to be associated with the resilience indicators and explained high proportions of their genetic variance. The genomic regions that were associated explained 27 and 5% of the genetic variance of ∆BW and ∆HP, respectively. These genomic regions harbour promising candidate genes that are involved in pathways related to immune response, response to stress, or signal transduction (CD6, PTGDR2, IKZF1, RNASEL and MYD88), and growth (GRB10 and LCORL).

Conclusions

Our study identified novel genomic regions that are associated with two resilience indicators (∆BW and ∆HP) in pigs. These associated genomic regions harbour potential candidate genes involved in immune response and growth pathways, which emphasise the strong relationship between resilience and immune response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00739-1.

Genetic factors of functional traits

Selection of functional traits is a challenge for researchers, but an increasingly necessary objective due to the growing concern regarding animal welfare and overcoming the problems of reducing antibiotic use in rabbit production without undermining the animals’ productivity. The aim of this review is to discuss the genetic control of resistance to diseases, longevity and variability of birth weight within a litter, or litter size variability at birth within doe, describing the selection programmes and the first results from a multi-omics analysis of resistance/susceptibility to diseases. The heritability is around 0.13 for longevity, 0.01 for uniformity in birth weight, 0.09 for litter size variability and around 0.11 for disease resistance. Genetic correlations between functional traits and production traits are mostly no different from zero, or are moderately favourable in some cases. Six selection programmes developed in three countries are reviewed. Line foundation with high pressure for selection or divergent selection experiments are different methodologies used, and favourable responses to selection have been achieved. Genomics studies have revealed associations in regions related to immune system functionality and stress in lines selected for litter size variability. Knowledge of the role of gut microbiota in the rabbit’s immune response is very limited. A multi-omics approach can help determine the microbial mechanisms in regulation immunity genes of the host.

Fatty Acid Profile of Blood Plasma at Mating and Early Gestation in Rabbit

The aim of this study was to analyse the fatty acid (FA) profile of blood plasma at mating and 72 hpm by gas chromatography. Moreover, the correlation between FA and ovulation rate, normal embryos and compacted morulae was estimated. Palmitic, linoleic, oleic and stearic were the highest FA concentrations at mating and 72 hpm. Most long chain saturated and PUFA were higher at 72 hpm than at mating, while MUFA were higher at mating. SFA, MUFA and PUFA were high and positively correlated. Correlation was 0.643 between MUFA at mating and ovulation rate, and 0.781 between MUFA and normal embryos, respectively. Compacted morulae were slightly correlated with SFA at mating (0.465). In conclusion, the FA profile of plasma varies depending on the reproductive cycle of the rabbit female, adapting to energetic requirements at mating and early gestation. Moreover, positive correlations are found between fatty acids and ovulation rate and embryo development and quality.

A Methodology to Quantify Resilience in Growing Pigs

Simple Summary

The concept of resilience can be defined as the ability of animals to maintain their productivity despite the stressors that might occur during the rearing period. Despite the growing interest in the genetic determinism of resilience and its possible inclusion in selection objectives, there is no straightforward method to measure this trait. Several quantifying methods estimate resilience based on productivity such as body weight or milk production, or non-productivity related traits such as immunity or stress responses. The objective of this study was to elaborate novel resilience indicators in growing pigs based on both productivity (body weight) and non-productivity (acute-phase proteins) related traits. We propose the deviation from the expected growth curve and the increment of the acute-phase protein haptoglobin, after applying a common vaccine, as resilience indicators in growing pigs under standard rearing conditions. We showed that the suggested resilience indicators are under a genetic control, show a substantial variability in the population, and may be improved through selection.

