Multiple-trait genomic prediction for swine meat quality traits using gut microbiome features as a correlated trait.

Traits such as meat quality and composition are becoming valuable in modern pork production; however, they are difficult to include in genetic evaluations because of the high phenotyping costs. Combining genomic information with multiple-trait indirect selection with cheaper indicator traits is an alternative for continued cost-effective genetic improvement. Additionally, gut microbiome information is becoming more affordable to measure using targeted rRNA sequencing, and its applications in animal breeding are becoming relevant. In this paper, we investigated the usefulness of microbial information as a correlated trait in selecting meat quality in swine. This study incorporated phenotypic data encompassing marbling, colour, tenderness, loin muscle and backfat depth, along with the characterization of gut (rectal) microbiota through 16S rRNA sequencing at three distinct time points of the animal's growth curve. Genetic progress estimation and cross-validation were employed to evaluate the utility of utilizing host genomic and gut microbiota information for selecting expensive-to-record traits in crossbred individuals. Initial steps involved variance components estimation using multiple-trait models on a training dataset, where the top 25 associated operational taxonomic units (OTU) for each meat quality trait and time point were included. The second step compared the predictive ability of multiple-trait models incorporating different numbers of OTU with single-trait models in a validation set. Results demonstrated the advantage of including genomic information for some traits, while in some instances, gut microbial information proved advantageous, namely, for marbling and pH. The study suggests further investigation into the shared genetic architecture between microbial features and traits, considering microbial data's compositional and high-dimensional nature. This research proposes a straightforward method to enhance swine breeding programs for improving costly-to-record traits like meat quality by incorporating gut microbiome information.

Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping.

BACKGROUND: Artificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of causal loci and the surrounding genomic regions. In population genetics, this type of selection is called polygenic selection. Researchers and managers of pig breeding programs are motivated to understand the genetic basis of phenotypic diversity across genetic lines, breeds, and populations using selection mapping analyses. Here, we applied generation proxy selection mapping (GPSM), a genome-wide association analysis of single nucleotide polymorphism (SNP) genotypes (38,294-46,458 markers) of birth date, in four pig populations (15,457, 15,772, 16,595 and 8447 pigs per population) to identify loci responding to artificial selection over a period of five to ten years. Gene-drop simulation analyses were conducted to provide context for the GPSM results. Selected loci within and across each population of pigs were compared in the context of swine breeding objectives. RESULTS: The GPSM identified 49 to 854 loci as under selection (Q-values less than 0.10) across 15 subsets of pigs based on combinations of populations. The number of significant associations increased when data were pooled across populations. In addition, several significant associations were identified in more than one population. These results indicate concurrent selection objectives, similar genetic architectures, and shared causal variants responding to selection across these pig populations. Negligible error rates (less than or equal to 0.02%) of false-positive associations were found when testing GPSM on gene-drop simulated genotypes, suggesting that GPSM distinguishes selection from random genetic drift in actual pig populations. CONCLUSIONS: This work confirms the efficacy and the negligible error rates of the GPSM method in detecting selected loci in commercial pig populations. Our results suggest shared selection objectives and genetic architectures across swine populations. The identified polygenic selection highlights loci that are important to swine production.

Genotyping and phenotyping strategies for genetic improvement of meat quality and carcass composition in swine.

BACKGROUND: Meat quality and composition traits have become valuable in modern pork production; however, genetic improvement has been slow due to high phenotyping costs. Combining genomic information with multi-trait indirect selection based on cheaper indicator traits is an alternative for continued cost-effective genetic improvement. METHODS: Data from an ongoing breeding program were used in this study. Phenotypic and genomic information was collected on three-way crossbred and purebred Duroc animals belonging to 28 half-sib families. We applied different methods to assess the value of using purebred and crossbred information (both genomic and phenotypic) to predict expensive-to-record traits measured on crossbred individuals. Estimation of multi-trait variance components set the basis for comparing the different scenarios, together with a fourfold cross-validation approach to validate the phenotyping schemes under four genotyping strategies. RESULTS: The benefit of including genomic information for multi-trait prediction depended on the breeding goal trait, the indicator traits included, and the source of genomic information. While some traits benefitted significantly from genotyping crossbreds (e.g., loin intramuscular fat content, backfat depth, and belly weight), multi-trait prediction was advantageous for some traits even in the absence of genomic information (e.g., loin muscle weight, subjective color, and subjective firmness). CONCLUSIONS: Our results show the value of using different sources of phenotypic and genomic information. For most of the traits studied, including crossbred genomic information was more beneficial than performing multi-trait prediction. Thus, we recommend including crossbred individuals in the reference population when these are phenotyped for the breeding objective.

Effect of rearing cross-fostered piglets in litters of differing size relative to sow functional teat number on preweaning growth and mortality.

