The genetic basis of natural antibody titers of young healthy pigs and relationships with disease resilience

The genetics of resilience and its relationships with egg production traits and antibody traits in chickens

BACKGROUND

Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to its initial state before exposure to a disturbance. Resilient livestock are desired because of their improved health and increased economic profit. Genetic improvement of resilience may also lead to trade-offs with production traits. Recently, resilience indicators based on longitudinal data have been suggested, but they need further evaluation to determine whether they are indeed predictive of improved resilience, such as disease resilience. This study investigated different resilience indicators based on deviations between expected and observed egg production (EP) by exploring their genetic parameters, their possible trade-offs with production traits, and their relationships with antibody traits in chickens.

METHODS

Egg production in a nucleus breeding herd environment based on 1-week-, 2-week-, or 3-week-intervals of two purebred chicken lines, a white egg-laying (33,825 chickens) and a brown egg-laying line (34,397 chickens), were used to determine deviations between observed EP and expected average batch EP, and between observed EP and expected individual EP. These deviations were used to calculate three types of resilience indicators for two life periods of each individual: natural logarithm-transformed variance (ln(variance)), skewness, and lag-one autocorrelation (autocorrelation) of deviations from 25 to 83 weeks of age and from 83 weeks of age to end of life. Then, we estimated their genetic correlations with EP traits and with two antibody traits.

RESULTS

The most promising resilience indicators were those based on 1-week-intervals, as they had the highest heritability estimates (0.02-0.12) and high genetic correlations (above 0.60) with the same resilience indicators based on longer intervals. The three types of resilience indicators differed genetically from each other, which indicates that they possibly capture different aspects of resilience. Genetic correlations of the resilience indicator traits based on 1-week-intervals with EP traits were favorable or zero, which means that trade-off effects were marginal. The resilience indicator traits based on 1-week-intervals also showed no genetic correlations with the antibody traits, which suggests that they are not informative for improved immunity or vice versa in the nucleus environment.

CONCLUSIONS

This paper gives direction towards the evaluation and implementation of resilience indicators, i.e. to further investigate resilience indicator traits based on 1-week-intervals, in breeding programs for selecting genetically more resilient layer chickens.

Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience

BACKGROUND

Disease resilience is the ability of an animal to maintain productive performance under disease conditions and is an important selection target. In pig breeding programs, disease resilience must be evaluated on selection candidates without exposing them to disease. To identify potential genetic indicators for disease resilience that can be measured on selection candidates, we focused on the blood transcriptome of 1594 young healthy pigs with subsequent records on disease resilience. Transcriptome data were obtained by 3'mRNA sequencing and genotype data were from a 650 K genotyping array.

RESULTS

Heritabilities of the expression of 16,545 genes were estimated, of which 5665 genes showed significant estimates of heritability (p < 0.05), ranging from 0.05 to 0.90, with or without accounting for white blood cell composition. Genes with heritable expression levels were spread across chromosomes, but were enriched in the swine leukocyte antigen region (average estimate > 0.2). The correlation of heritability estimates with the corresponding estimates obtained for genes expressed in human blood was weak but a sizable number of genes with heritable expression levels overlapped. Genes with heritable expression levels were significantly enriched for biological processes such as cell activation, immune system process, stress response, and leukocyte activation, and were involved in various disease annotations such as RNA virus infection, including SARS-Cov2, as well as liver disease, and inflammation. To estimate genetic correlations with disease resilience, 3205 genotyped pigs, including the 1594 pigs with transcriptome data, were evaluated for disease resilience following their exposure to a natural polymicrobial disease challenge. Significant genetic correlations (p < 0.05) were observed with all resilience phenotypes, although few exceeded expected false discovery rates. Enrichment analysis of genes ranked by estimates of genetic correlations with resilience phenotypes revealed significance for biological processes such as regulation of cytokines, including interleukins and interferons, and chaperone mediated protein folding.

CONCLUSIONS

These results suggest that expression levels in the blood of young healthy pigs for genes in biological pathways related to immunity and endoplasmic reticulum stress have potential to be used as genetic indicator traits to select for disease resilience.

