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Vitamin B and trace minerals are crucial molecular signals involved in many biological pathways, however, their bioavailability is compromised in high-producing ruminant animals. So far, studies have mainly focused on the effects of these micronutrients on animal performance, but their use in a rumen-protected form and their impact on liver metabolism in finishing beef cattle is poorly known. We used a shotgun proteomic approach combined with biological network analyses to assess the effects of a rumen-protected B-vitamin blend, as well as those of hydroxy trace minerals, on the hepatic proteome. A total of 20 non-castrated Nellore males with 353 ± 43 kg of initial body weight were randomly assigned to one of the following treatments: CTRL—inorganic trace minerals without supplementation of a protected vitamin B blend, or SUP—supplementation of hydroxy trace minerals and a protected vitamin B blend. All animals were fed the same amount of the experimental diet for 106 days, and liver biopsies were performed at the end of the experimental period. Supplemented animals showed 37 up-regulated proteins (p &lt, 0.10), and the enrichment analysis revealed that these proteins were involved in protein folding (p = 0.04), mitochondrial respiratory chain complex I (p = 0.01) and IV (p = 0.01), chaperonin-containing T-complex 2 (p = 0.01), glutathione metabolism (p &lt, 0.01), and other aspects linked to oxidative-stress responses. These results indicate that rumen-protected vitamin B and hydroxy trace mineral supplementation during the finishing phase alters the abundance of proteins associated with the electron transport chain and other oxidation–reduction pathways, boosting the production of reactive oxygen species, which appear to modulate proteins linked to oxidative-damage responses to maintain cellular homeostasis.

We investigated how feed restriction at 50% of maintenance requirements during different stages of gestation affects the transcriptome of newborn goats' skeletal muscle. Fourteen pregnant dams were randomly assigned into one of the following dietary treatments: animals fed at 50% of maintenance requirement from 8-84 d of gestation and then fed at 100% of maintenance requirement from day 85 of gestation to parturition (RM, n = 6), and animals fed at 100% of maintenance requirement from 8-84 d of gestation and then fed at 50% of maintenance requirement from day 85 of gestation to parturition (MR, n = 8). At birth, samples of offspring's Longissimus muscle were collected for total RNA extraction and sequencing. Our data showed 66 differentially expressed (DE) genes (FDR < 0.05). A total of 6 genes were upregulated and 60 downregulated (FDR < 0.05) in the skeletal muscle of the newborns resulting from treatment RM compared with MR. Our results suggest that the DE genes upregulated in newborn goats' skeletal muscle from the RM group compared to MR, included genes related to satellite cells, and genes that indicates impaired insulin sensitivity and changes in the composition of intramuscular fat. The DE genes upregulated in newborn goats' skeletal muscle from the MR group compared to RM, are also related to impaired insulin sensitivity, as well as a predominantly oxidative metabolism and cellular oxidative stress. However, protective mechanisms against insulin sensitivity and oxidative stress may have been augmented in the skeletal muscle of offspring from MR treatment compared to RM, in order to maintain cellular homeostasis.

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.

Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are two of the most significant pathogens affecting swine. Co-infections are common and result in respiratory disease and reduced weight gain in growing pigs. Although PRRS modified live virus (MLV) vaccines are widely used to decrease PRRS-associated losses, they are generally considered inadequate for disease control. The gut microbiome provides an alternative strategy to enhance vaccine efficacy and improve PRRS control. The objective of this study was to identify gut microbiome characteristics associated with improved outcome in pigs immunized with a PRRS MLV and co-challenged with PRRSV and PCV2b. Twenty-eight days after vaccination and prior to co-challenge, fecal samples were collected from an experimental population of 50 nursery pigs. At 42 days post-challenge, 20 pigs were retrospectively identified as having high or low growth outcomes during the post-challenge period. Gut microbiomes of the two outcome groups were compared using the Lawrence Livermore Microbial Detection Array (LLMDA) and 16S rDNA sequencing. High growth outcomes were associated with several gut microbiome characteristics, such as increased bacterial diversity, increased Bacteroides pectinophilus, decreased Mycoplasmataceae species diversity, higher Firmicutes:Bacteroidetes ratios, increased relative abundance of the phylum Spirochaetes, reduced relative abundance of the family Lachnospiraceae, and increased Lachnospiraceae species C6A11 and P6B14. Overall, this study identifies gut microbiomes associated with improved outcomes in PRRS vaccinated pigs following a polymicrobial respiratory challenge and provides evidence towards the gut microbiome playing a role in PRRS vaccine efficacy.