Abstract

There is a growing concern about the genetic determinism of resilience and its possible implementation in breeding programs. The objective of our study was to elaborate novel resilience indicators in growing pigs based on the deviation from the expected growth curve and the increment of the acute-phase protein haptoglobin (HP) after applying a common vaccine. A total of 445 pigs were vaccinated with an attenuated Aujeszky vaccine at 12 weeks of age. Deviation from the expected body weight (ΔBW) given the growth curve of unvaccinated pigs at 28 days post-vaccination (DPV) and the increment of HP at 4 DPV (ΔHP) were suggested as resilience indicators. Challenged pigs that maintained their productivity and had a minor activation of HP were deemed resilient, whereas pigs that had low ∆BW values and a high activation of HP were deemed susceptible. Pigs were also classified based on ∆BW and ∆HP relative to the expected BW at 28 DPV and to the basal level of HP, respectively. The concordance was high between both methods, indicating that ΔBW and ΔHP are not sensitive to the animal’s expected BW nor the basal level of HP. The heritability estimates were moderate for ∆BW (0.33) and low-to-moderate for ∆HP (0.16). Our study suggests ΔBW and ΔHP as novel resilience indicators in pigs. The suggested indicators capture different aspects of resilience, are easy to measure, and are genetically controlled. Thus, they may be improved through selective breeding. Further analyses are needed to validate our findings.

Selection for environmental variance of litter size in rabbits involves genes in pathways controlling animal resilience

Background

Environmental variance (V_E) is partially under genetic control, which means that the V_E of individuals that share the same environment can differ because they have different genotypes. Previously, a divergent selection experiment for V_E of litter size (LS) during 13 generations in rabbit yielded a successful response and revealed differences in resilience between the divergent lines. The aim of the current study was to identify signatures of selection in these divergent lines to better understand the molecular mechanisms and pathways that control V_E of LS and animal resilience. Three methods (F_ST, ROH and varLD) were used to identify signatures of selection in a set of 473 genotypes from these rabbit lines (377) and a base population (96). A whole-genome sequencing (WGS) analysis was performed on 54 animals to detect genes with functional mutations.

Results

By combining signatures of selection and WGS data, we detected 373 genes with functional mutations in their transcription units, among which 111 had functions related to the immune system, stress response, reproduction and embryo development, and/or carbohydrate and lipid metabolism. The genes TTC23L, FBXL20, GHDC, ENSOCUG00000031631, SLC18A1, CD300LG, MC2R, and ENSOCUG00000006264 were particularly relevant, since each one carried a functional mutation that was fixed in one of the rabbit lines and absent in the other line. In the 3ʹUTR region of the MC2R and ENSOCUG00000006264 genes, we detected a novel insertion/deletion (INDEL) variant.

Conclusions

Our findings provide further evidence in favour of V_E as a measure of animal resilience. Signatures of selection were identified for V_E of LS in genes that have a functional mutation in their transcription units and are mostly implicated in the immune response and stress response pathways. However, the real implications of these genes for V_E and animal resilience will need to be assessed through functional analyses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00653-y.

Effect of Postbiotic Based on Lactic Acid Bacteria on Semen Quality and Health of Male Rabbits

The aim of this study was to evaluate the effect of lactic acid bacteria-based postbiotic supplementation on semen characteristics and hematological and biochemical profiles in rabbits. A total of 28 males were randomly allocated into two groups. Males received a Control diet and Enriched diet supplemented with postbiotic for 15 weeks (4 weeks of adaptation period and 11 weeks of experimental period). Body weight, feed intake and semen characteristics were recorded weekly. Hematological profile was recorded at the beginning and end of the experiment and biochemical profile at 0, 5, 10 and 15 weeks. Bayesian methodology was used for the statistical analysis. Feed intake was higher in Control diet (125.2 g) than in the Enriched diet (118.6 g, p = 1.00). The percentages of abnormal spermatozoa were higher in Control diet than in Enriched diet (30% and 22%; p = 0.93) and the acrosome integrity percentage was lower (97% and 96%; p = 0.87). The hematological profile was within the range for healthy rabbits. The plasmatic level of alanine aminotransferase was higher in Control diet than Enriched diet at 5 and 10 weeks (p = 0.93 and p = 0.94, respectively) and alkaline phosphatase was similar in Control diet throughout the experiment, but decreased in Enriched diet (p = 0.97). No difference was found in kidney parameters (uric nitrogen and creatinine). Enriched diet showed higher total protein and globulin than Control diet (p = 0.99). Phosphorus was lower (p = 0.92) in Control diet than in Enriched diet. In conclusion, the addition of the postbiotic based on lactic acid bacteria seems to improve the quality of the semen and the liver profile in rabbits.