Litter sizes of commercial sows have increased considerably over recent decades, and often exceed the number of functional teats on the sow. The objective of this study was to evaluate the effect of litter size after cross-fostering relative to sow functional teat number on piglet preweaning growth and mortality. A total of 39 litters (561 piglets) were used in a randomized complete block design; blocking factors were farrowing day and sow parity, body condition score, and functional teat number. Three Litter Size treatments were compared (relative to sow functional teat number): Decreased (two piglets less); Control (same number of piglets); Increased (two piglets more). Piglets were randomly allotted to treatment at 24 h after birth to form litters of the appropriate size, with similar mean and CV of birth weight within block. Weaning weights (WW) were collected at 19.5 ± 0.50 d of age; preweaning mortality (PWM) was recorded. Litter sizes were between 11 and 17 piglets, depending on block and treatment. The Decreased treatment had lower (P ≤ 0.05) PWM than the Increased (7.7% and 17.9%, respectively); the Control was intermediate (11.5%) and not different (P > 0.05) from the other treatments. The rate of decline in litter size from birth to weaning was greater (P ≤ 0.05) for the Increased than the Decreased treatment (-0.16 vs. -0.05 piglets per day), with the Control (-0.09 piglets per day) being intermediate and different (P ≤ 0.05) to the other two treatments. Litter sizes at weaning were greater (P ≤ 0.05) for the Increased than the Decreased treatment (13.3 and 11.3, respectively); the Control treatment was intermediate (12.6) and not different (P > 0.05) to the other treatments. The log odds of PWM increased with the decreasing birth weight, at a similar rate (P > 0.05) for all Litter Size treatments. However, the intercept was greater (P ≤ 0.05) for the Increased compared with the Decreased treatment; the Control was intermediate and different (P > 0.05) to the other two treatments. Mean WW tended (P = 0.07) to be greater for the Decreased (6.17 kg) compared to the Control and Increased treatments (5.86 and 5.84 kg, respectively). In conclusion, increasing litter size after cross-fostering relative to the number of functional teats of the sow increased piglet PWM, and tended to decrease WW.

Effect of drying and warming piglets at birth on preweaning mortality.

Piglets are susceptible to hypothermia early after birth, which is a major predisposing factor for preweaning mortality (PWM). Drying and warming piglets at birth has been shown to reduce early postnatal temperature decline. This study evaluated the effect of drying and warming piglets at birth on PWM and weaning weight (WW) under commercial conditions. A completely randomized design was used with 802 sows/litters (10,327 piglets); sows/litters were randomly allotted at start of farrowing to one of two Intervention Treatments (applied at birth): Control (no drying or warming); Drying+Warming (dried with a cellulose-based desiccant and placed in a box under a heat lamp for 30 min). Piglets were weighed at birth and weaning; PWM was recorded. Rectal temperature was measured at 0 and 30 min after birth on all piglets in a subsample of 10% of litters. The effect of farrowing pen temperature (FPT) on WW and PWM was evaluated by comparing litters born under COOL (<25°C) to those born under WARM (≥25°C) FPT. The effect of birth weight on WW and PWM was evaluated by comparing three birth weight categories (BWC; Light: <1.0 kg, Medium: 1.0 to 1.5 kg, or Heavy: >1.5 kg). PROC GLIMMIX and MIXED of SAS were used to analyze mortality and other data, respectively. Litter was the experimental unit; piglet was a subsample of litter. The model included fixed effects of Intervention Treatment, and FPT or BWC as appropriate, the interaction, and the random effects of litter. Piglet rectal temperature at 30 min after birth was greater (P ≤ 0.05) for the Drying+Warming than the Control treatment (+2.33°C). Overall, there was no effect (P > 0.05) of Intervention Treatment on PWM or WW, and there were no Intervention Treatment by BWC interactions (P > 0.05) for these measurements. There was an Intervention Treatment by FPT interaction (P ≤ 0.05) for PWM. Drying and warming piglets reduced (P ≤ 0.05) PWM under COOL (by 2.4 percentage units) but not WARM FPT. In addition, WW were lower (P ≤ 0.05) under WARM (by 0.79 kg) than COOL FPT; however, there was no interaction (P > 0.05) with Intervention Treatment. In conclusion, this study suggests that drying and warming piglets at birth increases rectal temperature and may reduce PWM under cooler conditions, which are typically experienced in temperate climates during the majority of the year.

Effect of rearing cross-fostered piglets in litters of either uniform or mixed birth weights on preweaning growth and mortality.

