Breeding for resilience: new opportunities in a modern pig breeding program

Consistency of dry matter intake in Holstein cows: Heritability estimates and associations with feed efficiency

Resilience can be defined as the capacity to maintain performance or bounce back to normal functioning after a perturbation, and studying fluctuations in daily feed intake may be an effective way to identify resilient dairy cows. Our goal was to develop new phenotypes based on daily dry matter intake (DMI) consistency in Holstein cows, estimate genetic parameters and genetic correlations with feed efficiency and milk yield consistency, and evaluate their relationships with production, longevity, health, and reproduction traits. Data consisted of 397,334 daily DMI records of 6,238 lactating Holstein cows collected from 2007 to 2022 at 6 research stations across the United States. Consistency phenotypes were calculated based on the deviations from expected daily DMI for individual cows during their respective feeding trials, which ranged from 27 to 151 d in duration. Expected values were derived from different models, including simple average, quadratic and cubic quantile regression with a 0.5 quantile, and locally estimated scatterplot smoothing (LOESS) regression with span parameters 0.5 and 0.7. We then calculated the log of variance (log-Var-DMI) of daily deviations for each model as the consistency phenotype. Consistency of milk yield was also calculated, as a reference, using the same methods (log-Var-Milk). Genetic parameters were estimated using an animal model, including lactation, days in milk and cohort as fixed effects, and animal as random effect. Relationships between log-Var-DMI and traits currently considered in the US national genetic evaluation were evaluated using Spearman's rank correlations between sires' breeding values. Heritability estimates for log-Var-DMI ranged from 0.11 ± 0.02 to 0.14 ± 0.02 across models. Different methods (simple average, quantile regressions, and LOESS regressions) used to calculate log-Var-DMI yielded very similar results, with genetic correlations ranging from 0.94 to 0.99. Estimated genetic correlations between log-Var-DMI and log-Var-Milk ranged from 0.51 to 0.62. Estimated genetic correlations between log-Var-DMI and feed efficiency ranged from 0.55 to 0.60 with secreted milk energy, from 0.59 to 0.63 with metabolic body weight, and from 0.26 to 0.31 with residual feed intake (RFI). Relationships between log-Var-DMI and the traits in the national genetic evaluation were moderate and positive correlations with milk yield (0.20 to 0.21), moderate and negative correlations with female fertility (-0.07 to -0.20), no significant correlations with health and longevity, and favorable correlations with feed efficiency (-0.23 to -0.25 with feed saved and 0.21 to 0.26 with RFI). We concluded that DMI consistency is heritable and may be an indicator of resilience. Cows with lower variation in the difference between actual and expected daily DMI (more consistency) may be more effective in maintaining performance in the face of challenges or perturbations, whereas cows with greater variation in observed versus expected daily DMI (less consistency) are less feed efficient and may be less resilient.

Hotspots and bottlenecks for the enhancement of the environmental sustainability of pig systems, with emphasis on European pig systems

Although pig systems start from a favourable baseline of environmental impact compared to other livestock systems, there is still scope to reduce their emissions and further mitigate associated impacts, especially in relation to nitrogen and phosphorous emissions. Key environmental impact hotspots of pig production systems are activities associated with feed production and manure management, as well as direct emissions (such as methane) from the animals and energy use. A major contributor to the environmental impacts associated with pig feed is the inclusion of soya in pig diets, especially since European pig systems rely heavily on soya imported from areas of the globe where crop production is associated with significant impacts of land use change, deforestation, carbon emissions, and loss of biodiversity. The "finishing" pig production stage contributes most to these environmental impacts, due to the amount of feed consumed, the efficiency with which feed is utilised, and the amount of manure produced during this stage. By definition therefore, any substantial improvements pig system environmental impact would arise from changes in feed production and manure management. In this paper, we consider potential solutions towards system environmental sustainability at these pig system components, as well as the bottlenecks that inhibit their effective implementation at the desired pace and magnitude. Examples include the quest for alternative protein sources to soya, the limits (perceived or real) to the genetic improvement of pigs, and the implementation of alternative manure management strategies, such as production of biogas through anaerobic digestion. The review identifies and discusses areas that future efforts can focus on, to further advance understanding around the potential sustainability benefits of modifications at various pig system components, and key sustainability trade-offs across the environment-economy-society pillars associated with synergistic and antagonistic effects when joint implementation of multiple solutions is considered. In this way, the review opens a discussion to facilitate the development of holistic decision support tools for pig farm management that account for interactions between the "feed * animal * manure" system components and trade-offs between sustainability priorities (e.g., environmental vs economic performance of pig system; welfare improvements vs environmental impacts).

