Search

Vitamin B and trace minerals are crucial molecular signals involved in many biological pathways of energy metabolism and their bioavailability is compromised in high-producing ruminant animals. Despite the current knowledge of the effects of vitamin B complex and trace minerals on animal performance, their use as a rumen-protected form and its impact on liver metabolism in finishing beef cattle is poorly known. The present study aimed to assess the effects of ruminally protected B-vitamin blend (Trouw Nutrition, Italy) and hydroxy trace minerals (Cu and Zn; Micronutrients Inc., Indianapolis, IN) on hepatic proteome. A total of 20 non-castrated Nellore males with 353 ± 43 kg of initial BW were submitted in a high supplementation (1.7% of BW) in pasture and randomly assigned to one of the following treatments: CTRL – inorganic trace minerals without supplementation of vitamin B blend; SUP – supplementation of hydroxy trace minerals (Cu and Zn) and vitamin B blend (B5, B6, B7, B9, and B12). All animals were fed the same level of the experimental diet for 106 days and liver biopsy was performed at the end of the experimental period. We use shotgun proteomics combined with biological and network analyses of the protein differentially abundant between treatments, showing 37 proteins differentially abundant (P < 0.10) between treatment groups, where all proteins were up-regulated in the SUP treatment. These proteins were related to protein folding (P = 0.0456), oxidoreductase complex (P = 0.0155), mitochondrial respiratory chain complex IV (P = 0.0132), chaperonin-containing T-complex 2 (P = 0.0132), glutathione metabolism (P = 0.00026) and other linked to oxidative stress regulation. These results indicate that ruminal-protected vitamin B and hydroxy trace minerals supplementation during the finishing phase cause positive changes in the abundance of proteins related to oxidative metabolism and response to oxidative damage.

Most tall fescue [Lolium arundinaceum (Schreb.) Darbysh] in the Southeastern United States contains an endophyte that causes fescue toxicosis (FT) in grazing animals, a serious disease that causes approximately $1 billion in economic losses to the animal industries in the United States. Recently, a genetic test called T-Snip (AgBotanica, LCC, Columbia, MO), was developed with the objective of identifying animals with genetic variation for FT tolerance. The aim of this study was to validate the use of this genetic test in mature, pregnant cows. Over 13 wk, weekly phenotypic data, including body weight, rectal temperatures, hair coat scores, hair shedding scores, and body condition scores, were collected on 148 pregnant purebred Angus cows at 2 locations in NC where infected fescue was the primary source of feed. Birth weights (cBW) and 205-d adjusted weaning weights (adjWW) from these cow’s calves were recorded. All cows were genotyped for T-Snip. At the end of the trial, each phenotypic trait was calculated as the slope of the linear regression of performance on weeks. The effect of T-Snip rating genotypes (4 levels) on slope traits was tested using a linear model also including the fixed-effects of location, parity, and the initial measurement for each trait (covariate). For cBW and adjWW, the model also included the sex of the calf and the month of birth as categorical effects. Associations of T-Snip genotypes were observed for body weight gain (aBWd) of pregnant cows (P = 0.15; interaction with location), change in body condition score (aBCSd; P = 0.13), and adjWW (P = 0.06; interaction with location). For aBWd and adjWW, associations were found just within one location (P = 0.017 and 0.047, respectively), which was the location with higher endophyte infection rate. For all associations, the direction of the T-Snip genotypes was the same and as expected: the greater the genotype score, the better performance. No associations were found for the other traits (P > 0.10). These results indicate that the T-Snip test may be predictive of cow performance (aBWd, aBCSd, and adjWW) in an endophyte-infected tall fescue environment.

Microbial phytase is widely used to enhance digestibility of phytate-P. By tradition, diets with P content well below requirement are used to quantify phytate-P release by phytase, but P-adequate diets may be more physiologically relevant. The objective of this study was to investigate the effects of phytase on P digestion and metabolism and develop a P release curve for phytase in P-adequate diets (above requirement according to NRC, 2012), and to compare these effects in a P-deficient diet. Three replicates of 24 barrows each (BW = 23.0 ± 1.8 kg) were randomly assigned to 1 of 8 dietary treatments, housed in individual pens for 21 d, then moved to metabolism crates for 5 d urine and fecal collections. A basal corn-soybean meal diet (P-adequate, A) was formulated at 0.36% standardized total tract digestible (STTD) P and total Ca:STTD P of 1.83. Phytase was added to A at 200 (A200), 400 (A400), 600 (A600), and 800 (A800) phytase units (FTU)/kg. A positive control diet (PC) was formulated using monocalcium phosphate (MCP) to increase STTD P by 0.16% to 0.52%, the expected STTD P release of 800 FTU/kg. A P-deficient diet (D) was formulated by reducing MCP to achieve 0.21% STTD P, and 200 FTU phytase/kg was added to D for D200. Pig was the experimental unit, and replicate and dietary treatment were fixed effects. Orthogonal polynomial contrasts were used to test linear and quadratic effects of phytase within A, A200, A400, A600, and A800. Phytase increased percent apparent total tract digestibility (ATTD) and STTD of P (quadratic P < 0.001), and quantity of absorbed P (linear P < 0.001; quadratic P = 0.069). Urinary P increased linearly with phytase (P < 0.001) and retained P also increased (linear P = 0.001, quadratic P = 0.094). Phytate-P release was estimated to be 0.049, 0.080, 0.093, and 0.09% STTD P for 200, 400, 600, and 800 FTU/kg, respectively. It appears that the effect of phytase may be lower in P-adequate diets as compared to P-deficient diets, given that there was a 12% improvement for A200 versus A, and a 28% improvement in STTD P for D200 versus D. In conclusion, phytase improved P digestibility and retention in P-adequate diets, and P digestibility was used to estimate the quantity of P released by phytase. Further research investigating P release by phytase in P-adequate diets, rather than P-deficient diets, may be preferable.