Cross-fostering is a practice commonly used in the swine industry to equalize litter sizes, however, there is limited understanding of the optimum cross-fostering methods that will maximize piglet preweaning growth and survival. This study evaluated the effects of within-litter variation in birth weight after cross-fostering on piglet preweaning mortality (PWM) and weaning weight (WW) using litters of 15 piglets. A hierarchical incomplete block design was used (blocking factors: day of farrowing and sow parity, body condition score, and number of functional teats) with a 3 × 2 factorial arrangement of treatments: 1) Birth Weight Category (BWC): Light (<1.0 kg), Medium (1.0 to 1.5 kg), or Heavy (1.5 to 2.0 kg); 2) Litter Composition: UNIFORM (all 15 piglets in each litter of the same BWC), or MIXED (five piglets in each litter from each BWC, i.e., five Light, five Medium, and five Heavy piglets). At 24 h after birth, piglets were weighed and randomly allotted to litter composition treatments from within BWC. The experimental unit was five piglets of the same BWC; there were three experimental units within each Litter Composition treatment litter. There were 17 blocks, each of six litters (one UNIFORM litter of each BWC; three MIXED litters) and 51 replicates (three replicates per block of six litters) for a total of 102 cross-fostered litters and 1,530 piglets. Piglets were weaned at 19.7 ± 0.46 d of age; WW and PWM were measured. PROC GLIMMIX and MIXED of SAS were used to analyze PWM and WW, respectively. Models included BWC, Litter Composition, the interaction, and replicate within the block. There were BWC by Litter Composition treatment interactions (P ≤ 0.05) for PWM and WW. Preweaning mortality was greater (P ≤ 0.05) for Light piglets in MIXED than UNIFORM litters. In contrast, for Heavy piglets, PWM was greater (P ≤ 0.05) and WW was lower (P ≤ 0.05) in UNIFORM than MIXED litters. Medium piglets had similar (P > 0.05) PWM and WW in UNIFORM and MIXED litters. The results of this study, which involved large litter sizes typical of current commercial production, suggested that for piglet survival to weaning, using cross-fostering to form litters of piglets of similar birth weight was beneficial for light piglets, detrimental for heavy piglets, and neutral for medium piglets.

Effect of within-litter birth weight variation after cross-fostering on piglet preweaning growth and mortality.

Cross-fostering is commonly used in commercial swine production to equalize litter sizes and/or adjust piglet birth weights within litters. However, there is limited published information on optimum cross-fostering procedures. This study evaluated the effects of within-litter birth weight variation after cross-fostering (using litters of 14 piglets) on piglet preweaning mortality (PWM) and weaning weight (WW). An RCBD was used (blocking factors were day of farrowing and sow parity, body condition score, and functional teat number) with an incomplete factorial arrangement of the following two treatments: 1) birth weight category (BWC): light (<1.0 kg), medium (1.0 to 1.5 kg), or heavy (1.5 to 2.0 kg); 2) litter composition: uniform, all piglets in the litter of the same BWC [uniform light (14 light piglets); uniform medium (14 medium piglets); uniform heavy (14 heavy piglets)]; mixed, piglets in the litter of two or more BWC [L+M (seven light and seven medium piglets); M+H (seven medium and seven heavy piglets); L+M+H (three light, six medium, and five heavy piglets)]. Piglets were weighed at 24 h after birth and randomly allotted to litter composition treatment from within BWC; all piglets were cross-fostered. There were 47 blocks of six litters (total 282 litters and 3,948 piglets). Weaning weights were collected at 18.7 ± 0.64 d of age; all PWM was recorded. Individual piglet WW and PWM data were analyzed using PROC MIXED and PROC GLIMMIX of SAS, respectively; models included fixed effects of BWC, litter composition, and the interaction, and random effects of sow within the block. There was litter composition by BWC interactions (P ≤ 0.05) for WW and PWM. Within each BWC, WW generally increased and PWM generally decreased as littermate weight decreased. For example, WW was greatest (P ≤ 0.05) for light piglets in uniform light litters, for medium piglets in L+M litters, and for heavy piglets in L+M+H litters. Preweaning mortality was lowest (P ≤ 0.05) for medium piglets in L+M litters, and for heavy piglets in L+M+H litters; however, litter composition had no effect (P > 0.05) on PWM of light piglets. In conclusion, increasing the average birth weight of littermates after cross-fostering generally decreased WW and increased PWM for piglets of all birth weight categories. This implies that the optimum approach to cross-fostering that maximizes piglet preweaning growth and survival is likely to vary depending on the birth weight distribution of the population.

Effect of farrowing pen size on pre-weaning performance of piglets.