The WUR0000125 PRRS resilience SNP had no apparent effect on pigs' infectivity and susceptibility in a novel transmission trial

BACKGROUND

Porcine reproductive and respiratory syndrome (PRRS) remains one of the most important infectious diseases for the pig industry. A novel small-scale transmission experiment was designed to assess whether the WUR0000125 (WUR for Wageningen University and Research) PRRS resilience single nucleotide polymorphism (SNP) confers lower susceptibility and infectivity to pigs under natural porcine reproductive and respiratory syndrome virus (PRRSV-2) transmission.

METHODS

Commercial full- and half-sib piglets (n = 164) were assigned as either Inoculation, Shedder, or Contact pigs. Pigs were grouped according to their relatedness structure and WUR genotype, with R- and R+ referring to pigs with zero and one copy of the dominant WUR resilience allele, respectively. Barcoding of the PRRSV-2 strain (SD09-200) was applied to track pig genotype-specific transmission. Blood and nasal swab samples were collected and concentrations of PRRSV-2 were determined by quantitative (q)-PCR and cell culture and expressed in units of median tissue culture infectious dose (TCID₅₀). The Log₁₀TCID₅₀ at each sampling event, derived infection status, and area under the curve (AUC) were response variables in linear and generalized linear mixed models to infer WUR genotype differences in Contact pig susceptibility and Shedder pig infectivity.

RESULTS

All Shedder and Contact pigs, except one, became infected through natural transmission. There was no significant (p > 0.05) effect of Contact pig genotype on any virus measures that would indicate WUR genotype differences in susceptibility. Contact pigs tended to have higher serum AUC (p = 0.017) and log₁₀TCID₅₀ (p = 0.034) when infected by an R+ shedder, potentially due to more infectious R+ shedders at the early stages of the transmission trial. However, no significant Shedder genotype effect was found in serum (p = 0.274) or nasal secretion (p = 0.951) that would indicate genotype differences in infectivity.

CONCLUSIONS

The novel design demonstrated that it is possible to estimate genotype effects on Shedder pig infectivity and Contact pig susceptibility that are not confounded by family effects. The study, however, provided no supportive evidence that genetic selection on WUR genotype would affect PRRSV-2 transmission. The results of this study need to be independently validated in a larger trial using different PRRSV strains before dismissing the effects of the WUR marker or the previously detected GBP5 gene on PRRSV transmission.

Effect of early vs. late maturing sire lines and creep feeding on the cortisol response, intestinal permeability, and growth performance of nursery and finishing pigs