Residual feed intake (RFI) is the difference between observed and predicted feed intake of an animal, based on growth and maintenance requirements. In Yorkshire pigs, divergent selection for increased (Low RFI) and decreased (High RFI) RFI was carried out over 10 generations (G) while feeding a corn- and soybean-meal-based, higher-energy, lower-fiber (HELF) diet. In G8 to G10, representing 4 replicates, barrows and gilts (n = 649) of the RFI lines were fed the HELF diet and a diet incorporating coproducts that were lower in energy and higher in dietary fiber (LEHF). The diets differed in ME, 3.32 vs. 2.87 Mcal/kg, and in neutral detergent fiber (NDF), 9.4% vs. 25.9%, respectively. The impact of the LEHF diet on 1) performance and growth, 2) diet digestibility, 3) genetic parameter estimates, and 4) responses to selection for RFI, when fed the HELF, was assessed. In general, the LEHF diet reduced the performance of both lines. When fed the HELF diet, the Low RFI pigs had lower (P 0.05) loin muscle area (LMA; +5%); and greater (P < 0.05) feed efficiency (i.e., 8% higher G:F and 7% lower RFI) than the High RFI line. These patterns of line differences were still present under the LEHF diet but differences for ADFI (-11%), energy intake (-10%), G:F (+2%), and RFI (-6%) were reduced compared to the HELF diet. Apparent total tract digestibility (ATTD) of the HELF and LEHF diets was assessed using 116 barrows and gilts from G8. When fed the HELF diet, ATTD of DM, GE, N, and NDF were similar between lines (P ≥ 0.27), but when fed the LEHF diet, the Low RFI pigs had greater digestibility (7%, 7%, 10%, and 32%) than the High RFI line (P ≤ 0.04). To measure responses to selection for RFI and estimate genetic parameters, data from all 10 generations were used (HELF; n = 2,310; LEHF, n = 317). Heritability estimates of performance traits ranged from 0.19 to 0.63, and genetic correlations of traits between diets were high and positive, ranging from 0.87 (RFI) to 0.99 (LMA). By G10, RFI in the Low RFI line was 3.86 and 1.50 genetic SD lower than in the High RFI line when fed the HELF and LEHF diets, respectively. Taken together, the results of this study demonstrate that responses to selection for RFI when fed a HELF diet are not fully realized when pigs are fed an extremely LEHF diet. Thus, feeding diets that differ from those used for selection may not maximize genetic potential for feed efficiency.

Previous studies on genomics of antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) have reported a major quantitative trait locus (QTL) on the major histocompatibility complex (MHC) on chromosome 7, explaining ~25% of the genetic variance of this trait. S/P ratio following modified live PRRSV vaccination in crossbred commercial gilts has been proposed as genetic indicator for reproductive performance in non-infected purebred sows and PRRSV-vaccinated crossbred sows. This motivated further genomic study for this trait by performing haplotype-based genome-wide association study (GWAS). 906 naïve F1 (Landrace x Large White) had blood samples taken at ~50d after vaccination for measuring PRRSV ELISA S/P ratio and genotyping. Haplotype-based GWAS identified 8 genomic regions on chromosomes 4 (108 Mb), 7 (15, 21, and 24–27 Mb), and 9 (33 Mb) that were associated (q-value < 0.07) with S/P ratio. From those, only the MHC region (chromosome 7; 24 – 26 Mb) had been identified in the SNP based GWAS. The main SNP identified in the SNP based GWAS (H3GA0020505) was not in LD with the haplotype; thus, we added this SNP to the haplotype model. We observed that the haplotype explained more of the genetic variance compared to the H3GA0020505 SNP, indicating that the MHC haplotype is in stronger LD with the QTL than the H3GA0020505 SNP. All the significant regions associated with S/P ratio included immune-related candidate genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. This study validated the QTL identified on the MHC region, narrowing the search for causal genes in this region, and identified new genomic regions, along with candidate genes associated with S/P ratio. Identifying novel genomic regions provides more resources for marker-assisted selection and genomic prediction of S/P ratio in purebred and commercial pig populations.

Previous studies proposed the use of antibody response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV), measured as sample-to-positive (S/P) ratio, as a potential indicator trait to improve the reproductive performance of PRRSV-infected Landrace sows. However, this indicator trait has not yet been validated in Landrace sows or evaluated in a terminal sire line, such as Duroc. The main objective of this work was to perform host-genetic analyses of S/P ratio and reproductive traits during a PRRSV outbreak in maternal and terminal breeds. The data consisted of 690 Duroc and 541 Landrace multiparous sows (1.9±1.2 and 2.3±1.5, respectively) with S/P ratio collected at approximately 54 days after the predicted beginning of the outbreak. Of these, 644 Duroc and 528 Landrace sows also had reproductive data recorded during the PRRSV outbreak comprising number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NBM), number born dead (NBD; sum of NSB and NBM), total number born (TNB; sum of NBA and NBD), and number weaned (NW). All animals had genotype data on ~30K SNPs common across both breeds. Heritability estimates (± standard error) of S/P ratio during the PRRSV outbreak were moderate, with 0.33±0.06 for Duroc and 0.28±0.07 for Landrace. Reproductive traits during the PRRSV outbreak had overall low heritability estimates (≤0.18). Favorable genetic correlations of S/P ratio with NBA (0.65±0.33), in accordance with previous studies, and NBD (-0.33±0.28) were observed for Landrace sows only. Estimates of genetic correlation with other traits were -0.21±0.30 (NBM), -0.12±0.29 (NSB), 0.10±0.38 (NW), and 0.54±1.29 (TNB) for Landrace. For Duroc, these estimates were weaker: -0.33±0.40 (NBA), 0.26±0.27 (NBA), and 0.28±0.30 (NW), with convergence issues for mortality traits. These results further support the use of S/P ratio as an indicator trait for improved reproductive performance during a PRRSV outbreak in Landrace sows.