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.

Nucleotides are important to cell growth and division and are crucial to the rapid proliferation of such cells as the intestinal mucosa and immune cells. Accordingly, the nucleotide requirements of animals are high during periods of rapid growth and periods of stress like post-weaning period. Thus, nucleotide supplementation may be a possible alternative to in-feed antibiotics as growth promoter in this phase. The study aimed to evaluate dietary nucleotide supplementation as an alternative to in-feed antibiotics on performance and gut health of weaned piglets. Ninety-six 21-day-old piglets, weighing 7.44 ± 0.65 kg, were allocated into 1 of 3 treatments (8 pens per treatment; 4 pigs per pen) in a 14-day trial. Dietary treatments consisted of control: corn-soybean meal-based diet; nucleotides: control +2 g/kg of a nutritional additive with purified nucleotides; and antibiotic: control +0.8 g/kg of antibiotic growth promoter based on colistin and tylosin. Performance variables and fecal score were not affected (P > 0.05) by supplementing nucleotide or antibiotic. Nucleotides treatment had similar effect to antibiotic and superior to control (P 0.05) by treatments. In the ileal, antibiotic supplementation reduced total bacteria quantification compared to nucleotide supplementation or the control (P

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.

Reproductive performance is critical for efficient swine production. A relationship between the size of the vulva measured in gilts prior to puberty at 15 weeks of age and subsequent reproductive performance has been demonstrated. The objective of this study was to estimate genetic parameters and perform genomic analysis on vulva size traits. A total of 1411 animals from Landrace (n=587) and Yorkshire (n=824) breeds were used for this trial. Measurements including vulva width (VW), vulva height (VH), and vulva area (VA) were taken at an average age of 21.5 weeks. Genotype data (Geneseek GGP-HD) was available for all animals by imputation. Genetic parameters were estimated using measurement week, breed, line, and body weight (covariate) as fixed effects in an animal model. For genomic analyses, BayesCp was used to estimate the p to be used in genome-wide association (GWA) analyses using BayesB. Heritability estimates for both breeds grouped were 0.42 ± 0.08, 0.26 ± 0.06, and 0.41 ± 0.07 for VA, VW, and VH, respectively. Estimates of genetic correlations were 0.93 ± 0.02 between VA and VH, 0.95 ± 0.02 between VA and VW, and 0.78 ± 0.08 between VH and VW. The GWA analyses identified QTL associated with vulva measurements. For VH in Landrace, a QTL located on Sus scrofa chromosome (SSC) 7 at 107Mb accounted for 9% of the genetic variance. This region harbors FLRT2, a gene that regulates early embryonic vascular development. For VW in Landrace, a QTL on SSC2 (154Mb) and SSC8 (60Mb) explained 4% and 1.5% of the genetic variance, respectively. For VW in Yorkshire, a QTL on SSC2 (28Mb) explained 2% of the genetic variance. Our results support a large genetic variability for vulva measurements at approximately 21.5 weeks of age and that a genomic region on SSC7, including a gene associated with embryonic development, accounts for 9% of genetic variability for VH in Landrace gilts.