A total of 21 litters (11 early and 10 late maturing Duroc × DNA 241) resulting in 241 pigs were used in 170 d trial to determine the effect of sire lines selected for either early or late maturing growth rates and creep feeding on the cortisol concentration, intestinal permeability, and growth performance of nursery and finishing pigs. Treatments were arranged in a 2 × 2 factorial with main effect of Duroc sire line (early or late maturing) and creep feeding (with or without). Creep feed was provided for 14 d prior to weaning. After weaning (approximately 21 d of age; initially 6.4 kg), no interactions were observed for blood cortisol. However, blood cortisol levels were increased (P = 0.011) in late maturing pigs compared to early maturing pigs. A lower percentage (P < 0.001) of early maturing pigs lost weight 3 d post-weaning compared to late maturing pigs. Likewise, early maturing pigs had improved (P < 0.001) average daily gain (ADG) and average daily feed intake (ADFI) during the first 3 d in the nursery and also had increased ADFI (P < 0.001) from days 2 to 14 in the nursery. Creep feeding had no effect on initial nursery performance. On day 7, after a 2-h fast, a subsample of pigs was administered an oral gavage of lactulose and mannitol dissolved in distilled water. No differences by sire line, creep feeding, or their interactions were observed in lactulose:mannitol ratio. For overall nursery growth performance, an interaction was observed for ADG (P = 0.007) and ADFI (P < 0.001), with creep feed providing a benefit in late maturing pigs, but not in early maturing pigs. Early maturing pigs had poorer gain-to-feed ratio (G:F) (P < 0.001) than late maturing pigs. For overall finishing performance, an interaction was observed for ADG (P = 0.037) and ADFI (P = 0.007), with creep feed providing a benefit in late maturing pigs, but not in early maturing pigs. This resulted in an interaction for final body weight (P = 0.005), with late maturing pigs that did not receive creep feed having decreased market weights (P ≤ 0.003) compared to the other treatments. In summary, early maturing pigs had decreased cortisol concentration at weaning and improved ADG and ADFI until approximately 100 kg, at which point late maturing pigs began to exhibit greater ADG. Late maturing pigs had improved G:F from 46 d of age until market. Interestingly, creep feeding late maturing pigs resulted in increased day 170 weight compared with providing no creep feed, whereas creep feed did not impact early maturing pigs (sire line × creep feed interaction, P < 0.005).

Genetic and phenotypic correlations between Aleutian disease tests with body weight, growth, and feed efficiency traits in mink

The ineffectiveness of vaccination, medicine, and culling strategy leads mink farmers to control Aleutian disease (AD) by selecting AD-resilient mink based on AD tests. However, the genetic background of AD tests and their correlations with economically important or AD-resilient traits are limited. This study estimated the genetic and phenotypic correlations between four AD tests and seven body weight (BW) traits, six growth parameters from the Richards growth model, and eight feed-related traits. Univariate models were used to test the significance (P < 0.05) of fixed effects (sex, color type, AD test year, birth year, and row-by-year), random effects (additive genetic, maternal genetic, and permanent environmental), and a covariate of age using ASReml 4.1. Likewise, pairwise bivariate analyses were conducted to estimate the phenotypic and genetic correlations among the studied traits. Both antigen- and virus capsid protein-based enzyme-linked immunosorbent assay tests (ELISA-G and ELISA-P) showed significant (P < 0.05) moderate positive genetic correlations (±SE) with maturation rate (from 0.36 ± 0.18 to 0.38 ± 0.19). ELISA-G showed a significant negative genetic correlation (±SE) with average daily gain (ADG, -0.37 ± 0.16). ELISA-P showed a significant positive moderate genetic correlation (±SE) with off-feed days (DOF, 0.42 ± 0.17). These findings indicated that selection for low ELISA scores would reduce the maturation rate, increase ADG (by ELISA-G), and minimize DOF (by ELISA-P). The iodine agglutination test (IAT) showed significant genetic correlations with DOF (0.73 ± 0.16), BW at 16 weeks of age (BW16, 0.45 ± 0.23), and BW at harvest (HW, -0.47 ± 0.20), indicating that selection for lower IAT scores would lead to lower DOF and BW16, and higher HW. These estimated genetic correlations suggested that the selection of AD tests would not cause adverse effects on the growth, feed efficiency, and feed intake of mink. The estimates from this study might strengthen the previous finding that ELISA-G could be applied as a reliable and practical indicator trait in the genetic selection of AD-resilient mink in AD-positive farms.

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.

Genetic parameters of drinking and feeding traits of wean-to-finish pigs under a polymicrobial natural disease challenge

Background

The pork industry faces unprecedented challenges from disease, which increases cost of production and use of antibiotics, and reduces production efficiency, carcass quality, and animal wellbeing. One solution is to improve the overall resilience of pigs to a broad array of common diseases through genetic selection. Behavioral changes in feeding and drinking are usually the very first clinical signs when animals are exposed to stressors such as disease. Changes in feeding and drinking behaviors in diseased pigs may reflect the way they cope with the challenge and, thus, could be used as indicator traits to select for disease resilience. The objectives of this study were to estimate genetic parameters of feeding and drinking traits for wean-to-finish pigs in a natural polymicrobial disease challenge model, to estimate genetic correlations of feeding and drinking traits with growth rate and clinical disease traits, and to develop indicator traits to select for disease resilience.