Studies on differences in resilience to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) between breeds are scarce in the literature. Thus, the objective of this work was to assess PRRSV resilience in PRRSV wild-type infected sows from two breeds. Farrowing data included 2546 and 2522 litters from 894 Duroc and 813 Landrace sows, respectively, which were housed together and experienced the same PRRSV outbreak. Traits used for this study were number of piglets born alive (NBA), number born dead (NBD), total number born (TNB), and number weaned (NW). The impact of PRRSV infection was evaluated by comparing the reproductive performance of breeds between PRRS phases (pre-PRRS, PRRS, and post-PRRS). PRRS phases were defined based on the reproductive performance data. NBA, NBD, and NW were analyzed as a proportion of TNB using a Poisson mixed model. Pre-defined contrasts were used to evaluate the effect of breed on PRRSV resilience and on return to PRRSV-free performance, representing the differences between breeds for the difference between pre-PRRS and PRRS phases, and pre-PRRS and post-PRRS phases, respectively. There was a significant (P ≤ 0.003) interaction between PRRS phase and breed for all traits, as shown in Table 1. In general, reproductive performance reduced from pre-PRRS to PRRS, and then increased from PRRS to post-PRRS, as expected. The resilience contrast was significant for all traits (P ≤ 0.003). In all cases, the drop in percent reproductive performance from pre-PRRS to PRRS was lower for Duroc than for Landrace, indicating that Duroc sows have greater PRRSV resilience than Landrace sows. The return to PRRSV-free performance contrast had a trending effect for NBD (P = 0.055), and it was not significant for the other traits (P ≥ 0.515). These results indicate that Duroc sows have overall greater phenotypic PRRSV resilience for reproductive performance than Landrace sows.

This study aimed to evaluate the effects of dietary chromium, CLA, and ractopamine on performance, carcass traits, and pork quality of finishing pigs slaughtered at 115 kg BW. Ninety-six crossbred barrows (initial BW = 70.21 ± 1.98 kg) were randomly assigned to 1 of 6 dietary treatments. There were 8 replicates per treatment (48 pens; 2 pigs/pen). A diet formulated according to the nutritional requirements was used as the control (CON). The other 5 diets were based on the CON and supplemented as follows: 0.4 mg/kg Cr yeast (CrY); 0.5% CLA; 0.4 mg/kg CrY and 0.5% CLA (CrY + CLA); 20 mg/kg ractopamine (RAC); 0.4 mg/kg CrY and 20 mg/kg RAC (CrY + RAC). Lysine levels on diets containing ractopamine were raised by 20% compared to CON to meet the greater requirements of pigs fed ractopamine. Pigs fed RAC and CrY + RAC were fed CON for the first 17 d, and then the respective diets for the last 28 d on trial. Data were analyzed in a model including the fixed effect of treatment (6 levels) and initial BW as a covariate for all characteristics, with the exception of carcass traits, in which final BW was used as a covariate. Least-squares means were separated using Tukey-Kramer's method. Differences were considered when probability values were lower than 0.05. Pigs fed RAC and CrY + RAC had the greatest ( 0.05) pork quality, except for color. No differences ( > 0.05) were observed for carcasses pH and temperature. The values for pigs fed RAC were greater ( = 0.01) than pigs fed other diets. Pigs fed RAC had lower ( < 0.01) values compared to pigs fed other experimental diets. Serum urea nitrogen concentration (SUN) was lower ( = 0.02) in pigs fed CrY + RAC than in pigs fed CON and RAC and similar to pigs fed the other feeding additives. In summary, it was demonstrated that, when combined, CrY and RAC increase LM area and carcass yield, and reduce SUN, suggesting that chromium could improve nutrient utilization by muscle cells in RAC-fed pigs. Additionally, the additives have no major effects on pork quality.

The vaginal microbiome of gilts vaccinated for porcine reproductive and respiratory syndrome (PRRS) has been previously associated with first-parity reproductive performance in absence of PRRS outbreak. However, associations using multiparous sows have not been investigated. The objective of this study was to associate the vaginal microbiota of PRRS-vaccinated gilts with longevity. Vaginal swabs from 251 commercial F1 gilts (Landrace/Large-White) were collected on days 4 and 52 after PRRS vaccination (dpv) for 16S rRNA sequencing. Sequences were clustered into operational taxonomic unit (OTU). Sows were assigned to one of four groups according to the maximum parity reached (number of animals): without parity (13), first-parity (45), second-parity (47), and 3 or more parities (146). A negative binomial mixed model including fixed effects of group, dpv, group*dpv, and collection age (covariate), and random effect of animal, was used to identify OTUs with differential abundance. The false discovery rate method was used for multiple test correction. Canonical discriminant analysis (CDA) was performed to classify animals into the four parity groups by including significant OTUs in stepwise selection (P < 0.05) using the whole data. A leave-one-out-cross-validation was used to assess the predictive ability of OTUs to correctly classify animals into the parity groups. Abundance of five and four OTUs was associated (q < 0.05) with group and with group*dpv (q < 0.05), respectively. In the CDA analysis, 220 OTUs identified in the vaginal microbiome were included (P < 0.05). The first and second canonical variables explained 96.6 and 3.4% of the variation, respectively. All animals were correctly classified into their respective parity groups. This study indicates that the vaginal microbiome composition of gilts collected after PRRS-vaccination may be used to predict longevity in commercial sow herds. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (Capes) – Finance Code 001.