The objective of this study was to estimate genetic parameters of antibody response and reproductive traits after exposure to porcine reproductive and respiratory syndrome virus. Blood samples were taken approximately 60 d after the outbreak. Antibody levels were quantified as the sample-to-positive ratio (S/P ratio) using a fluorescent microsphere assay. Reproductive traits included total number born (TNB), number born alive (NBA), number stillborn (NSB), number mummified (NBM), and number born dead (NBD). Mortality traits were log transformed for genetic analyses. Data were split into prior, during, and after the disease outbreak phases using visual appraisal of the estimates of farm-year-week effects for each reproductive trait. For NBA, data from all phases were combined into a reaction norm analysis with regression on estimates of farm-year-week effects for NBA. Heritability for S/P ratio was estimated at 0.17 ± 0.05. Heritability estimates for reproduction traits were all low and were lower during the outbreak for NBA but greater for mortality traits. TNB was not greatly affected during the outbreak, as many sows that farrowed during the outbreak were mated prior to the outbreak. Heritability for TNB decreased from 0.13 (prior) to 0.08 (after). Genetic correlation estimates between prior to and during the outbreak were high for TNB (0.86 ± 0.23) and NBA (0.98 ± 0.38) but lower for mortality traits: 0.65 ± 0.43, -0.42 ± 0.55, and 0.29 ± 1.39 for LNSB, LNBM, and LNBD, respectively. TNB prior to and after the outbreak had a lower genetic correlation (0.32 ± 0.33). In general, genetic correlation estimates of S/P ratio with reproductive performance during the outbreak were below 0.20 in absolute value, except for LNSB (-0.73 ± 0.29). Based on the reaction norm model, estimates of genetic correlations between the intercept and slope terms ranged from 0.24 ± 0.50 to 0.54 ± 0.35 depending on the parameterization used, indicating that selection for the intercept may result in indirect selection for steeper slopes, and thus, less resilient animals. In general, estimates of genetic correlations between farm-year-week effect classes based on the reaction norm model resembled estimates of genetic correlations from the multivariate analysis. Overall, compared to previous studies, antibody S/P ratios showed a lower heritability (0.17 ± 0.05) and low genetic correlations with reproductive performance during a porcine reproductive and respiratory syndrome outbreak, except for the LNSB.

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.

International audience; AbstractBackgroundGenomic prediction of the pig’s response to the porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) would be a useful tool in the swine industry. This study investigated the accuracy of genomic prediction based on porcine SNP60 Beadchip data using training and validation datasets from populations with different genetic backgrounds that were challenged with different PRRSV isolates.ResultsGenomic prediction accuracy averaged 0.34 for viral load (VL) and 0.23 for weight gain (WG) following experimental PRRSV challenge, which demonstrates that genomic selection could be used to improve response to PRRSV infection. Training on WG data during infection with a less virulent PRRSV, KS06, resulted in poor accuracy of prediction for WG during infection with a more virulent PRRSV, NVSL. Inclusion of single nucleotide polymorphisms (SNPs) that are in linkage disequilibrium with a major quantitative trait locus (QTL) on chromosome 4 was vital for accurate prediction of VL. Overall, SNPs that were significantly associated with either trait in single SNP genome-wide association analysis were unable to predict the phenotypes with an accuracy as high as that obtained by using all genotyped SNPs across the genome. Inclusion of data from close relatives into the training population increased whole genome prediction accuracy by 33% for VL and by 37% for WG but did not affect the accuracy of prediction when using only SNPs in the major QTL region.ConclusionsResults show that genomic prediction of response to PRRSV infection is moderately accurate and, when using all SNPs on the porcine SNP60 Beadchip, is not very sensitive to differences in virulence of the PRRSV in training and validation populations. Including close relatives in the training population increased prediction accuracy when using the whole genome or SNPs other than those near a major QTL.

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.

Mutations in >30 genes are known to result in impairment of the adaptive immune system, causing a group of disorders collectively known as SCID. SCID disorders are split into groups based on their presence and/or functionality of B, T, and NK cells. Piglets from a line of Yorkshire pigs at Iowa State University were shown to be affected by T−B−NK+ SCID, representing, to our knowledge, the first example of naturally occurring SCID in pigs. In this study, we present evidence for two spontaneous mutations as the molecular basis for this SCID phenotype. Flow cytometry analysis of thymocytes showed an increased frequency of immature T cells in SCID pigs. Fibroblasts from these pigs were more sensitive to ionizing radiation than non-SCID piglets, eliminating the RAG1 and RAG2 genes. Genetic and molecular analyses showed that two mutations were present in the Artemis gene, which in the homozygous or compound heterozygous state cause the immunodeficient phenotype. Rescue of SCID fibroblast radiosensitivity by human Artemis protein demonstrated that the identified Artemis mutations are the direct cause of this cellular phenotype. The work presented in the present study reveals two mutations in the Artemis gene that cause T−B−NK+ SCID in pigs. The SCID pig can be an important biomedical model, but these mutations would be undesirable in commercial pig populations. The identified mutations and associated genetic tests can be used to address both of these issues.