Correlated Response to Selection for Litter Size Residual Variability in Rabbits’ Body Condition

A divergent selection experiment for residual variance of litter size at birth was carried out in rabbits during twelve generations. Residual variance of litter size was estimated as the within-doe variance of litter size after pre-correction for year and season as well as parity and lactation status effects. The aim of this work was to study the correlated response to selection for litter size residual variability in body condition from mating to weaning. Body condition is related directly to an animal’s fat deposits. Perirenal fat is the main fat deposit in rabbits. Individual body weight (IBW) and perirenal fat thickness (PFT) were used to measure body condition at second mating, delivery, 10 days after delivery, and weaning. Litter size of the first three parities was analyzed. Both lines decreased body condition between mating to delivery; however, the decrease in body condition at delivery was lower in the low line, despite this line having higher litter size at birth (+0.54 kits, p = 0.93). The increment of body condition between delivery and early lactation was slightly higher in the low line. On the other hand, body condition affected success of females’ receptivity and fertility at the third mating, e.g., receptive females showed a higher IBW and PFT than unreceptive ones (+129 g and +0.28 mm, respectively), and fertile females had a higher IBW and PFT than unfertile ones (+82 g and +0.28 mm, respectively). In conclusion, the does selected for reducing litter size variability showed a better deal with situations of high-energy demand, such as delivery and lactation, than those selected for increasing litter size variability, which would agree with the better health and welfare condition in the low line.

Inflammatory Correlated Response in Two Lines of Rabbit Selected Divergently for Litter Size Environmental Variability

A divergent selection experiment for environmental variance of litter size variance was carried out in rabbits over thirteen generations. The aim of this study was to evaluate the inflammatory response in the two lines of the experiment, in order to analyse the effect of selection on susceptibility to diseases after challenging to stressful situations, such as 24 h after the first delivery. A total of 78 females were used in this study, 39 from each line. The line selected for litter size heterogeneity (the high line) showed lower white blood leukocyte count (WBC; -0.87 × 103/µL), lower percentage of basophils (-0.11%), higher concentration of TNF-α (+13.8 pg/mL), and greater concentration of CRP (+38.1 µg/mL) than the line selected for litter size homogeneity (the low line). The high line had also higher concentrations of bilirubin, cholesterol, gamma-glutamyl transferase (GGT) and alkaline phosphatase (ALP) compared to the low line (difference between lines were +0.08 µmol/L, +0.14 µmol/L, +0.35 U/L and +2.4 U/L, respectively). The high line showed higher inflammatory response than the low line, in accordance with a larger susceptibility to infectious disorders. In conclusion, the line selected to increase litter size environmental variability seems to have poor capacity coping with environmental stressors. Therefore, selection for litter size environmental variability can be a useful way to improve animal welfare.

Selection Response in a Divergent Selection Experiment for Birth Weight Variability in Mice Compared with a Control Line

Birth weight (BW) in animal production is an economically important trait in prolific species. The laboratory mouse (Mus musculus) is used as an experimental animal because it is considered a suitable model for prolific species such as rabbits and pigs. Two mouse lines were divergently selected for birth weight variability with a third line of non-selected control population of the same origin as the animals starting the experiment. The objective of this study was, therefore, to compare and evaluate the differential response of each line. The animals were from the 17th generation of both low and high BW variability lines of the divergent selection experiment, including in addition animals from the control line. The dataset contained 389 records from 48 litters of the high line, 734 records from 73 litters of the low line, and 574 records from 71 litters of the control line. The studied traits were as follows: the BW, the BW variance, the BW standard deviation, the BW coefficient of variation within-litter, the weaning weight (WW), the litter size at birth and at weaning, the weight gain, and the preweaning survival. The model included the line effect jointly with the parturition number and its interaction, the linear and quadratic LS as covariates except for the LS trait itself when analyzing litter traits, as well as the pup sex when analyzing individual traits. The low line had a lower BW and WW, but a higher litter size, and greater robustness owing to a higher survival at weaning. As a model of livestock animals, the findings from this experiment led to a proposal of selection for pig production that would combine an increase in litter size with higher survival and welfare. Compared with the control line, a much higher response was observed in the low variability line than in the high line, making it extremely satisfactory given that homogeneity provides advantages in terms of animal welfare and robustness.