Litter sizes in commercial pig production have increased substantially over recent years; however, farrowing pen sizes have generally not changed over the same time period. The objective of this study was to evaluate the effect of farrowing pen size on piglet pre-weaning growth and mortality. Differences in pen size were created by varying the width of pens of the same length, increasing the creep area available to the piglets. The study used a total of 1,786 litters in a randomized complete block design to compare two farrowing pen size treatments (FPS): Standard (pen width 1.52 m) and Increased (pen width 1.68 m). Litter sizes were equalized across treatments (12.9 ± 1.95 piglets) at 24 h after birth using cross-fostering. Litter weights were collected at birth and weaning (21.3 ± 2.08 d); pre-weaning mortality was recorded. The experimental unit was the litter; models for statistical analysis included FPS and replicate. Farrowing pen size had no effect (P > 0.05) on litter size at birth (12.8 and 13.0 for the Standard and Increased FPS, respectively), after cross-fostering (12.9 for both treatments), or at weaning (11.2 and 11.3, respectively). There was no effect (P > 0.05) of FPS on total litter or average piglet weight at birth, after cross-fostering, and at weaning. These results suggest no benefit in piglet performance from increasing the width of farrowing pens. As litter sizes continue to increase in commercial production, further research is warranted to re-evaluate the impact of farrowing pen size on pre-weaning mortality.

Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs.

BACKGROUND: The role of the microbiome in livestock production has been highlighted in recent research. Currently, little is known about the microbiome's impact across different systems of production in swine, particularly between selection nucleus and commercial populations. In this paper, we investigated fecal microbial composition in nucleus versus commercial systems at different time points. RESULTS: We identified microbial OTUs associated with growth and carcass composition in each of the two populations, as well as the subset common to both. The two systems were represented by individuals with sizeable microbial diversity at weaning. At later times microbial composition varied between commercial and nucleus, with species of the genus Lactobacillus more prominent in the nucleus population. In the commercial populations, OTUs of the genera Lactobacillus and Peptococcus were associated with an increase in both growth rate and fatness. In the nucleus population, members of the genus Succinivibrio were negatively correlated with all growth and carcass traits, while OTUs of the genus Roseburia had a positive association with growth parameters. Lactobacillus and Peptococcus OTUs showed consistent effects for fat deposition and daily gain in both nucleus and commercial populations. Similarly, OTUs of the Blautia genus were positively associated with daily gain and fat deposition. In contrast, an increase in the abundance of the Bacteroides genus was negatively associated with growth performance parameters. CONCLUSIONS: The current study provides a first characterization of microbial communities' value throughout the pork production systems. It also provides information for incorporating microbial composition into the selection process in the quest for affordable and sustainable protein production in swine.

Effects of drying and providing supplemental oxygen to piglets at birth on rectal temperature over the first 24 h after birth.

Neonatal piglets can experience both a decrease in body temperature and hypoxia, increasing risks for pre-weaning mortality. This research evaluated the effects of drying and providing supplemental oxygen to newborn piglets on rectal temperature (RT) over the first 24 h after birth. The study used a CRD with three Intervention Treatments (IT; applied at birth): Control (no intervention), Drying (dried using a desiccant), Oxygen [dried using a desiccant and placed in a chamber (at 40% oxygen concentration) for 20 min]. A total of 42 litters (485 piglets) were randomly allotted to treatments at the start of farrowing. At birth, each piglet was given a numbered ear tag, weighed, and the treatment was applied; RT was measured at 0, 20, 30, 45, 60, 120, and 1440 min after birth. Blood was collected from one piglet from each birth weight quartile within each litter at 24 h after birth to measure plasma immunocrit concentration. There was no effect (P > 0.05) of IT on piglet RT at 0 or 1440 min after birth. Between 20 and 60 min after birth, piglet RT was lower (P ≤ 0.05) for the Control than the Drying treatment, with the Oxygen treatment being intermediate and different (P ≤ 0.05) from the other two IT. The effect of piglet birth weight on responses to IT were evaluated by classifying piglets into Birth Weight Categories (BWC): Light (<1.0 kg), Medium (1.0 to 1.5 kg), or Heavy (>1.5 kg). There were IT by BWC interactions (P ≤ 0.05) for piglet RT at all measurement times between 20 and 120 min after birth. Relative to the Control, the effects of the Drying and Oxygen treatments on RT were greater (P ≤ 0.05) for Light than heavier piglets. Plasma immunocrit concentrations tended (P = 0.07) to be greater for piglets on the Control treatment compared to the other two IT and were lower (P ≤ 0.05) for Light than Heavy piglets, with Medium piglets being intermediate and different (P ≤ 0.05) to the other BWC. In conclusion, drying piglets at birth reduced the extent and duration of RT decline in piglets in the early postnatal period compared to undried piglets, especially for those of low birth weight. However, the combination of drying and placing piglets in an oxygen-rich environment provided no additional benefit over drying alone.

Effect of drying and/or warming piglets at birth under warm farrowing room temperatures on piglet rectal temperature over the first 24 h after birth.

