Resistance to infectious diseases is a heritable trait in rabbits

Genome-wide association studies for diarrhoea outcomes identified genomic regions affecting resistance to a severe enteropathy in suckling rabbits

Selection and breeding strategies to improve resistance to enteropathies are essential to reaching the sustainability of the rabbit production systems. However, disease heterogeneity (having only as major visible symptom diarrhoea) and low disease heritability are two barriers for the implementation of these strategies. Diarrhoea condition can affect rabbits at different life stages, starting from the suckling period, with large negative economic impacts. In this study, from a commercial population of suckling rabbits (derived from 133 litters) that experienced an outbreak of enteropathy, we first selected a few animals that died with severe symptoms of diarrhoea and characterized their microbiota, using 16S rRNA gene sequencing data. Clostridium genus was consistently present in all affected specimens. In addition, with the aim to identify genetic markers in the rabbit genome that could be used as selection tools, we performed genome-wide association studies for symptoms of diarrhoea in the same commercial rabbit population. These studies were also complemented with FST analyses between the same groups of rabbits. A total of 332 suckling rabbits (151 with severe symptoms of diarrhoea, 42 with mild symptoms and 129 without any symptoms till the weaning period), derived from 45 different litters (a subset of the 133 litters) were genotyped with the Affymetrix Axiom OrcunSNP Array. In both genomic approaches, rabbits within litters were paired to constitute two groups (susceptible and resistant, including the mildly affected in one or the other group) and run case and control genome-wide association analyses. Genomic heritability estimated in the designed experimental structure integrated in a commercial breeding scheme was 0.19-0.21 (s.e. 0.09-0.10). A total of eight genomic regions on rabbit chromosome 2 (OCU2), OCU3, OCU7, OCU12, OCU13, OCU16 and in an unassembled scaffold had significant single nucleotide polymorphisms (SNPs) and/or markers that trespassed the FST percentile distribution. Among these regions, three main peaks of SNPs were identified on OCU12, OCU13 and OCU16. The QTL region on OCU13 encompasses several genes that encode members of a family of immunoglobulin Fc receptors (FCER1G, FCRLA, FCRLB and FCGR2A) involved in the immune innate system, which might be important candidate genes for this pathogenic condition. The results obtained in this study demonstrated that resistance to an enteropathy occurring in suckling rabbits is in part genetically determined and can be dissected at the genomic level, providing DNA markers that could be used in breeding programmes to increase resistance to enteropathies in meat rabbits.

Robustness scores in fattening pigs based on routinely collected phenotypes: determination and genetic parameters

The objective was to determine operational proxies for robustness based on data collected routinely on farm that allow phenotyping of these traits in fattening pigs, and to estimate their genetic parameters. A total of 7,256 pigs, from two Piétrain paternal lines (Pie and Pie NN), were tested at the AXIOM boar testing station (Azay-sur-Indre, France) from 2019 to 2021. During the fattening period (from 75 to 150 d of age), individual performance indicators were recorded (growth, backfat, loin depth, feed intake, and feed conversion ratio [FCR]) together with indicators such as insufficient growth, observable defect, symptoms of diseases, and antibiotic and anti-inflammatory injections. These indicators were combined into three categorical robustness scores: R1, R2, and R3. Genetic parameters were estimated using an animal linear model. The robustness score R2 (selectable or not selectable animal) that combined information from status at testing and mortality had the highest heritability estimates of 0.08 ± 0.03 for Pie NN line and a value of 0.09 ± 0.02 for Pie line, compared with traits R1 and R3. The score R3 that combines information from the score R2 with antibiotic and anti-inflammatory injections presented slightly lower heritability estimates (0.05 ± 0.02 to 0.07 ± 0.03). Genetic correlations between R2 and R3 were high and favorable (0.93 ± 0.04 to 0.95 ± 0.03) and R2 and R3 can be considered identical with regard to the confidence interval. These two robustness scores were also highly and favorably genetically correlated with initial body weight and average daily gain, and unfavorably correlated with daily feed intake (ranging from 0.73 ± 0.06 to 0.90 ± 0.08). Estimates of genetic correlations of R2 and R3 with backfat depth and raw FCR (not standardized between starting and finishing weights) were moderate and unfavorable (0.20 ± 0.13 to 0.46 ± 0.20). A part of these genetic correlations, that are of low precision due to the number of data available, have to be confirmed on larger datasets. The results showed the interest of using routine phenotypes collected on farm to build simple robustness indicators that can be applied in breeding.