Comparative effects of soy protein concentrate, enzyme-treated soybean meal, and fermented soybean meal replacing animal protein supplements in feeds on growth performance and intestinal health of nursery pigs

BACKGROUND

Soy protein supplements, with high crude protein and less antinutritional factors, are produced from soybean meal by different processes. This study evaluated the comparative effects of various soy protein supplements replacing animal protein supplements in feeds on the intestinal immune status, intestinal oxidative stress, mucosa-associated microbiota, and growth performance of nursery pigs.

METHODS

Sixty nursery pigs (6.6 ± 0.5 kg BW) were allotted to five treatments in a randomized complete block design with initial BW and sex as blocks. Pigs were fed for 39 d in 3 phases (P1, P2, and P3). Treatments were: Control (CON), basal diet with fish meal 4%, 2%, and 1%, poultry meal 10%, 8%, and 4%, and blood plasma 4%, 2%, and 1% for P1, P2, and P3, respectively; basal diet with soy protein concentrate (SPC), enzyme-treated soybean meal (ESB), fermented soybean meal with Lactobacillus (FSBL), and fermented soybean meal with Bacillus (FSBB), replacing 1/3, 2/3, and 3/3 of animal protein supplements for P1, P2, and P3, respectively. Data were analyzed using the MIXED procedure in SAS 9.4.

RESULTS

The SPC did not affect the BW, ADG, and G:F, whereas it tended to reduce (P = 0.094) the ADFI and tended to increase (P = 0.091) crypt cell proliferation. The ESM did not affect BW, ADG, ADFI, and G:F, whereas tended to decrease (P = 0.098) protein carbonyl in jejunal mucosa. The FSBL decreased (P < 0.05) BW and ADG, increased (P < 0.05) TNF-α, and Klebsiella and tended to increase MDA (P = 0.065) and IgG (P = 0.089) in jejunal mucosa. The FSBB tended to increase (P = 0.073) TNF-α, increased (P < 0.05) Clostridium and decreased (P < 0.05) Achromobacter and alpha diversity of microbiota in jejunal mucosa.

CONCLUSIONS

Soy protein concentrate, enzyme-treated soybean meal, and fermented soybean meal with Bacillus could reduce the use of animal protein supplements up to 33% until 7 kg body weight, up to 67% from 7 to 11 kg body weight, and entirely from 11 kg body weight without affecting the intestinal health and the growth performance of nursery pigs. Fermented soybean meal with Lactobacillus, however, increased the immune reaction and oxidative stress in the intestine consequently reducing the growth performance.

Levels of Circulating IgM and IgY Natural Antibodies in Broiler Chicks: Association with Genotype and Farming Systems

Naturally occurring antibodies (NAbs), which are major components of innate immunity, exist in circulation under healthy conditions without prior antigenic stimulation and are able to recognize both self- and non-self-constituents. The present study aimed at identifying potential immunological differences between commercial fast- and slow-growth broilers (n = 555) raised in conventional and free-range systems, respectively, through the use of the specificity, isotypes and levels of circulating NAbs. The possible beneficial effect of oregano-based dietary supplementation was also evaluated. To this end, serum IgM and IgY NAbs against self- (actin and DNA) and non-self- antigens (trinitrophenol and lipopolysaccharide) were measured by ELISA and further correlated with genotype, season and performance. Significantly higher levels of IgM NAbs against all antigens were found in slow-growth compared to fast-growth broilers. IgM NAb levels were also significantly increased in dietarily supplemented slow-growth broilers versus those consuming standard feed. Moreover, significantly elevated levels of anti-DNA IgY NAbs were found in fast-growth compared to slow-growth broilers, whereas the opposite was observed for anti-LPS IgY NAbs. Multivariate linear regression analysis confirmed multiple interactions between NAb levels, genotype, season and performance. Overall, serum NAbs have proven to be valuable innovative immunotools in the poultry industry, efficiently differentiating fast-growing versus slow-growing broilers, and dietary supplementation of plant extracts can enhance natural immunity.