Piglets experience a decline in body temperature immediately after birth, and both drying and warming piglets at birth reduce this. However, these interventions may be less effective at higher farrowing room temperatures. This study was carried out at a commercial facility to compare the effect of drying and/or warming piglets at birth on postnatal rectal temperature (RT) under relatively warm farrowing room temperatures (26.6 ± 2.09 °C). Forty-five sows/litters were used in a completely randomized design to compare three Intervention Treatments (applied at birth): Control (no treatment); Warming (piglets placed in a plastic box under a heat lamp for 30 min); and Drying+Warming (piglets dried with desiccant and warmed as above). Temperatures in the warming boxes over the study period averaged 37.7 ± 2.75 °C. At birth, piglets were weighed; RT temperature was measured at 0, 10, 20, 30, 45, 60, 120, and 1,440 min after birth. Blood samples were collected at 24 h after birth from a subsample of one piglet from each birth weight quartile within each litter to measure plasma immunocrit concentration. Data were analyzed using PROC MIXED of SAS with litter as the experimental unit, and piglet as a subsample of litter. The model for analysis of piglet rectal temperature included fixed effects of Intervention Treatment, measurement time (repeated measure), the interaction, and the random effect of sow. Compared with the Control, piglet RT were higher (P ≤ 0.05) for the Warming treatment between 10 and 60 min, and higher (P ≤ 0.05) for the Drying+Warming treatment between 10 and 120 min after birth. Rectal temperatures were higher (P ≤ 0.05) for the Drying+Warming than the Warming treatment between 20 and 120 min. Responses to drying and/or warming were greater for low-birth-weight piglets (<1.0 kg) than heavier littermates, but were generally less than observed in previous experiments with similar treatments carried out under cooler temperatures. Piglet immunocrit values were lower (P ≤ 0.05) for the Drying+Warming treatment compared to the other Intervention Treatments, which were similar (P > 0.05). Immunocrit values tended (P = 0.10) to be lower for light (<1.0 kg) compared with heavier birth weight piglets. In conclusion, drying and warming piglets at birth was more effective for reducing piglet RT decline after birth than warming alone, though the effect was less than observed in previous studies carried out under cooler farrowing room temperatures.

Gut microbiome mediates host genomic effects on phenotypes: a case study with fat deposition in pigs.

A large number of studies have highlighted the importance of gut microbiome composition in shaping fat deposition in mammals. Several studies have also highlighted how host genome controls the abundance of certain species that make up the gut microbiota. We propose a systematic approach to infer how the host genome can control the gut microbiome, which in turn contributes to the host phenotype determination. We implemented a mediation test that can be applied to measured and latent dependent variables to describe fat deposition in swine (Sus scrofa). In this study, we identify several host genomic features having a microbiome-mediated effects on fat deposition. This demonstrates how the host genome can affect the phenotypic trait by inducing a change in gut microbiome composition that leads to a change in the phenotype. Host genomic variants identified through our analysis are different than the ones detected in a traditional genome-wide association study. In addition, the use of latent dependent variables allows for the discovery of additional host genomic features that do not show a significant effect on the measured variables. Microbiome-mediated host genomic effects can help understand the genetic determination of fat deposition. Since their contribution to the overall genetic variance is usually not included in association studies, they can contribute to filling the missing heritability gap and provide further insights into the host genome - gut microbiome interplay. Further studies should focus on the portability of these effects to other populations as well as their preservation when pro-/pre-/anti-biotics are used (i.e. remediation).

Effect of method of drying piglets at birth on rectal temperature over the first 24 h after birth.

Piglets are born wet, and evaporation of that moisture decreases body temperature, increasing the risk of mortality. The objective of this study was to compare the effect of two commercially applicable methods for drying piglets at birth on piglet rectal temperature over 24 h after birth. The study was carried out in standard commercial farrowing facilities with 52 litters, using a completely randomized design with three Drying Treatments: Control (not dried); Desiccant (dried at birth using a cellulose-based desiccant); Paper Towel (dried at birth using paper towels). Litters were randomly allotted to treatments at the birth of the first piglet. At birth, piglets were individually identified, and the treatment was applied. Rectal temperature was measured at 0, 10, 20, 30, 45, 60, 120, and 1,440 min (24 h) after birth. Data were analyzed using a repeated measures model with PROC MIXED of SAS, with litter as the experimental unit and piglet a subsample of the litter. The model included the fixed effects of treatment and time (as a repeated measure), and the interaction. There was no effect (P > 0.05) of treatment on temperature at birth, or 10 or 1,440 min after birth. Piglet temperatures between 20 and 120 min after birth were similar (P > 0.05) for the Desiccant and Paper Towel treatments, but were greater (P ≤ 0.05) than the Control. The effect of birth weight on the response to Drying Treatment was evaluated by dividing the data into Light (<1.0 kg), Medium (1.0 to 1.5 kg), or Heavy (>1.5 kg) piglet Birth Weight Categories. Piglet rectal temperature data at each measurement time were analyzed using a model that included the fixed effects of Birth Weight Category, Drying Treatment, and the interaction. Temperatures of Light piglets were lower (P ≤ 0.05) than those of Heavy piglets between 20 and 120 min after birth, with Medium piglets being intermediate and generally different to the other two weight categories at these times. The difference in temperature between Light as compared with Medium or Heavy piglets was greater for the Control than the other two Drying Treatments at 60 min after birth. These results suggest that drying piglets at birth is an effective method to reduce rectal temperature decline in the early postnatal period, especially for low birth weight piglets.