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.

High Heritabilities for Antibiotic Usage Show Potential to Breed for Disease Resistance in Finishing Pigs

The use of antimicrobials in animal production is under public debate, mainly due to the risk of transfer of resistance to pathogenic bacteria in humans. Therefore, measures have been taken during the last few decades to reduce antibiotic usage in animals, for instance, by national monitoring programmes and by improving animal health management. Although some initiatives exist in molecular genetic selection, quantitative genetic selection of animals towards decreased antibiotic usage is an underexplored area to reduce antibiotic usage. However, this strategy could yield cumulative effects. In this study, we derived new phenotypes from on-farm parenteral antibiotic records from commercially grown crossbred finishing pigs used in the progeny test of Piétrain terminal sires to investigate the heritability of antibiotics usage. Parenteral antibiotic records, production parameters and pedigree records of 2238 full-sib pens from two experimental farms in Belgium between 2014 and 2020 were analysed. Heritability estimates were moderate (18–44%) for phenotypes derived from all antibiotic treatments, and low (1–15%) for phenotypes derived from treatments against respiratory diseases only. Moreover, genetic correlations between these new phenotypes and mortality were low to moderate (0.08–0.60) and no strong adverse genetic correlations with production traits were found. The high heritabilities and favourable genetic correlations suggest these new phenotypes, derived from on-farm antibiotics records, to be promising for inclusion in future pig breeding programs to breed for a decrease in antibiotics usage.

Genetic parameters of resistance to pasteurellosis using novel response traits in rabbits

Background

Pasteurellosis (Pasteurella infection) is one of the most common bacterial infections in rabbits on commercial farms and in laboratory facilities. Curative treatments using antibiotics are only partly efficient, with frequent relapses. Breeding rabbits for improved genetic resistance to pasteurellosis is a sustainable alternative approach. In this study, we infected 964 crossbred rabbits from six sire lines experimentally with Pasteurella multocida. After post-mortem examination and bacteriological analyses, abscess, bacteria, and resistance scores were derived for each rabbit based on the extent of lesions and bacterial dissemination in the body. This is the first study to use such an experimental design and response traits to measure resistance to pasteurellosis in a rabbit population. We investigated the genetic variation of these traits in order to identify potential selection criteria. We also estimated genetic correlations of resistance to pasteurellosis in the experimental population with traits that are under selection in the breeding populations (number of kits born alive and weaning weight).

Results

Heritability estimates for the novel response traits, abscess, bacteria, and resistance scores, ranged from 0.08 (± 0.05) to 0.16 (± 0.06). The resistance score showed very strong negative genetic correlation estimates with abscess (− 0.99 ± 0.05) and bacteria scores (− 0.98 ± 0.07). A very high positive genetic correlation of 0.99 ± 0.16 was estimated between abscess and bacteria scores. Estimates of genetic correlations of the resistance score with average daily gain traits for the first and second week after inoculation were 0.98 (± 0.06) and 0.70 (± 0.14), respectively. Estimates of genetic correlations of the disease-related traits with average daily gain pre-inoculation were favorable but with high standard errors. Estimates of genetic and phenotypic correlations of the disease-related traits with commercial selection traits were not significantly different from zero.

Conclusions

Disease response traits are heritable and are highly correlated with each other, but do not show any significant genetic correlations with commercial selection traits. Thus, the prevalence of pasteurellosis could be decreased by selecting more resistant rabbits on any one of the disease response traits with a limited impact on the selection traits, which would allow implementation of a breeding program to improve resistance to pasteurellosis in rabbits.