Reproductive efficiency is critical to maximizing productivity in the swine industry. A recent study indicated that vulva score (VSC) assessed prior to puberty may be predictive of reproductive performance in sows, in which gilts with greater VSC had greater reproductive performance. The objective of this study was to validate the effect of VSC on reproductive performance, to estimate genetic parameters, and to perform genomic analysis of VSC. A total of 5494 phenotypes and 1326 genotypes (~50K SNPs) from two farms were available for this study. Measurements included VSC assessed using a three-point scale: small (VSC-S), medium (VSC-M), and large (VSC-L), at 15 and 14 weeks of age, for Farm 1 and 2, respectively, and subsequent first parity performance. Genetic parameters were estimated using single-step GBLUP. Genome-wide association study (GWAS) was performed for VSC using BayesB (p=0.999). For Farm1, VSC-L was associated with a greater (P-value=0.04) farrow rate (0.68±0.03) than VSC-S (0.53±0.07). For Farm2, VSC-L was associated with greater (P-value=0.04) number of piglets born alive (NBA; 11.4±0.17) and less mummified fetuses (P-value=0.03; 0.09±0.01) than VSC-S (10.9±0.14; 0.14±0.01). Heritability estimates of VSC were 0.35±0.06 for Farm1 and 0.34±0.05 for Farm2. Moderate genetic correlations between VSC with reproductive traits were found for total number born (0.61±0.21) and NBA (0.62±0.19). The GWAS identified multiple genomic regions associated with VSC. Of these, a QTL located on chromosome 1 at 85Mb accounted for >3% of the genetic variance. This region harbors ADAM21, a gene that has been associated with early embryonic development in pigs. These results validated the use of VSC for prediction of first-parity performance, identified genomic regions controlling VSC, and indicate that selection for increased VSC is possible and could improve reproductive efficiency in swine. We are grateful to Fast Genetics for providing the data and the Iowa Pork Industry Center for financial support.

Allocation of treatments to experimental units (EUs) is done at random. In the presence of a concomitant variable (e.g., initial body weight; iBW), one strategy is to block WUs into iBW groups. However, in some scientific manuscripts, EUs are sorted by iBW and then allocated to treatments (e.g., treatments “A” and “B”) based on iBW, such that the lightest EU receives “A,” the second and third lightest receive “B,” etc. Although this strategy guarantees similar iBW between treatments, this ignores the random process required for statistical analysis of the data. We aimed to quantify the impact of lack of randomization on the statistical power and type I error of completely randomized designs (CRD). Data were simulated for ADG using two treatments (“A” having 50 g/d more than “B,” and MSE=1250 g2/d2). Data were simulated for different replicates per treatment (RepsPerTreat; from 3 to 18, every 3). We used two scenarios for the correlations between iBW and ADG (ρ ADG,iBW): 0 and 0.5. Treatments were allocated to EUs at random (CRD) or according to the order of EUs based on iBW (completely non-randomized design; CNRD). The model included the fixed-effects of intercept and treatment. For ρ ADG,iBW=0, results showed that CRD had greater statistical power (POW) than CNRD for RepsPerTreat from 3 to 9, whereas CNRD had greater from 12 to 18. For ρ ADG,iBW=0.5, CNRD had an even greater POW than CRD starting at 9 RepsPerTreat. Although the type I error (ERROR) of CRD were close to 5% across all scenarios with different RepsPerTreat, CNRD had consistently greater and lower ERROR than CRD with =0 and 0.5, respectively. Having ERROR deviating from 5% is not expected. Visual inspection of the F-values of these models when the null hypothesis was true showed that a distribution other than the theoretical F-distribution, indicating that the statistical test is not valid. Sorting EUs by iBW does not guarantee greater statistical power but results in invalid F-tests.

The use of corn coproducts increases the concentration of fiber and, often, the use of supplemental lipids in swine diets, which may affect energy and nutrient digestibility. An experiment was conducted to determine the effects of reduced-oil distillers' dried grains with solubles (DDGS) and soybean oil (SBO) on dietary AA, acid hydrolyzed ether extract (AEE), and NDF digestibility in corn-based diets fed to growing pigs. Eighteen growing pigs (33.8 ± 2.2 kg BW) were surgically fitted with a T-cannula in the distal ileum and allocated to 1 of 6 dietary treatment groups in a 3-period incomplete Latin square design, with 9 observations per treatment. Six dietary treatments were obtained by adding 0, 20, and 40% DDGS to corn-casein diets formulated with 2 and 6% SBO. Ileal digesta and fecal samples were collected and the apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of AEE and NDF and the AID of AA were determined. Apparent values were corrected for endogenous losses of lipids, and true ileal (TID) and true total tract digestibility (TTTD) values of lipids were calculated. Results showed that the AID of Lys decreased (0.001) with the inclusion of DDGS but was not affected ( = 0.63) by the inclusion of SBO. An interaction between DDGS and SBO on the AID ( = 0.002) and ATTD ( = 0.009) of NDF was observed, where the AID and ATTD of NDF decreased with DDGS at 6% SBO but no effect was observed at 2% SBO. The AID of NDF increased with SBO at 0% DDGS, but no effect was observed at 20 or 40% DDGS. An interaction between DDGS and SBO on the AID ( = 0.011) and ATTD ( = 0.008) of AEE was observed, where the AID and ATTD of AEE increased with SBO. The AID and ATTD of AEE increased with DDGS at 2% SBO, but no effect was observed at 6% SBO. Correction by ileal and fecal endogenous loss of AEE (9.5 and 13.6 g/kg of DMI, respectively) showed that increasing dietary AEE had no effect on the TID and TTD of AEE (0.05). In conclusion, the AID of Lys decreased with DDGS and was not affected by lipids from SBO. The greatest AID and ATTD of NDF was observed in diets with a high AEE and low NDF content. Low values of apparent digestibility of AEE in lower-lipid diets are possibly the result of endogenous losses of lipids, because the true digestibility of AEE was not affected by the dietary increase of AEE.