Feed efficiency is of great importance to the swine industry, yet few studies have evaluated the robustness of pigs selected for increased feed efficiency based on residual feed intake (RFI) when challenged with disease. RFI is calculated as the difference between the observed and expected feed intake. The objective of this study was to assess the effect of porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) infection on lines of pigs divergently selected for RFI. Hypothesizing that the more feed efficient low RFI (LRFI) pigs would be more affected by PRRSV-infection, 97 piglets from LRFI and 99 piglets from high RFI (HRFI) selection lines were experimentally infected with the NVSL 97-7985 PRRSV isolate 1 to 3 weeks post-weaning. Pig body weight was recorded weekly and used to calculate average daily gain (ADG). For comparison, ADG was also evaluated on 489 non-challenged LRFI and HRFI pigs housed in a separate facility. Viral load (VL) was quantified as area under the curve for 0–21 days post-infection (dpi) of the log of PCR-based serum viremia. Antibody level was analyzed from serum samples collected at 4, 7, and 11 dpi by PRRS ELISA and MAGPIX assays to quantify PRRSV-specific IgG antibody and total antibody, respectively, during the early stages of PRRSV-infection. There was a tendency for pigs from the LRFI line to have lower VL (P=0.09), greater ADG (P=0.10), and be more likely to survive the PRRSV-challenge (P=0.06) than pigs from the HRFI line. However, joint analysis of challenged and non-challenged pigs showed a significant interaction between RFI line and challenge status (P=0.04), which demonstrated that growth of the LRFI line was less affected by PRRSV-challenge than growth of the HRFI line. Additionally, a significant interaction between RFI line and dpi for the ELISA (P

Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower—DFF; Days for flowering—DTF; Days to end of flowering—DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons. Plants were genotyped for 384 SNPs. Traditional single-SNP and 9 QR models, ranging from equally spaced quantiles (τ) 0.1 to 0.9, were used to associate SNPs to phenotype. Heritabilities were moderate high, ranging from 0.32 to 0.58. Genetic and phenotypic correlations were all high, averaging 0.66 and 0.98, respectively. Traditional single-SNP GWAS model was not able to find any SNP-trait association. On the other hand, when using QR methodology considering one extreme quantile (τ = 0.1) we found, respectively 1 and 7, significant SNPs associated for DFF and DTF. Significant SNPs were found on Pv01, Pv02, Pv03, Pv07, Pv10 and Pv11 chromosomes. We investigated potential candidate genes in the region around these significant SNPs. Three genes involved in the flowering pathways were identified, including Phvul.001G214500, Phvul.007G229300 and Phvul.010G142900.1 on Pv01, Pv07 and Pv10, respectively. These results indicate that GWAS-based QR was able to enhance the understanding on genetic architecture of phenological traits (DFF and DTF) in common bean.

Background Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficiency in the fetus and impact the fetal regulation of genes associated with myogenesis and immune response. Methods Forty days before the expected calving date, cows were assigned to one of two diets: 100% (control) or 70% (restricted group) of the daily energy requirement. Muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. The objective of this work was to identify and to assess the biological relevance of differentially expressed genes (DEG) in the skeletal muscle and blood of beef calves born from cows that experienced [or not] a 30% energy restriction during the last 40 days of gestation. Results A total of 160, 164, and 346 DEG (q-value

SUMMARYThe present study aimed to explore the molecular factors underlying differences in Calpain/Calpastatin proteolytic system in Nellore and Angus cattle. Longissimus muscle samples were collected in Nellore (n= 6; body weight (BW) = 373 ± 37·3 kg) and Angus (n= 6; BW = 383 ± 23·9 kg) cattle at slaughter for analysis of gene and protein expression, and Calpastatin enzyme activity. Additionally, the myofibrillar fragmentation index was used to quantify the extension of proteolysis in longissimus muscle samples. A greater myofibrillar fragmentation was observed in skeletal muscle of Angus compared with Nellore cattle. Conversely, no differences were found between breeds for mRNA expression of Calpain 1 (CAPN1) and Calpastatin (CAST). Similarly, no differences were observed for the abundance of Calpain and Calpastatin proteins between skeletal muscles of Nellore and Angus cattle. Despite the lack of differences in mRNA and protein abundance, a greater activity of Calpastatin was observed in skeletal muscle of Nellore compared with Angus cattle. These data indicate that the greater proteolysis in skeletal muscle of Angus compared with Nellore cattle is mainly driven by a greater Calpastatin activity rather than Calpain or Calpastatin mRNA and protein expression.