Results

In general, drinking traits had moderate to high estimates of heritability, especially average daily water dispensed, duration, and number of visits (0.44 to 0.58). Similar estimates were observed for corresponding feeding traits (0.35 to 0.51). Most genetic correlation estimates among drinking traits were moderate to high (0.30 to 0.92) and higher than among feeding traits (0 to 0.11). Compared to other drinking traits, water intake duration and number of visits had relatively stronger negative genetic correlation estimates with treatment rate and mortality, especially across the challenge nursery and finisher (− 0.39 and − 0.45 for treatment rate; − 0.20 and − 0.19 for mortality).

Conclusion

Most of the recorded drinking and feeding traits under a severe disease challenge had moderate to high estimates of heritability, especially for feed or water intake duration and number of visits. Phenotypic and genetic correlations among the recorded feeding traits under disease were generally low but drinking traits showed high correlations with each other. Water intake duration and number of visits are potential indicator traits to select for disease resilience because of their high heritability and had moderate genetic correlations with treatment and mortality rates under severe disease.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00622-x.

A Comparison of the Behavior, Physiology, and Offspring Resilience of Gestating Sows When Raised in a Group Housing System and Individual Stalls

Simple Summary

The housing patterns of gestating sows affect their health and welfare. In this study, the differences between behavior and stress hormone levels were assessed when sows were housed in a group housing system compared to individual stalls; in addition, the disease resistance and resilience of their piglets were compared. In our investigation, the group-housed sows showed more exploratory behavior, less vacuum chewing, less sitting behavior, and lower stress hormone levels throughout pregnancy. A lipopolysaccharide (LPS) injection test revealed that the offspring of group-housed sows showed better resistance and resilience to disease. Therefore, the gestating sows raised in a group housing system and their piglets are healthier and have improved welfare. Our results show that a group housing system provides higher welfare standards, with conditions that are more suitable for gestating sows in modern pig production.

Abstract

Being in a confined environment causes chronic stress in gestating sows, which is detrimental for sow health, welfare and, consequently, offspring physiology. This study assessed the health and welfare of gestating sows housed in a group housing system compared to individual gestation stalls. After pregnancy was confirmed, experimental sows were divided randomly into two groups: the group housing system (GS), with the electronic sow feeding (ESF) system; or individual stall (IS). The behavior of sows housed in the GS or IS was then compared; throughout pregnancy, GS sows displayed more exploratory behavior, less vacuum chewing, and less sitting behavior (p < 0.05). IS sows showed higher stress hormone levels than GS sows. In particular, at 41 days of gestation, the concentration of the adrenocorticotropic hormone (ACTH) and adrenaline (A) in IS sows was significantly higher than that of GS sows, and the A level of IS sows remained significantly higher at 71 days of gestation (p < 0.01). The lipopolysaccharide (LPS) test was carried out in the weaned piglets of the studied sows. Compared with the offspring of gestating sows housed in GS (PG) or IS (PS), PG experienced a shorter period of high temperature and showed a quicker return to the normal state (p < 0.05). Additionally, their lower levels of stress hormone (p < 0.01) suggest that PG did not suffer from as much stress as PS. These findings suggested that gestating sows housed in GS were more able to carry out their natural behaviors and, therefore, had lower levels of stress and improved welfare. In addition, PG also showed better disease resistance and resilience. These results will provide a research basis for the welfare and breeding of gestating sows.