The use of pooled semen (PS), standard procedure at the commercial level of the swine industry, limits genetic progress, since the offspring parentage is unknown. Literature suggests that some boars have a greater number of progeny than others in the same litter when PS is used. The objective of this study was to evaluate different pedigree-relationship matrices for selection purposes when PS is used. Data on a trait with heritability of 0.4 were simulated 1,000 times for 12 scenarios: combination of sires per pool (2 or 3), number of phenotyped progeny (1 or 12), and three boar dominance levels: no dominance (equal probability of parentage), medium dominance, and complete dominance (all progeny from one boar). Ten pools were created for each scenario based on 5 sires and used for 5 dams each. Breeding values (BV) of the progeny were estimated (EBV) using three relationship matrices: known parents (A), using equal probabilities of parentage (E), and probabilities based on known boar dominance (D). Results for each relationship matrix were compared using the average of the true BV (TBV) of the 10% best animals selected based on EBV. Results are presented as percentage TBV of the selected animals compared to using A (Table). In general, D resulted in better results than E as boar dominance increased. Similar results between E and D were obtained when 12 progenies were phenotyped. When one was phenotyped, D was superior than E in the presence of boar dominance. Knowing the probability of each sire contributing to the progeny increases response to selection when pooled semen is used.

Antibody (Ab) response to natural infection with porcine reproductive and respiratory syndrome (PRRS) virus has been shown to be highly heritable (~0.40), to be genetically correlated with farrowing performance in PRRSV-infected sows, be controlled by two major QTL on chromosome 7, among others, and have moderate genomic prediction accuracy. However, waiting for PRRS outbreaks to occur to collect data limits the use of Ab response to select for increased PRRS resilience. Thus, we investigated the genomic basis of Ab response to PRRS vaccination with a modified live PRRSV vaccine as a strategy to generate data for this purpose. Nine hundred and six commercial F1 replacement gilts (189±16 days old) were vaccinated with a commercial PRRS modified live virus vaccine. Blood samples were collected 52 days after vaccination to measure Ab response, as sample-to-positive (S/P) ratio using a commercial ELISA, and for SNP genotyping (~50K). BayesC0 was used to estimate heritability for S/P ratio using in a model with contemporary group (CG) as fixed effect and SNP effects as random. Genome-wide association study and genomic prediction for S/P ratio were performed with BayesB (Pi=0.99). For genomic prediction, a three-fold cross-validation was used, in which each CG (n=3) was used as validation dataset. Accuracy of genomic prediction was defined as the correlation between genomic estimated breeding values and phenotypes adjusted for estimates of fixed effects, weighed by the number of individuals in the validation dataset. Heritability of S/P was moderate (0.35±0.04). A QTL was identified on chromosome 7 (25 Mb) explaining ~28% of the genetic variance. Accuracy of genomic prediction was fairly high (0.60±0.15). This is the first study describing the genomic basis of Ab response to PRRS vaccination with modified-live virus vaccine. Additional work is needed to evaluate the genetic correlation of Ab response to vaccination with resilience traits in pigs.

The use of R-squared as a measurement of prediction in regression is a common practice in animal nutrition studies. Generally, studies use data used to estimate the prediction equation to calculate the R-squared of the equation, which does not represent prediction. The objective was to evaluate the predictive ability of prediction equations using independent datasets. Data were simulated in based on previously reported prediction equations for ADG in nursery pigs: 152 + 195(SID_Lysine%). A completely randomized design with SID_Lysine% levels of 1.2, 1.3, and 1.4% was used. Data were simulated for three CVs representing low, moderate, and high variation in ADG, for low number of replicates per treatment (RepTreat; 4 to 10, every 2). Data were simulated and analyses performed 300 times for each scenario. Prediction equations were estimated for each scenario when significant effect of SID_Lysine% was followed by a significant orthogonal contrast testing the linear effect of SID_Lysine% (P-value< 0.05), and their R-squared were calculated (R2_training). The prediction equation was used to test the fit of the other datasets, and their R-squared were calculated and averaged for each prediction equation (R2_prediction). The relationship between R2_training and R2_prediction was assessed through Spearmen’s correlation and regression of R2_prediction on R2_training, across scenarios. The R2_training and R2_prediction averages were similar with 94.5% and 93.9%, 66.0% and 63.5%, and 46.1% and 42.7%, for low, moderate, and high CVs, respectively. The rank-correlation between R2_training and R2_prediction increased with CV: 0.23, 0.67, and 0.77, for low, moderate, and high CV, respectively. From regression analysis of R2_prediction on R2_training, as CV increased bias increased, with prediction equations with greater R2_training overestimating R2_prediction, and prediction equations with lower R2_training underestimating R2_prediction. These results indicate that in small sample sizes (≤10 per treatment), as CV increases, models with high R-squared are overestimated, and are not as predictable.