A major QTL for host response to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) infection was identified in a previous study. Single nucleotide polymorphism WUR10000125 (WUR), which is in complete linkage disequilibrium with the putative causative mutation, can be used as a tag SNP for the QTL. However, the effect of WUR following PRRS vaccination and/or coinfection with other pathogens is not known. Therefore, objectives of this study were to estimate the effect of WUR on host response following PRRS vaccination and coinfection of PRRSV with porcine circovirus type 2b (PCV2b), to estimate genetic parameters for host response to vaccination and coinfection, and to estimate the effect of previously identified candidate SNP under PRRSV-only or PCV2b-only infection on host response to coinfection. Data from 2 trials, comprising a total of 396 commercial crossbred nursery pigs from a single genetic source, were used for all analyses. Pigs were preselected based on WUR genotype: approximately half AA and half AB, where B is the favorable and dominant allele. At weaning, pigs were shipped to Kansas State University, where half of the pigs were vaccinated with a PRRS modified live virus vaccine. Four weeks later, all pigs were coinfected with field strains of PRRSV and PCV2b and followed for 42 d. Body weight and serum viremia measurements were collected following vaccination and coinfection to calculate ADG and viral load (VL), respectively. Average heritability estimates for PRRS VL, PCV2b VL, and ADG were 0.29, 0.09, and 0.40, respectively. After vaccination, AB pigs had lower vaccination VL ( = 0.03) and faster gain ( = 0.004) than AA pigs, as expected. After coinfection, AB pigs had lower PRRSV VL ( < 0.001) but did not significantly differ from AA pigs in growth rate ( = 0.86). For PCV2b VL, suggestive evidence of an interaction between vaccination and WUR genotype ( = 0.11) was detected, where AB pigs had significantly lower PCV2b VL when vaccinated ( = 0.007) but not when they were not vaccinated ( = 0.87). In addition to WUR, several PRRS-associated SNP and a PCV2b-associated SNP had significant effects on host response to coinfection. In conclusion, marker-assisted selection based on WUR genotype alone, or along with other candidate SNP for PRRSV and PCV2b infection, is a promising strategy to select for improved host response to not just PRRS but also coinfection of PRRSV with PCV2b and perhaps other pathogens.

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

This study was developed aiming to evaluate the effects of maternal feed-restriction ond evelopment of gastrointestinal tract (GIT) of bovine fetus at different gestational stages. Feed-restricted cows were fed 1.2 times the maintenance level while the control group was fed ad libitum. Pregnant cows were slaughtered at 136, 189, 239, and 269 days of gestation and gastrointestinal tracts of the fetuses were evaluated. No effects of maternal nutrition on body weight (P 1⁄4 0.17) and body length (P 1⁄40.13) of the fetuses were observed. No major effects of feed restriction on GIT mass of the fetuses were observed (P 1⁄4 0.51). However, the weight of small intestine per unit of body weight was 11.24% greater (P 1⁄40.04) in fetuses from restricted dams. Additionally, the length of small intestine and its villi were 12.93% and 16.44% respectively greater (P o .001) in fetuses from restricted dams compared to those from non-restricted dams. These data indicates that maternal feed-restriction does not affect the development of most of fetal gastrointestinal parts besides small intestine which in turn increases its surface area as a response of maternal feed restriction.

Gene expression time series (GETS) analysis aims to characterize sets of genes according to their longitudinal patterns of expression. Due to the large number of genes evaluated in GETS analysis, an useful strategy to summarize biological functional processes and regulatory mechanisms is through clustering of genes that present similar expression pattern over time. Traditional cluster methods usually ignore the challenges in GETS, such as the lack of data normality and small number of temporal observations. Independent Component Analysis (ICA) is a statistical procedure that uses a transformation to convert raw time series data into sets of values of independent variables, which can be used for cluster analysis to identify sets of genes with similar temporal expression patterns. ICA allows clustering small series of distribution-free data while accounting for the dependence between subsequent time-points. Using temporal simulated and real (four libraries of two pig breeds at 21, 40, 70 and 90 days of gestation) RNA-seq data set we present a methodology (ICAclust) that jointly considers independent components analysis (ICA) and a hierarchical method for clustering GETS. We compare ICAclust results with those obtained for K-means clustering. ICAclust presented, on average, an absolute gain of 5.15% over the best K-means scenario. Considering the worst scenario for K-means, the gain was of 84.85%, when compared with the best ICAclust result. For the real data set, genes were grouped into six distinct clusters with 89, 51, 153, 67, 40, and 58 genes each, respectively. In general, it can be observed that the 6 clusters presented very distinct expression patterns. Overall, the proposed two-step clustering method (ICAclust) performed well compared to K-means, a traditional method used for cluster analysis of temporal gene expression data. In ICAclust, genes with similar expression pattern over time were clustered together. All dataset related to simulation (replicate1.docx, replicate2.docx,...,replicate10.docx) and real data (RNA_seq_Pig.docx), as well as the R software codes (ICAclust.docx) are available.