Effect of drying and/or warming piglets at birth on rectal temperature over the first 24 h after birth.

Piglets experience a rapid decrease in body temperature immediately after birth, increasing the risk of mortality. The objective of this study was to determine the effect of drying and/or warming piglets at birth on rectal temperature over the first 24 h after birth. The study was carried out at a commercial sow facility using a completely randomized design with four treatments (applied to piglets at birth): Control (no drying or warming), Desiccant (dried using a desiccant), Warming Box (placed in a box under a heat lamp for 30 min), and Desiccant + Warming Box (both dried and warmed as above). Farrowing pens had one heat lamp, temperatures under which were similar to the warming box (35 °C). A total of 68 litters (866 piglets) were randomly allotted to a treatment at the birth of the first piglet. At birth, each piglet was identified with a numbered ear tag and weighed; rectal temperature was measured at 0, 10, 20, 30, 45, 60, 120, and 1,440 min after birth. Data were analyzed using a repeated-measures model using PROC MIXED of SAS. Litter was the experimental unit, piglet was a subsample of the litter; and the model included the fixed effects of treatment, time (the repeated measure), and the interaction. Rectal temperatures at birth and 1,440 min after birth were similar (P > 0.05) for all treatments. At all times between 10 and 120 min after birth, Control piglets had lower (P ≤ 0.05) temperatures than the other three treatments. The Desiccant and Warming Box treatments had similar (P > 0.05) temperatures at most measurement times, but the Desiccant + Warming Box treatment had the highest (P ≤ 0.05) rectal temperatures at most times between 10 and 60 min. In addition, for all treatments, light (<1.0 kg) birth weight piglets had lower (P ≤ 0.05) temperatures than medium (1.0-1.5 kg) or heavy (>1.5 kg) piglets at all times between 10 and 120 min. In addition, at these measurement times, the deviation in temperature between the Control and the other three treatments was greater for light than medium or heavy piglets. In conclusion, both drying and warming piglets at birth significantly increased rectal temperatures between 10 and 120 min after birth, with the combination of the two interventions having the greatest effect, especially for low birth weight piglets.

Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters.

Despite recent efforts to characterize longitudinal variation in the swine gut microbiome, the extent to which a host's genome impacts the composition of its gut microbiome is not yet well understood in pigs. The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. A total of 1,028 pigs were characterized. Animals were genotyped with the Illumina PorcineSNP60 Beadchip. Microbiome samples from fecal swabs were obtained at weaning (Wean), at mid-test during the growth trial (MidTest), and at the end of the growth trial (OffTest). Average daily gain was calculated from birth to week 14 of the growth trial, from weaning to week 14, from week 14 to week 22, and from week 14 to harvest. Backfat and loin depth were also measured at weeks 14 and 22. Heritability estimates (±SE) of Operational Taxonomic Units ranged from 0.025 (±0.0002) to 0.139 (±0.003), from 0.029 (±0.003) to 0.289 (±0.004), and from 0.025 (±0.003) to 0.545 (±0.034) at Wean, MidTest, and OffTest, respectively. Several SNP were significantly associated with taxa at the three time points. These SNP were located in genomic regions containing a total of 68 genes. This study provides new evidence linking gut microbiome composition with growth and carcass traits in swine, while also identifying putative host genetic markers associated with significant differences in the abundance of several prevalent microbiome features.

Increasing the ratio of SID lysine to metabolizable energy improves pig performance during a viral challenge.