Recent studies on host-genetics of response to porcine reproductive and respiratory syndrome virus (PRRSV) infection have shown that genetic markers can be used to predict performance in growing pigs. On the other hand, no work has been done on the genomic prediction of reproductive performance in PRRSV-infected sows. Thus, the objective of this work was to assess the accuracies of genomic prediction for reproductive traits in PRRSV-infected sows. A total of 475 Duroc and 405 Landrace sows with ~30K SNP genotypes had farrowing performance data during the outbreak on: number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NM), piglets born dead (NBD; NSB+NM), total number of piglets born (TNB; NBA+NBD), and piglets weaned (NW). Genomic prediction was performed by Bayes-B with a model fitting parity as fixed-effect and SNP effects as random. Analyses were performed for two scenarios: within-breed and between-breed. For the within-breed prediction, 4-fold cross-validation was used. For the between-breed prediction, all data for each breed were used. Accuracy of genomic prediction (AGP) was calculated as the correlation between genomic estimated breeding values and pre-adjusted phenotype, divided by square-root of heritability. For the within-breed prediction, AGP (± standard deviation) for NBA, NBD, NM, NSB, NW, and TNB were 0.24±0.05, 0.07±0.10, -0.27±0.06, -0.24±0.09, -0.05±0.05, 0.19±0.03, respectively, for Duroc, and 0.37±0.02, 0.38±0.11, 0.30±0.07, 0.60±0.10, 0.09±0.11, 0.15±0.10, respectively, for Landrace. For the between-breed prediction, AGP for NBA, NBD, NM, NSB, NW, and TB were 0.28, -0.17, -0.01, 0.37, 0.27, and 0.29, respectively, when training on Landrace and validating on Duroc, and 0.28, -0.14, 0.01, 0.15, 0.23, and -0.01, respectively, when training on Duroc and validating on Landrace. Results show that the accuracies of genomic prediction for reproductive traits during a PRRSV outbreak are low to moderate.

The objective of this study was to investigate host-genetic contributions to the vaginal microbiome of commercial gilts vaccinated for Porcine Reproductive and Respiratory Syndrome (PRRS). Vaginal swab samples (n = 576) from 308 F1 gilts (183±12 days old) were collected on day 4 (D4) and 52 (D52) post-vaccination with a commercial modified live virus PRRS vaccine. Samples were used to profile the vaginal microbiome by 16S rRNA gene sequencing, with sequences clustered into operational taxonomic units (OTUs) and taxonomically classified. All animals were genotyped for 45,536 SNPs. Arcsine of the square root-transformed OTUs abundance data were analyzed using a linear mixed animal model with age at vaccination as a covariate and animal (random) for estimation of genetic parameters. The same model was used for GWAS for the 100 most abundant OTUs but with addition of genotype of SNPs as a covariate, one at a time. For D4, heritability estimates ranged from < 0.001±0.01(13 OTUs) to 0.60±0.13 (Fusobacterium), with OTUs corresponding to the genera Fusobacterium, Pasteurellaceae, Clostridiales, Prevotellaceae, and Lactobacillus having high estimates (0.41±0.13 to 0.60±0.13). For D52, heritability estimates ranged from < 0.001±0.01 (10 OTUs) to 0.63±0.12 (Terrisporobacter), with OTUs corresponding to Clostridium, Terrisporobacter, Romboutsia, Turicibacter, Phascolarctobacterium, Muribaculaceae, and Ruminococcaceae having high estimates (0.42±0.14 to 0.63±0.12). Forty-six QTLs were significantly (P < 0.00001) associated with OTU across days. Among these, one main QTL on chromosome 12 (20–23Mb), a gene-rich region with previously identified QTL for immune-related traits, was identified for 5 and 6 OTUs on D4 and D52, respectively. These OTUs were mainly of the phyla Proteobacteria and Firmicutes on D4 and D52, respectively. In conclusion, there is evidence of substantial host genetic variation for vaginal microbiome in commercial PRRS-vaccinated gilts, including the identification of many QTLs. Additional research is needed to investigate the genetic relationship between vaginal microbiome, health, and production in pigs.

Fescue toxicosis is a multifaceted syndrome common in cattle grazing endophyte-infected tall fescue. However, varying responses among cattle potentially implies genetic tolerance to the syndrome. Therefore, the objective was to evaluate the cytokine response of cows deemed either tolerant or susceptible to endophyte-infected fescue. Angus cows, 2–4 yrs old, grazed endophyte-infected tall fescue at two locations for 13 weeks starting mid-April 2016. A post-hoc analysis of animal performance was utilized to designate cattle into either tolerant (n = 20) or susceptible (n = 20) groups, based on physiological responses (changes in ADG) to chronic exposure to endophyte-infected fescue. Blood samples collected on weeks 1, 7, and 13 were used to evaluate serum prolactin (PRL) concentration. Cytokine concentrations were evaluated via Quantibody Bovine Cytokine Arrays. Data were analyzed using PROC MIXED of SAS with repeated measures. There were no differences by location or week. Tolerant cows tended to have decreased overall PRL concentrations compared to susceptible cows (98.3 and 138.4 ng/mL, respectively; P = 0.08). G protein-coupled receptor associated sorting protein (GASP)-1, a down-regulator of G protein-coupled receptors including D2-dopamine receptor a regulator of PRL secretion, was greater in tolerant cows when compared to susceptible cows (4.7 and 4.2 ng/mL; P = 0.03). Vascular endothelial growth factor (VEGF)-A was greater in tolerant cows when compared to susceptible cows (0.5 and 0.2 ng/mL; P = 0.02). Finally, interleukin (IL)-4, an anti-inflammatory cytokine, tended to be greater in tolerant cows when compared to susceptible cows (2.2 and 0.8 ng/mL, respectively; P = 0.07). Based on these data, greater concentrations of GASP-1, VEGF-A, and IL-4 in tolerant compared to susceptible cattle may mitigate the detrimental effects of fescue toxicosis, including suppressed PRL and vasoconstriction, leading to improved animal performance in a fescue environment. Additionally, these cytokines may serve as potential biomarkers for determining an animal’s tolerance or susceptibility to negative effects associated with endophyte-infected tall fescue