Research Note: Genome-wide association study for natural antibodies and resilience in a purebred layer chicken line

Resilience is the capacity of an animal to be minimally affected by disturbances or rapidly return to the state pertained before exposure to a disturbance. Resilience indicators can be estimated from longitudinal production data, using deviations of observed from expected production levels. One component of resilience is disease resilience, which includes general disease resistance. Natural antibodies (NAbs) are an indicator trait for general disease resistance. The aim of this study was to perform a genome-wide association study (GWAS) for resilience indicators and NAbs in a Rhode Island purebred layer line and study potential overlap in genomic regions detected for these traits. For 2,494 hens, deviations (i.e., differences) between observed weekly egg production and expected weekly egg production were calculated. Resilience indicators were then defined as the natural logarithm of the variance of deviations, skewness of deviations, and lag-one autocorrelation of deviations. For a subset of 1,221 hens genotyped with the 60 K Illumina SNP BeadChip, NAbs binding keyhole-limpet hemocyanin were available (isotypes IgM and IgG). Heritabilities, estimated with a linear mixed animal model, were 0.39 for IgM and 0.20 for IgG, and ranged from 0.03 to 0.18 for the resilience indicators. No significant associations were found in the GWAS, except for a single chromosomal region for the skewness of egg deviations in wk 25 to 83 of the laying period. The absence of significant peaks for NAbs and resilience indicators suggests that there are no genes with major effect and that the traits are likely under polygenic control in this line.

Genetic Analyses of Response of Local Ghanaian Tanzanian Chicken Ecotypes to a Natural Challenge with Velogenic Newcastle Disease Virus

Simple Summary

Newcastle disease (ND) is a global threat to poultry production and often has a major impact on chicken welfare and the livelihoods of rural poultry farmers. We exposed unvaccinated Ghanaian and Tanzanian local chicken ecotypes to velogenic Newcastle disease virus strains, and measured response traits to understand the genetic basis of ND. We identified heritable ND response traits and revealed differences in survival between Ghanaian and Tanzanian local chicken ecotype birds. Our findings indicate that velogenic ND resistance could be improved through selective breeding of local chicken ecotypes in regions where the disease is endemic.

Abstract

Newcastle disease is a devastating poultry disease that often causes significant economic losses in poultry in the developing countries of Africa, Asia, as well as South and Central America. Velogenic Newcastle disease virus (NDV) outbreaks are associated with high mortalities, which can threaten household livelihoods, especially in the rural areas, and lead to loss of high-quality proteins in the form of meat and eggs, as well as household purchasing power. In this study, we exposed unvaccinated Ghanaian and Tanzanian chickens of six local ecotypes to velogenic NDV strains, measured NDV response traits, sequenced their DNA on a genotyping-by-sequencing platform, and performed variance component analyses. The collected phenotypes included: growth rates (pre- and post-exposure); lesion scores (gross lesion severity) in the trachea, proventriculus, intestine, and cecal tonsils; natural antibody levels; anti-NDV antibody levels at 7 days post exposure (dpe); tear and cloacal viral load at 2, 4, and 6 dpe; and survival time. Heritability estimates were low to moderate, ranging from 0.11 for average lesion scores to 0.36 for pre-exposure growth rate. Heritability estimates for survival time were 0.23 and 0.27 for the Tanzanian and Ghanaian ecotypes, respectively. Similar heritability estimates were observed when data were analyzed either separately or combined for the two countries. Survival time was genetically negatively correlated with lesion scores and with viral load. Results suggested that response to mesogenic or velogenic NDV of these local chicken ecotypes could be improved by selective breeding. Chickens that are more resilient to velogenic NDV can improve household livelihoods in developing countries.

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.