Health and welfare of rabbits farmed in different production systems

The AGRI committee of the European Parliament requested EFSA to assess the welfare of rabbits farmed in different production systems, including organic production, and to update its 2005 scientific opinion about the health and welfare of rabbits kept for meat production. Considering reproducing does, kits and growing rabbits, this scientific opinion focusses on six different housing systems, namely conventional cages, structurally enriched cages, elevated pens, floor pens, outdoor/partially outdoor systems and organic systems. To compare the level of welfare in the different housing systems and rabbit categories, welfare impact scores for 20 welfare consequences identified from the literature were calculated, taking their occurrence, duration and severity into account. Based on the overall welfare impact score (sum of scores for the single welfare consequences), obtained via a 2‐step expert knowledge elicitation process, the welfare of reproducing does is likely (certainty 66–90%) to be lower in conventional cages compared to the five other housing systems. In addition, it is likely to extremely likely (certainty 66–99%) that the welfare of kits is lower in outdoor systems compared to the other systems and that the welfare is higher in elevated pens than in the other systems. Finally, it is likely to extremely likely (certainty 66–99%) that the welfare of growing rabbits is lower in conventional cages compared to the other systems and that the welfare is higher in elevated pens than in the other systems. Ranking of the welfare consequences allowed an analysis of the main welfare consequences within each system and rabbit category. It was concluded that for reproducing does, as well as growing rabbits, welfare consequences related to behavioural restrictions were more prominent in conventional cages, elevated pens and enriched cages, whereas those related to health problems were more important in floor pens, outdoor and organic systems. Housing in organic rabbit farming is diverse, which can result in different welfare consequences, but the overall welfare impact scores suggest that welfare in organic systems is generally good.

Quantifying the health challenges in an Australian piggery using medication records for the definition of disease resilience1

Disease resilience is the ability to maintain performance and health, despite infection challenges in the environment. The evaluation of disease resilience requires measures of environment infection challenges, along with other environmental challenges. The overall objective of this study was to define disease resilience using pedigree, production, and medication records from an Australian herd of Large White pigs. The extent to which the infection challenges were captured by environmental descriptors based on contemporary group (CG) estimates of growth was assessed (n = 8,835). There were moderately negative linear relationships (r = -0.29, p = 0.08) between CG estimates (39 CGs) of growth and the frequency of medicated pigs (n = 812 medicated pigs). This suggests that CG estimates of growth partly capture health challenges. However, because the health challenges were not of the pathogenic nature for this herd, these environmental descriptors may not be appropriate for the evaluation of disease resilience. Subsequently, an alternative approach to select for health was provided, where health was defined as a binary outcome of medication status, fitted in a generalized linear mixed sire model. Two health-trait definitions were explored, which differed in the number of control (nonmedicated) pigs per litter. The 'reduced-control' health trait had a representative sample of littermates with available performance records, and the 'full-control' health trait included all piglets weaned per litter (i.e., performance-tested and non-performance-tested pigs). All 812 medicated pigs had performance records available. The remaining 8,023 pigs in the reduced-control and 21,352 pigs in the full-control health traits were assumed to have not been medicated (controls). Male pigs from litters with a higher number of postweaning deaths were more likely to be medicated for both health traits. Heritability was consistent for both trait definitions, at 0.06 ± 0.04 (± SE) (reduced-control) and 0.04 ± 0.03 (full-control). While results may be specific for individual herds depending on health status, these estimates align with those presented in literature for other health traits. Together, these results demonstrate that routinely collected medication records may be useful for pig breeding programs and their economic importance and genetic background should be explored further.