The objective of this study was to perform genome-wide association studies (GWAS) to identify Quantitative Trait Loci (QTL) associated with antibody response to infectious diseases in commercial sows. A total of 2,848 Large White x Landrace replacement gilts were sourced from 17 high-health multipliers (7 breeding companies; BC) and introduced to 23 commercial farms with a history of common pig diseases, following the standard acclimation procedures with an average of 53 animals per entry group (CG). Serum was used to quantify antibody response to swine influenza virus (SIV), Mycoplasma hyopneumoniae (MH), porcine circovirus type-2 (PCV2), and 8 serotypes of Actinobacillus pleuropneumoniae (APP1-3, 5, 7, 10, 12, and 13) at entry (S/PEntry), following acclimation (S/PAcclimation), and during parities 1 (S/PParity1) and 2 (S/PParity2). All animals were genotyped for 38,191 SNPs. GWAS was performed using BayesB (pi=0.99), with the fixed effect of CG and the random effects of SNPs in the model. For APP, QTL were only identified at S/PAcclimation; on SSC14 (2Mb) for APP3, APP7, APP10, and APP13 that explained 5.6, 4.7, 2.8, and 3.6% of the genetic variance, respectively. A gene within this QTL region is SYK, involved in the control of immune-receptors. For APP5, a QTL that explained 4.2% of the genetic variance was identified on SSC4 (105Mb), which co-localizes with two genes associated with immune-response: SIKE1and NRAS. For SIV, no QTL was identified. A QTL on SSC7 (130-131Mb) was identified for MH (S/PParity1, 5.1%) and PCV2 (S/PEntry, 34%; S/PAcclimation, 43.4%). These results provide new information on the genetic basis of response to infectious diseases in sows. The identified QTL have the potential to be used to select for improved immune response. The authors thanks PigGen Canada, Genome Canada, and the Canadian Swine Health Board for financial support, and the late Dr. Stephen Bishop for his scientific contributions.

Twenty-four pregnant Nellore cows were randomly assigned into 2 feeding level groups (control [CTL]; fed 1.0 times the maintenance requirement; n = 12; and overnourished [ON]; fed at 1.5 times the maintenance requirement; n = 12) to evaluate effects of maternal overnutrition on fetal skeletal muscle development. Cows were slaughtered at 135, 190, and 240 d of gestation and samples of fetal LM were collected for analysis of mRNA expression analysis and for histological evaluation of collagen content and number of muscle cells. There was no interaction between gestational period and maternal nutrition for the variables evaluated (P > 0.05). The mRNA expression of Cadherin-associated protein, β 1 (β-catenin) tended to be greater in fetuses from ON cows (P = 0.08), while myogenic differentiation 1 (MyoD; P = 0.56), myogenin (MyoG; P = 0.70), and the number of muscle cells (P = 0.90) were not affected by maternal overnutrition. Gestational period did not affect the mRNA expression of β-catenin (P = 0.60) and MyoG (P = 0.21). The mRNA expression of MyoD tended to increase with days of gestation (P = 0.06). The mRNA expression of zinc finger protein 423 (Zfp423; P < 0.0001), C/EBPα (P = 0.01), and PPARγ (P < 0.0001) were enhanced in ON fetuses. No effects of days of gestation were observed for mRNA expression of Zfp423 (P = 0.75) and C/EBPα (P = 0.48). The mRNA expression of PPARγ in fetuses at 190 d of gestation tended to be greater than those at 135 and 240 d of gestation (P = 0.06). The mRNA expression of transforming growth factor β (TGF-β; P < 0.0001), collagen type III, α I (COL3A1; P < 0.0001), and collagen content (P = 0.01) were increased in ON fetuses. Gestational period did not affect the mRNA expression of collagen type I, α I (COL1A1; P = 0.65). The mRNA expression of COL3A1 (P = 0.09) in fetuses at 190 d of gestation tended to be greater than fetuses at 135 and 240 d of gestation. The mRNA expression of TGF-β in fetuses at 190 d of gestation was greater than in fetuses at 135 d of gestation (P = 0.03), and the values observed in fetuses at 240 d of gestation did not differ from the other gestational time points. The least value of collagen content (P = 0.01) was observed in fetuses at 135 d of gestation, and no differences were observed among the other gestational time points. These data shows that maternal overnutrition enhances fibrogenesis and likely adipogenesis without compromising myogenesis in fetal skeletal muscle of cattle.