Impact of Enrichment and Repeated Mixing on Resilience in Pigs

Resilience, the capacity of animals to be minimally affected by a disturbance or to rapidly bounce back to the state before the challenge, may be improved by enrichment, but negatively impacted by a high allostatic load from stressful management procedures in pigs. We investigated the combined effects of diverging environmental conditions from weaning and repeated mixing to create high allostatic load on resilience of pigs. Pigs were either exposed to barren housing conditions (B) from weaning onwards or provided with sawdust, extra toys, regular access to a “play arena” and daily positive human contact (E). Half of the pigs were exposed to repeated mixing (RM) and the other half to one mixing only at weaning (minimal mixing, MM). To assess their resilience, the response to and recovery from a lipopolysaccharide (LPS) sickness challenge and a Frustration challenge were studied. In addition, potential long-term resilience indicators, i.e. natural antibodies, hair cortisol and growth were measured. Some indications of more favorable responses to the challenges in E pigs were found, such as lower serum reactive oxygen metabolite (dROM) concentrations and a smaller area under the curve of dROM after LPS injection. In the Frustration challenge, E pigs showed less standing alert, escape behaviors and other negative behaviors, a tendency for a smaller area under the curve of salivary cortisol and a lower plasma cortisol level at 1 h after the challenge. Aggression did not decrease over mixings in RM pigs and was higher in B pigs than in E pigs. Repeated mixing did not seem to reduce resilience. Contrary to expectations, RM pigs showed a higher relative growth than MM pigs during the experiment, especially in the week of the challenges. Barren RM pigs showed a lower plasma cortisol concentration than barren MM pigs after the LPS challenge, which may suggest that those RM pigs responded less detrimentally than MM pigs. Enriched RM pigs showed a higher level of IgM antibodies binding keyhole limpet hemocyanin (KLH) than enriched MM and barren RM pigs, and RM pigs showed a sharper decline in IgG antibodies binding Bovine Serum Albumin (PC-BSA) over time than MM pigs. Hair cortisol concentrations were not affected by enrichment or mixing. To conclude, enrichment did not enhance the speed of recovery from challenges in pigs, although there were indications of reduced stress. Repeated as opposed to single mixing did not seem to aggravate the negative effects of barren housing on resilience and for some parameters even seemed to reduce the negative effects of barren housing.

Breeding for disease resilience: opportunities to manage polymicrobial challenge and improve commercial performance in the pig industry

Disease resilience, defined as an animal's ability to maintain productive performance in the face of infection, provides opportunities to manage the polymicrobial challenge common in pig production. Disease resilience can deliver a number of benefits, including more sustainable production as well as improved animal health and the potential for reduced antimicrobial use. However, little progress has been made to date in the application of disease resilience in breeding programs due to a number of factors, including (1) confusion around definitions of disease resilience and its component traits disease resistance and tolerance, and (2) the difficulty in characterizing such a complex trait consisting of multiple biological functions and dynamic elements of rates of response and recovery from infection. Accordingly, this review refines the definitions of disease resistance, tolerance, and resilience based on previous studies to help improve the understanding and application of these breeding goals and traits under different scenarios. We also describe and summarize results from a "natural disease challenge model" designed to provide inputs for selection of disease resilience. The next steps for managing polymicrobial challenges faced by the pig industry will include the development of large-scale multi-omics data, new phenotyping technologies, and mathematical and statistical methods adapted to these data. Genome editing to produce pigs resistant to major diseases may complement selection for disease resilience along with continued efforts in the more traditional areas of biosecurity, vaccination and treatment. Altogether genomic approaches provide exciting opportunities for the pig industry to overcome the challenges provided by hard-to-manage diseases as well as new environmental challenges associated with climate change.

Concentration and heritability of immunoglobulin G and natural antibody immunoglobulin M in dairy and beef colostrum along with serum total protein in their calves