A natural knockout of the MYO7A gene leads to pre-weaning mortality in pigs

The pig breeding system provides a unique framework to study recessive defects and the consequence on the phenotype. We examined a commercial synthetic Duroc population for recessive defects and identified a haplotype on chromosome 9 significantly affecting pre‐weaning mortality. To identify the causal variant underlying the mortality, we examined sequence data of four carrier animals and 21 non‐carrier animals from the same population. The results yield a strong candidate causal stop‐gained variant (NM_001099928.1:c.541C>T) affecting the MYO7A gene in complete linkage disequilibrium with the lethal haplotype. The variant leads to an impaired (p.Gln181*) MYO7A protein that truncates 2032 amino acids from the protein. We examined a litter from a carrier sow inseminated by a carrier boar. From the resulting piglets, two confirmed homozygous piglets suffered from severe balance difficulties and the inability to walk properly. The variant segregates at a carrier frequency of 8.2% in the evaluated population and will be gradually purged from the population, improving animal welfare. Finally, this 'natural knockout' will increase our understanding of the functioning of the MYO7A gene and provides a potential model for Usher syndrome in humans.

Organoids: a promising new in vitro platform in livestock and veterinary research

Organoids are self-organizing, self-renewing three-dimensional cellular structures that resemble organs in structure and function. They can be derived from adult stem cells, embryonic stem cells, or induced pluripotent stem cells. They contain most of the relevant cell types with a topology and cell-to-cell interactions resembling that of the in vivo tissue. The widespread and increasing adoption of organoid-based technologies in human biomedical research is testament to their enormous potential in basic, translational- and applied-research. In a similar fashion there appear to be ample possibilities for research applications of organoids from livestock and companion animals. Furthermore, organoids as in vitro models offer a great possibility to reduce the use of experimental animals. Here, we provide an overview of studies on organoids in livestock and companion animal species, with focus on the methods developed for organoids from a variety of tissues/organs from various animal species and on the applications in veterinary research. Current limitations, and ongoing research to address these limitations, are discussed. Further, we elaborate on a number of fields of research in animal nutrition, host-microbe interactions, animal breeding and genomics, and animal biotechnology, in which organoids may have great potential as an in vitro research tool.

Using PRRSV-Resilient Sows Improve Performance in Endemic Infected Farms with Recurrent Outbreaks

Simple Summary

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease responsible for huge economic losses to the pig industry. The selection of PRRSV resilient sows has been proposed as a strategy to control this disease. A simulation model was developed to test the differences in reproductive performance and economic outcome of resilient or susceptible sows under farm PRRSV endemic conditions with or without recurrent PRRSV outbreaks. The data from phenotyped sows came from a PRRSV-positive farm with 1500 sows that suffered a PRRSV outbreak that lasted 24 weeks within three years. The reproductive parameters were generally better for resilient than for susceptible sows in PRRSV-positive farms suffering recurrent PRRSV outbreaks. Consequently, the piglet production cost was lower for resilient than for susceptible sows in any condition but showed only significant differences in PRRSV endemic farms suffering recurrent outbreaks. Finally, the annual gross margin by sow is significantly better for resilient than for susceptible sows under endemic conditions with or without recurrent outbreaks. Thus, the selection of PRRSV resilient sows is always a profitable approach for producers supporting the control of this disease.

Abstract

The selection of porcine reproductive and respiratory syndrome (PRRS) resilient sows has been proposed as a strategy to control this disease. A discrete event-based simulation model was developed to mimic the outcome of farms with resilient or susceptible sows suffering recurrent PRRSV outbreaks. Records of both phenotypes were registered in a PRRSV-positive farm of 1500 sows during three years. The information was split in the whole period of observation to include a PRRSV outbreak that lasted 24 weeks (endemic/epidemic or En/Ep) or only the endemic phase (En). Twenty simulations were modeled for each farm: Resilient/En, Resilient/En_Ep, Susceptible/En, and Susceptible/En_Ep during twelve years and analyzed for the productive performance and economic outcome, using reference values. The reproductive parameters were generally better for resilient than for susceptible sows in the PRRSV En/Ep scenario, and the contrary was observed in the endemic case. The piglet production cost was always lower for resilient than for susceptible sows but showed only significant differences in the PRRSV En/Ep scenario. Finally, the annual gross margin by sow is significantly better for resilient than for susceptible sows for the PRRSV endemic (12%) and endemic/epidemic scenarios (17%). Thus, the selection of PRRSV resilient sows is a profitable approach for producers to improve disease control.