Porcine reproductive and respiratory syndrome (PRRS) is the most economically significant disease impacting pig production in North America, Europe, and Asia, causing reproductive losses such as increased rates of stillbirth and mummified piglets. The objective of this study was to explore the genetic basis of host response to the PRRS virus (PRRSV) in a commercial multiplier sow herd before and after a PRRS outbreak, using antibody response and reproductive traits. Reproductive data comprising number born alive (NBA), number alive at 24 h (NA24), number stillborn (NSB), number born mummified (NBM), proportion born dead (PBD), number born dead (NBD), number weaned (NW), and number of mortalities through weaning (MW) of 5,227 litters from 1,967 purebred Landrace sows were used along with a pedigree comprising 2,995 pigs. The PRRS outbreak date was estimated from rolling averages of farrowing traits and was used to split the data into a pre-PRRS phase and a PRRS phase. All 641 sows in the herd during the outbreak were blood sampled 46 d after the estimated outbreak date and were tested for anti-PRRSV IgG using ELISA (sample-to-positive [S/P] ratio). Genetic parameters of traits were estimated separately for the pre-PRRS and PRRS phase data sets. Sows were genotyped using the PorcineSNP60 BeadChip, and genome-wide association studies (GWAS) were performed using method Bayes B. Heritability estimates for reproductive traits ranged from 0.01 (NBM) to 0.12 (NSB) and from 0.01 (MW) to 0.12 (NBD) for the pre-PRRS and PRRS phases, respectively. S/P ratio had heritability (0.45) and strong genetic correlations with most traits, ranging from -0.72 (NBM) to 0.73 (NBA). In the pre-PRRS phase, regions associated with NSB and PBD explained 1.6% and 3% of the genetic variance, respectively. In the PRRS phase, regions associated with NBD, NSB, and S/P ratio explained 0.8%, 11%, and 50.6% of the genetic variance, respectively. For S/P ratio, 2 regions on SSC 7 (SSC7) separated by 100 Mb explained 40% of the genetic variation, including a region encompassing the major histocompatibility complex, which explained 25% of the genetic variance. These results indicate a significant genomic component associated with PRRSV antibody response and NSB in this data set. Also, the high heritability and genetic correlation estimates for S/P ratio during the PRRS phase suggest that S/P ratio could be used as an indicator of the impact of PRRS on reproductive traits.

Recent results indicated that vulva size measured prior to puberty may be predictive of reproductive performance in sows. Therefore, the objective of this study was to estimate genomic prediction accuracies for vulva size traits in purebred gilts. A total of 1,185 Landrace (n = 477) and Yorkshire (n = 708) gilts originated from two different lines were used in this study. All animals had vulva size measurements taken at an average 21.5 weeks of age (SD = 5.8). Measurements included vulva width (VW), vulva height (VH), and vulva area (VA). Genotype data (Geneseek GGP-HD) was available for all animals, for ~40K SNPs. Marker allele substitution effects were estimated using Bayes-B (pi = 0.99) in a model including the fixed effects of contemporary group, line, breed (for multi-breed analysis only) and body weight (covariate), and the random effect of SNPs. Genomic prediction accuracies were estimated using three training and validation strategies: between-breed, within-breed (4 and 6 cross-validation folds for Landrace and Yorkshire, respectively), and multi-breed (10-fold cross-validation, using one-fold per breed for validation at a time). Between-breed accuracies were low and consistently negative, with -0.02, -0.10, and -0.05 in Landrace and -0.05, -0.04 and -0.03 in Yorkshire, for VW, VH, and VA, respectively. Within Landrace, these were moderate, with 0.35 (VW), 0.42 (VH), and 0.56 (VA), whereas lower accuracies were obtained for Yorkshire, with 0.07 (VW), 0.20 (VH), and 0.14 (VA). Multi-breed accuracies were low with 0.14 (VW), 0.14 (VH), and 0.24 (VA) for Landrace, and 0.03 (VW), 0.16 (VH), and 0.09 (VA) for Yorkshire. These results indicate that genomic selection for vulva size traits is possible in Landrace, but limited in Yorkshire gilts. The low between- and multi-breed results suggest that QTL for these traits are in opposite phases between breeds and/or do not segregate in both breeds. Financial support from the Iowa Pork Industry Center is appreciated.

The objective of this study was to identify differentially expressed genes (DEG) and functions associated with tolerance to fescue toxicosis (FT). Forty pregnant purebred Angus cows were selected based on their growth at two locations in North Carolina (Butner Beef Cattle Field Laboratory, BBFCL; Upper Piedmont Research Station, UPRS) and classified as either high tolerant (HT) or low tolerant (LT) to FT with 20 cows in each group balanced by location. Blood samples were collected on weeks 1, 5, 9, and 13 for RNA sequencing. Counts were analyzed using a negative binomial model including the effects of genetic group, location, time, all possible interactions of these effects, flow cell, covariate of RNA integrity number, and normalized library size as offset. Genotype-by-location-by-time interaction was evident with a high number (4,453) of DEG (q-value

The female reproductive ability is crucial to the efficiency of swine production, but genetic progress is limited by its low heritability and sex-limited expression. Thus, the objective of this study was to understand the relationship between testis size in boars and reproductive traits in sows. In this study, Yorkshire and Landrace boars (161) and sows (420) were analyzed for testis (boars) width (TW) and area (TA) and reproductive traits (sows): total born (TB), number born alive (NBA), alive 48h (alive48), total born dead (TBD), stillborn, and mummies. Genetic analyses were performed including the fixed effects of age, breed, contemporary group, and parity (for sow traits only), and a random animal effect in the models. The 420 sows were daughters of 13 of the 161 boars. For the phenotypic analysis, we performed a Poisson regression of the reproductive traits of the 420 daughters on the testis size of their 13 sires, with parity and breed of the sow as fixed effect and sow as random effect, and TW or TA as fixed covariates (linear and quadratic). The heritability estimates of TA and TW were 0.69 ± 0.22 and 0.66 ± 0.21, respectively, and the reproductive traits ranged from 0.01 ± 0.01 (TBD) to 0.09 ± 0.04 (NBA). The phenotypic analysis showed quadratic (P < 0.05) and linear (P < 0.05) relationships between reproductive traits in sows with TA and TW, respectively. The optimum TA ranged from 17.09cm2 to 18.55cm2 associated with higher number of TB, NBA, and alive48 (P < 0.05), which did not overlap with the range related to higher number of TBD, mummies, and stillborn (16.0cm2 to 16.57cm2; P < 0.05). Also, increasing the testis width is associated with an increase in TB, NBA, and alive48 (P < 0.05) but not TBD, mummies, and stillborn (P>0.05). Phenotypic assessment of testis size of sires may be a useful tool to select/cull animals for breeding, improving female performance.