Porcine reproductive and respiratory syndrome virus (PRRSV) compromises pig performance. However, increasing standardized ileal digestible Lys per Mcal metabolizable energy (SID Lys:ME) above requirement has been shown to mitigate reduced performance seen during a porcine reproductive and respiratory syndrome (PRRS) virus challenge. The objective of this study was to evaluate the effects of increasing the dietary SID Lys:ME from 100% National Research Council (NRC) requirement to 120% of the requirement in vaccinated (vac+; modified live vaccine Ingelvac PRRS) and non-vaccinated (vac-; no PRRS vaccine) grower pigs subjected to a PRRSV challenge. In addition, the dietary formulation approach to achieve the 120% ratio by increasing Lys relative to energy (HL) or diluting energy in relation to Lys (LE) was evaluated. This allowed us to test the hypothesis that pigs undergoing a health challenge would have the ability to eat to their energy needs. Within vaccine status, 195 mixed-sex pigs, vac+ (35.2 ± 0.60 kg body weight [BW]) and vac- (35.2 ± 0.65 kg BW) were randomly allotted to one of three dietary treatments (2.67, 3.23, or 3.22 g SID Lys:ME) for a 42-d PRRS virus challenge study representing 100%, 120%, and 120% of NRC requirement, respectively. Pigs were randomly allotted across two barns, each containing 24 pens with 7 to 10 pigs per pen (8 pens per diet per vaccine status). On day post-inoculation 0, both barns were inoculated with PRRSV and started on experimental diets. Within vaccine status, weekly and overall challenge period pig performance were assessed. In both vac+ (P < 0.05) and vac- (P < 0.05) pigs, the HL and LE diets increased end BW and overall average daily gain (ADG) ADG compared with pigs fed the control diet (P < 0.05). Overall, average daily feed intake (ADFI) during the challenge period was greater (P < 0.05) for pigs fed the LE diet compared with pigs fed control and HL treatments, regardless of vaccine status (20% and 17% higher ADFI than the control in vac+ and vac- pigs, respectively). The HL vac+ pigs had the greatest gain to feed (G:F) compared with the control and LE pigs (0.438 vs. 0.394 and 0.391 kg/kg, respectively; P < 0.01). Feed efficiency was not impacted (P > 0.10) by treatment in the vac- pigs. In summary, PRRSV-challenged grower pigs consumed feed to meet their energy needs as indicated by the increase in ADFI when energy was diluted in the (LE) diet, compared with control pigs. In both PRRS vac+ and vac- pigs subsequently challenged with PRRSV, regardless of formulation approach, fed 120% SID Lys:ME diets resulted in enhanced overall growth performance.

Genetic Parameters for Tolerance to Heat Stress in Crossbred Swine Carcass Traits.

Data for loin and backfat depth, as well as carcass growth of 126,051 three-way crossbred pigs raised between 2015 and 2019, were combined with climate records of air temperature, relative humidity, and temperature-humidity index. Environmental covariates with the largest impact on the studied traits were incorporated in a random regression model that also included genomic information. Genetic control of tolerance to heat stress and the presence of genotype by environment interaction were detected. Its magnitude was more substantial for loin depth and carcass growth, but all the traits studied showed a different impact of heat stress and different magnitude of genotype by environment interaction. For backfat depth, heritability was larger under comfortable conditions (no heat stress), as compared to heat stress conditions. Genetic correlations between extreme values of environmental conditions were lower (∼0.5 to negative) for growth and loin depth. Based on the solutions obtained from the model, sires were ranked on their breeding value for general performance and tolerance to heat stress. Antagonism between overall performance and tolerance to heat stress was moderate. Still, the models tested can provide valuable information to identify genetic material that is resilient and can perform equally when environmental conditions change. Overall, the results obtained from this study suggest the existence of genotype by environment interaction for carcass traits, as a possible genetic contributor to heat tolerance in swine.

Predicting Growth and Carcass Traits in Swine Using Microbiome Data and Machine Learning Algorithms.

In this paper, we evaluated the power of microbiome measures taken at three time points over the growth test period (weaning, 15 and 22 weeks) to foretell growth and carcass traits in 1039 individuals of a line of crossbred pigs. We measured prediction accuracy as the correlation between actual and predicted phenotypes in a five-fold cross-validation setting. Phenotypic traits measured included live weight measures and carcass composition obtained during the trial as well as at slaughter. We employed a null model excluding microbiome information as a baseline to assess the increase in prediction accuracy stemming from the inclusion of operational taxonomic units (OTU) as predictors. We further contrasted performance of models from the Bayesian alphabet (Bayesian Lasso) as well machine learning approaches (Random Forest and Gradient Boosting) and semi-parametric kernel models (Reproducing Kernel Hilbert space). In most cases, prediction accuracy increased significantly with the inclusion of microbiome data. Accuracy was more substantial with the inclusion of microbiome information taken at weeks 15 and 22, with values ranging from approximately 0.30 for loin traits to more than 0.50 for back fat. Conversely, microbiome composition at weaning resulted in most cases in marginal gains of prediction accuracy, suggesting that later measures might be more useful to include in predictive models. Model choice affected predictions marginally with no clear winner for any model/trait/time point. We, therefore, suggest average prediction across models as a robust strategy in fitting microbiome information. In conclusion, microbiome composition can effectively be used as a predictor of growth and composition traits, particularly for fatness traits. The inclusion of OTU predictors could potentially be used to promote fast growth of individuals while limiting fat accumulation. Early microbiome measures might not be good predictors of growth and OTU information might be best collected at later life stages. Future research should focus on the inclusion of both microbiome as well as host genome information in predictions, as well as the interaction between the two. Furthermore, the influence of the microbiome on feed efficiency as well as carcass and meat quality should be investigated.