Background Our recent research showed that antibody response to porcine reproductive and respiratory syndrome (PRRS), measured as sample-to-positive (S/P) ratio, is highly heritable and has a high genetic correlation with reproductive performance during a PRRS outbreak. Two major quantitative trait loci (QTL) on Sus scrofa chromosome 7 (SSC7; QTLMHC and QTL130) accounted for ~40 % of the genetic variance for S/P. Objectives of this study were to estimate genetic parameters for PRRS S/P in gilts during acclimation, identify regions associated with S/P, and evaluate the accuracy of genomic prediction of S/P across populations with different prevalences of PRRS and using different single nucleotide polymorphism (SNP) sets. Methods Phenotypes and high-density SNP genotypes of female pigs from two datasets were used. The outbreak dataset included 607 animals from one multiplier herd, whereas the gilt acclimation (GA) dataset included data on 2364 replacement gilts from seven breeding companies placed on health-challenged farms. Genomic prediction was evaluated using GA for training and validation, and using GA for training and outbreak for validation. Predictions were based on SNPs across the genome (SNPAll), SNPs in one (SNPMHC and SNP130) or both (SNPSSC7) QTL, or SNPs outside the QTL (SNPRest). Results Heritability of S/P in the GA dataset increased with the proportion of PRRS-positive animals in the herd (from 0.28 to 0.47). Genomic prediction accuracies ranged from low to moderate. Average accuracies were highest when using only the 269 SNPs in both QTL regions (SNPSSC7, with accuracies of 0.39 and 0.31 for outbreak and GA validation datasets, respectively. Average accuracies for SNPALL, SNPMHC, SNP130, and SNPRest were, respectively, 0.26, 0.39, 0.21, and 0.05 for the outbreak, and 0.28, 0.25, 0.22, and 0.12, for the GA validation datasets. Conclusions Moderate genomic prediction accuracies can be obtained for PRRS antibody response using SNPs located within two major QTL on SSC7, while the rest of the genome showed limited predictive ability. Results were obtained using data from multiple genetic sources and farms, which further strengthens these findings. Further research is needed to validate the use of S/P ratio as an indicator trait for reproductive performance during PRRS outbreaks. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0230-0) contains supplementary material, which is available to authorized users.

Carcasses of sixty-three Nellore bulls slaughtered at a commercial beef plant were randomly selected by dental classification (2, 4, 6 or 8 permanent incisors) in order to evaluate the influence of dental maturity on carcass traits and meat quality. Carcasses with 8 permanent incisors (p.i.) had greatest values (P0.05) of carcass weight and longissimus area. Carcasses with 4 and 6 p.i. presented similar values of rib fat thickness being greater (P0.05) than the other groups. Carcasses with 6 and 8 p.i. presented greater (P0.05) values of shear force than the other groups. Conversely, carcasses with 2 and 4 p.i. displayed greater (P0.05) myofibrillar fragmentation index and collagen solubility. Greatest values of thawing loss were observed in carcasses with 2 p.i. (P0.05) while carcasses with 8 p.i. presented greatest values (P0.05) of drip loss. Regarding longissimus color, carcasses with 8 p.i presented greatest value (P0.05) of b*. Data suggests that dental maturity influences carcass traits and meat quality of Nellore bulls.

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.

Coinfections involving porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) contribute to a group of disease syndromes known as porcine circovirus-associated disease (PCVAD). Presumably, PRRSV infection enhances PCV2 replication as a result of modulation of host immunity. The purpose of this study was to evaluate PCV2 replication and pathogenesis in pigs vaccinated with a PRRS modified live virus (MLV) vaccine and subsequently challenged with a combination of PRRSV and PCV2. During the early postchallenge period, the number of pigs with PRRSV-associated clinical signs was decreased, and average daily gain (ADG) was increased, in the vaccinated group, demonstrating the protective effect of PRRS vaccination. However, during the later postchallenge period, more pigs in the vaccinated group showed increased PCV2 viremia, decreased ADG, increased PCVAD clinical signs, and increased mortality. In this disease model, the early benefits of PRRSV vaccination were outweighed by the later amplification of PCVAD.