Immunoglobulin (Ig) G and natural antibody (NAb) IgM are passively transferred to the neonatal calf through bovine colostrum. Maternal IgG provides pathogen- or vaccine-specific protection and comprises about 85 percent of colostral Ig. Natural antibody IgM is less abundant but provides broad and non-specific reactivity, potentially contributing to protection against the dissemination of pathogens in the blood (septicemia) in a calf's first days of life. In the dairy and beef industries, failure of passive transfer (FPT) of colostral Ig (serum total protein (STP) <5.2 g/dL) is still a common concern. The objectives of this study were to, i) compare colostral IgG concentrations and NAb-IgM titers between dairy and beef cows; ii) assess the effect of beef breed on colostral IgG; iii) compare passive transfer of colostral Ig in dairy and beef calves; and iv) estimate the heritability of colostral IgG and NAb-IgM. Colostrum was collected from Holstein dairy (n=282) and crossbred beef (n=168) cows at the University of Guelph dairy and beef research centres. Colostral IgG was quantified by radial immunodiffusion and NAb-IgM was quantified by an enzyme-linked immunosorbent assay. In dairy (n=308) and beef (n=169) calves, STP was estimated by digital refractometry. Beef cows had significantly greater colostral IgG (146.5 ± 9.5 SEM g/L) than dairy cows (92.4 ± 5.2 g/L, p <0.01). Beef cows with a higher proportion of Angus ancestry had significantly lower colostral IgG (125.5 ± 5.8 g/L) than cows grouped as "Other" (142.5 ± 4.9 g/L, p= 0.02). Using the FPT cut-off, 13% of dairy and 16% of beef calves had FPT; still, beef calves had a significantly larger proportion with excellent passive transfer (STP ≥6.2 g/dL, p <0.01). The heritability of colostral IgG was 0.04 (± 0.14) in dairy and 0.14 (± 0.32) in beef. Colostral NAb-IgM titers in dairy (12.12 ± 0.22, log2 (reciprocal of titer)) and beef cows (12.03 ± 0.19) did not differ significantly (p=0.71). The range of NAb-IgM titers was 9.18 to 14.60, equivalent to a 42-fold range in antibody concentration. The heritability of colostral NAb was 0.24 (± 0.16) in dairy and 0.11 (± 0.19) in beef cows. This study is the first to compare colostral NAb-IgM between dairy and beef cows. Based on the range in NAb-IgM titers and the heritability, selective breeding may improve colostrum quality and protection for neonatal calves in the early days of life.

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.

Genetic and phenotypic parameters for Aleutian disease tests and their correlations with pelt quality, reproductive performance, packed-cell volume, and harvest length in mink

Aleutian disease (AD), caused by the Aleutian mink disease virus (AMDV), is a major health concern that results in global economic losses to the mink industry. The unsatisfactory outcome of the culling strategy, immunoprophylaxis, and medical treatment in controlling AD have urged mink farmers to select AD resilient mink based on several detection tests, including enzyme-linked immunosorbent assay (ELISA), counterimmunoelectrophoresis (CIEP), and iodine agglutination test (IAT). However, the genetic analysis of these AD tests and their correlations with pelt quality, reproductive performance, packed-cell volume (PCV), and harvest length (HL) have not been investigated. In this study, data on 5,824 mink were used to estimate the genetic and phenotypic parameters of four AD tests, including two systems of ELISA, CIEP, and IAT, and their genetic and phenotypic correlations with two pelt quality, five female reproductive performance, PCV, and HL traits. Significances (P < 0.05) of fixed effects (sex, year, dam age, and color type), covariates (age at harvest and blood sampling), and random effects (additive genetic, permanent environmental, and maternal effects) were determined under univariate models using ASReml 4.1 software. The genetic and phenotypic parameters for all traits were estimated under bivariate models using ASReml 4.1 software. Estimated heritabilities (±SE) were 0.39 ± 0.06, 0.61 ± 0.07, 0.11 ± 0.07, and 0.26 ± 0.05 for AMDV antigen-based ELISA (ELISA-G), AMDV capsid protein-based ELISA, CIEP, and IAT, respectively. The ELISA-G also showed a moderate repeatability (0.58 ± 0.04) and had significant negative genetic correlations (±SE) with reproductive performance traits (from -0.41 ± 0.16 to -0.49 ± 0.12), PCV (-0.53 ± 0.09), and HL (-0.45 ± 0.16). These results indicated that ELISA-G had the potential to be applied as an indicator trait for genetic selection of AD resilient mink in AD endemic ranches and therefore help mink farmers to reduce the adverse effects caused by AD.