Identification of functional mutations associated with environmental variance of litter size in rabbits

Background

Environmental variance (V_E) is partly under genetic control and has recently been proposed as a measure of resilience. Unravelling the genetic background of the V_E of complex traits could help to improve resilience of livestock and stabilize their production across farming systems. The objective of this study was to identify genes and functional mutations associated with variation in V_E of litter size (LS) in rabbits. To achieve this, we combined the results of a genome-wide association study (GWAS) and a whole-genome sequencing (WGS) analysis using data from two divergently selected rabbit lines for high and low V_E of LS. These lines differ in terms of biomarkers of immune response and mortality. Moreover, rabbits with a lower V_E of LS were found to be more resilient to infections than animals with a higher V_E of LS.

Results

By using two GWAS approaches (single-marker regression and Bayesian multiple-marker regression), we identified four genomic regions associated with V_E of LS, on chromosomes 3, 7, 10, and 14. We detected 38 genes in the associated genomic regions and, using WGS, we identified 129 variants in the splicing, UTR, and coding (missense and frameshift effects) regions of 16 of these 38 genes. These genes were related to the immune system, the development of sensory structures, and stress responses. All of these variants (except one) segregated in one of the rabbit lines and were absent (n = 91) or fixed in the other one (n = 37). The fixed variants were in the HDAC9, ITGB8, MIS18A, ENSOCUG00000021276 and URB1 genes. We also identified a 1-bp deletion in the 3′UTR region of the HUNK gene that was fixed in the low V_E line and absent in the high V_E line.

Conclusions

This is the first study that combines GWAS and WGS analyses to study the genetic basis of V_E. The new candidate genes and functional mutations identified in this study suggest that the V_E of LS is under the control of functions related to the immune system, stress response, and the nervous system. These findings could also explain differences in resilience between rabbits with homogeneous and heterogeneous V_E of litter size.

Litter Survival Differences between Divergently Selected Lines for Environmental Sensitivity in Rabbits

Simple Summary

Two rabbit lines are divergently selected for increasing or decreasing the variability of litter size at birth. Decreasing the litter size variability produces more resilient females with less sensitivity to diseases, being an indirect selection way to improve environmental sensitivity. The kits’ survival rate at weaning was higher in the homogeneous line. Moreover, this line led to a greater uniformity of the kits’ weight at weaning, although the weight variability at birth was higher, which could be due to a higher lactation capacity of the homogeneous line.

Abstract

A divergent selection experiment on environmental sensitivity was performed in rabbits. The aim was to estimate the correlated response in kit weight and survival, litter weight, and weight distance from birth to weaning. The weight distance was calculated as the absolute value of the differences between the individual value and the mean value of its litter. The relationship between the probability of survival at 4 d of age, and the weight at birth, was studied. Environmental sensitivity was measured as litter size variability. A total of 2484 kits from 127 does from the low line, and 1916 kits of 114 does from the high line of the 12th generation were weighed. Both of the lines showed similar individual and litter weights at birth and weaning, and a similar survival rate at birth, and at 4 d of age. The survival rate at weaning was higher in the low line (0.67 and 0.62; P = 0.93). The weight distance was higher at birth, but lower at weaning in the low line (47.8 g and 54.1 g; P = 0.98). When the weight at birth was high, the kits had a higher survival rate. In conclusion, selection for environmental sensitivity showed a correlated response in the kits’ survival, and in the homogeneity of litter weight at weaning.