An experiment was conducted to determine the quantitative relationships between stan- dardized total tract digestible P (STTD P) and total Ca intakes with their retention and excretion by growing pigs fed corn-soybean meal diets. Forty-eight cross- bred barrows (BW = 22.7 ± 2.9 kg) were allotted to 1 of 8 diets, housed individually in pens for 3 wk, and then moved to metabolism crates and allowed 4 d for adaptation and 5 d for collection of urine and fecal samples. Eight corn-soybean meal diets were formu- lated for similar NE, fat, and AA concentrations but to increase the STTD P from 0.16 to 0.62% using monocalcium phosphate. Dietary treatments were for- mulated for a constant Ca:STTD P ratio (2.2:1). The STTD P intake increased (P < 0.001) from 64 to 242% of the daily requirement (4.59 g/d of STTD P). Fecal and total excretion of P and Ca were linearly associat- ed with mineral intake (P < 0.001). Constant urinary P excretion of 0.03 g/d P was observed, but at 4.96 g/d of STTD P intake, the urinary P excretion increased (P < 0.001). In contrast, Ca excretion in urine decreased (P < 0.001) with Ca intake, but constant excretion of 0.40 g/d Ca was reached at 17.97 g/d of Ca intake. The daily intakes of STTD P and Ca moderately explained the variation in urinary excretion of P (R 2 = 0.41) and Ca (R 2 = 0.64). The absorption and retention of P increased linearly (P < 0.001) with dietary P intake, whereas absorption and retention of Ca showed a qua- dratic response (P < 0.001). Absorption and retention of P and Ca were highly predictable from the STTD P and Ca intakes, with R 2 of 0.87 and 0.90, respec- tively. The femur mineral content (FMC) increased by 2.71 g with STTD P intake (P < 0.001) but reached a plateau (29.54 g of FMC) at 8.84 g/d of STTD P intake. The FMC was highly predictable from the STTD P intake (R 2 = 0.89). The FMC affected the urinary P excretion (P < 0.01), but moderately (R 2 = 0.19) explained the variation in urinary P. In conclu- sion, constant excretion of P in urine was observed but excretion increased linearly at STTD P intake levels above the requirement for maximum growth of grow- ing pigs. The FMC increased with STTD P intake, but a plateau was reached at a STTD P intake level above the requirement. Dietary STTD P was used for growth and accumulated in bones until a plateau was reached and excess was excreted in urine. The predictability of P and Ca excretion in urine from the dietary STTD P and Ca intakes was moderate.

Adding tannins to the dietary protein source will cause complexation between the tannin and protein, which may increase dietary ruminal undegraded protein. Thus, this study aimed to evaluate the effects of replacing soybean meal (SM) with soybean meal treated with tannin (SMT) on the intake, partial and total nutrient digestibility, and protein dietary efficiency of young cattle fed a high-concentrate diet. Five Nellore bulls with bodyweights of 290 ± 11.2 kg were fitted with ruminal and abomasal cannulas and were used in the study. The experimental diets included 7.5% SM, with a proportion of that SM (0%, 33%, 66% or 100%) replaced with SMT. Another treatment (SMT+urea) with only 2.5% SM treated with tannins was tested. The intake of ether extract and the intake of neutral detergent fibre ash and protein were the only parameters related to feed intake that were affected by the replacement of SM with SMT. Ruminal and intestinal digestibility each showed a linear effect on crude protein, which decreased with ruminal digestibility and increased with intestinal digestibility. The intake of ruminal undegraded protein and metabolisable protein showed a positive linear correlation with the amount of SMT in the diet. SMT substitution showed no effect on methane emission. The replacement of traditional SM with SM treated with 2.5% tannins (85% condensed tannins and 15% hydrolysable tannins) for cattle that were fed high-concentrate diets showed increased amounts of metabolisable protein and decreased nitrogen loss per unit of crude protein, without changing the methane emission.

Background Previously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4). Results Within this QTL, guanylate binding protein 5 (GBP5) was differentially expressed (DE) (p