Increased lysine: metabolizable energy ratio improves grower pig performance during a porcine reproductive and respiratory syndrome virus challenge.

Porcine reproductive and respiratory syndrome virus (PRRSV) reduces grower pig performance. The amino acid (AA) requirements and lysine:metabolizable energy ratio (Lys:ME) of health-challenged pigs for optimum performance are poorly understood. Two experiments were conducted to evaluate the effect of increasing standardized ileal digestible (SID) Lys:ME (g SID Lys per Mcal ME) on growth performance during a PRRSV challenge. In Exp. 1, a total of 379 barrows (51.3 ± 0.3 kg body weight [BW]) were allotted to one of six diets (1.87 to 3.41 Lys:ME) for a 35-d growth study. In Exp. 2, a total of 389 barrows (29.2 ± 0.23 kg BW) were allotted to one of six diets (2.39 to 3.91 Lys:ME) for a 49-d growth study. These isocaloric diets represented 80% to 130% of National Research Council (NRC) SID Lys requirement. For each experiment, pigs were randomly allotted across two barns of 24 pens each with seven to nine pigs per pen (four pens per diet per health status). On day 0, one barn was inoculated with live PRRSV, one barn sham inoculated (control), and all pigs were started on experimental diets. Pen growth performance and feed intake were recorded weekly and gain-to-feed ratio (G:F) was calculated. Breakpoint analysis was used to determine the Lys:ME that maximized average daily gain (ADG) and G:F over the 35 or 49-d test periods for Exp. 1 and 2, respectively. In Exp. 1, increasing Lys:ME increased ADG (quadratic P = 0.01) and G:F (linear and quadratic P = 0.04) in control pigs over 35 d. In PRRSV-infected pigs, ADG and G:F increased linearly with increasing Lys:ME (P < 0.01). The Lys:ME for optimum ADG and G:F during PRRSV challenge was 2.83 and 3.17, respectively, compared to 2.24 and 2.83, respectively, in control pigs using a one-slope broken-line model. In Exp. 2, pigs in the control barn became naturally infected after 21 days post inoculation. Before infection, ADG and G:F increased with increasing Lys:ME in control and PRRSV-infected pigs (linear and quadratic P < 0.05), and optimum ADG and G:F were achieved at 3.02 and 2.92 Lys:ME, respectively, in PRRSV-infected pigs compared to 2.82 and 3.22 Lys:ME, respectively, in control pigs. Over the 49-d period, increasing Lys:ME improved ADG (P < 0.01, linear and quadratic) and G:F (linear P < 0.01) in naturally infected pigs. The response was similar in experimental infection for ADG (P < 0.01, linear and quadratic) and G:F (linear P = 0.01). The optimum ratio for ADG (2.86 vs. 3.12 Lys:ME) and G:F (3.18 vs. 3.08 Lys:ME) were similar between natural and experimental infection. In summary, increasing Lys:ME by 10% to 20% above NRC requirements improved performance and feed efficiency during an experimental and natural PRRSV challenge.

Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth.

BACKGROUND: In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated. RESULTS: Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter "week 15"), and end-of-feeding test (hereafter "off-test"), were used to evaluate changes in the composition of the fecal microbiome of each animal over time. This study used 1205, 1295, and 1283 samples collected at weaning, week 15, and off-test, respectively. There were 1039 animals that had samples collected at all three time points and also had phenotypic records on back fat thickness (BF) and average daily body weight gain (ADG). Firmicutes and Bacteroidetes were the most abundant phyla at all three time points. The most abundant genera at all three time points included Clostridium, Escherichia, Bacteroides, Prevotella, Ruminococcus, Fusobacterium, Campylobacter, Eubacterium, and Lactobacillus. Two enterotypes were identified at each time point. However, only enterotypes at week 15 and off-test were significantly associated with BF. We report herein two novel findings: (i) alpha diversity and operational taxonomic unit (OTU) richness were moderately heritable at week 15, h2 of 0.15 ± 0.06 to 0.16 ± 0.07 and 0.23 ± 0.09 to 0.26 ± 0.08, respectively, as well as at off-test, h2 of 0.20 ± 0.09 to 0.33 ± 0.10 and 0.17 ± 0.08 to 0.24 ± 0.08, respectively, whereas very low heritability estimates for both measures were detected at weaning; and (ii) alpha diversity at week 15 had strong and negative genetic correlations with BF, - 0.53 ± 0.23 to - 0.45 ± 0.25, as well as with ADG, - 0.53 ± 0.32 to - 0.53 ± 0.29. CONCLUSIONS: These results are important for efforts to genetically improve the domesticated pig because they suggest fecal microbiota diversity can be used as an indicator trait to improve traits that are expensive to measure.