Genetic Parameters for Resistance to Non-specific Diseases and Production Traits Measured in Challenging and Selection Environments; Application to a Rabbit Case

Breeding for disease resistance is a challenging but increasingly necessary objective to overcome the issues with the reduced use of antibiotics and growing concern for animal welfare while limiting economic losses. However, implementing such strategies is a complex process because animals face numerous diseases, and the environments on selection farms differ from those on commercial farms. We evaluated whether selection for resistance to non-specific diseases based on a single visual record in selection (S) and challenging (Ch) environments is possible. Records from 23,773 purebred rabbits born between 2012 and 2016 were used in this study. After weaning (at 32 days of age), 17,712 rabbits were raised in the S environment and 6,061 sibs were raised in the Ch environment. Clinical signs of disease were recorded for all animals at the end of the test, at a single time point, at 70 or 80 days of age. The causes of mortality occurring before the end of the test were also recorded. Three disease traits were analyzed: signs of respiratory disease, signs of digestive disease, and a composite trait (Resist) taking into account signs of digestive, respiratory and various infectious diseases. This latter composite trait is proposed to capture the global resistance to disease. All disease traits were binary, with 0 being the absence of symptoms. Two production traits were also recorded: the number of kits born alive (4,121 litters) and the weaning weight (13,090 rabbits). Disease traits were analyzed with animal threshold models, assuming that traits are different in the two environments. Bivariate analyses were carried out using linear animal models. The heritabilities of the disease traits ranged from 0.04 ± 0.01 to 0.11 ± 0.03. The genetic correlations between disease traits in both environments were below unity (≤ 0.84), indicating genotype by environment interactions. Most of the genetic correlations between disease and production traits were not significantly different from zero, except between the weaning weight and Resist_S, with a favorable correlation of -0.34 ± 0.12. Given these genetic parameters, for the same level of exposure of rabbits to pathogens, the expected response to selection is a reduction of disease incidence of 4-6% per generation.

Data capture through Australian beef cattle and meat sheep value chains: opportunities for enhanced feedback to commercial producers

Technologies for capturing and transmitting data from different points in livestock value chains are developing very rapidly, and interest is growing in how best to use such technologies. While new data-capture technology comes with the promise of producers and others being more informed about a system, what usually results is large and complex datasets. A key challenge is to make use of the data or information. The present paper initially outlines the data-capture points and flow of information that occurs throughout the Australian beef cattle and meat sheep value chain. The avenues through which feedback can be delivered to commercial producers are briefly summarised, along with the value of this feedback and the factors that affect its value. Finally, practical principles for effective feedback systems are provided. While data capture is occurring throughout the value chain, the main focus of the paper is on carcass- and eating-quality feedback from processors to commercial producers. There is significant variation in the volume, nature and quality of data collected, and also the flow of information among members of the chain. Further, there appears to be an inconsistency in the levels of demand or desire for the feedback. The value of feedback ultimately depends on the producer’s ability to make better business decisions as a result of having that data or information. Increasing market specifications and compliance will result in greater profitability for the producer, as well as processor. The value of feedback also depends on several other factors, including its accuracy, its granularity, whether or not it can be connected to other data, and what options the producer has to use that information in the future. Feedback must be interpretable and enable better business decisions. The value of feedback will also increase if extended further upstream along the supply chain for genetic evaluation, provided there is enough information on genetically informed animals and their identifications can be tracked across the supply chain. For efficient feedback systems, every member in the chain needs to see value in the feedback, and there needs to be a mutual commitment and shared vision between all value-chain partners. Further, feedback must be provided in an efficient and practical manner, so as to increase the willingness of the information providers to deliver the feedback. Producers should be involved in any attempts to enhance feedback systems. Since there is variability in the needs, wants and capabilities of processors and producers, multiple dynamic and flexible feedback systems are required. An incentive to enhance feedback systems is to provide a value proposition by calculating the monetary value of the feedback to all members of the chain. Better objective measurements and Meat Standards Australia for lamb is likely to also contribute to better feedback value propositions. Communication and fostering of relationships among supply-chain members will always remain critical. While data permissions add a complication to information sharing across the chain, benefits can be gained by not only the commercial producer, but the entire industry.