The genetic basis of host response to experimental infection with the porcine reproductive and respiratory syndrome virus in pigs

Porcine reproductive and respiratory syndrome (PRRS) is the most economically important disease in the swine industry. The effects of PRRS are two fold in that it causes reproductive problems in breeding females and respiratory problems in growing animals. Vaccination has generally not been effective in the prevention of PRRS, partially due to the rapid mutation rate and evolution of the virus. The overall objective of this thesis was to discover the genetic basis of host response to PRRS virus (PRRSV) using data from the PRRS Host Genetics Consortium PRRS-CAP project by conducting genome-wide association analyses and estimating genetic parameters. Eight groups of ~200 commercial crossbred pigs from 5 breeding companies and 6 unrelated populations were infected between 25 and 35 days of age. Blood samples and body weights were collected up to 42 days post infection (dpi). Pigs were genotyped with the Illumina Porcine 60k Beadchip. Whole genome analyses focused on serum viremia and weight gain from 0 to 42 dpi (WG). Virus load (VL) was quantified as area under the curve of log viremia from 0 to 21 dpi. VL and WG were found to be moderately heritable at 0.44 and 0.39, respectively. A quantitative trait loci (QTL) was identified on Sus scrofa chromosome (SSC) 4 for VL and WG using data from the first 3 trials and validated in trials 4 through 8. The SSC4 QTL explained 13% of genetic variance for VL and 9% for WG. The favorable allele at the QTL had a dominance mode of action and resulted in reduced VL (0.50 phenotypic SD) and increased WG (0.49 phenotypic SD). The favorable allele was identified in all breeds represented in the trials but at a low frequency. Additional genomic regions were identified on SSCX and SSC1 for VL and SSC5 and 7 for WG, each explaining less than 3% of the genetic variance. The QTL on SSC1 was also associated with mortality in one trial where death loss was ~50% due to secondary infections. In conclusion, host response to PRRSV infection has a sizable genetic component. Estimates of heritability were moderate and, with a frequency of 0.17 for the favorable allele for the SSC4 QTL across trials, there is opportunity for genetic improvement of pigs for response to PRRS infection

The effects of ad libitum and restricted feeding on Yorkshire pigs selected for reduced residual feed intake

Residual feed intake (RFI), defined as the differences between observed and expected feed intake based on growth and backfat, has been used to select for improved feed efficiency in beef cattle, poultry, and now swine. However, little is known about the main biological factors that contribute to the variation in RFI in swine. The objectives of the experiments in this thesis were to compare the 5th generation of a line of pigs selected for reduced RFI (Select) against a randomly selected control (Control) line for performance parameters and to examine the biological contribution of visceral mass, carcass and chemical carcass composition, and predicted maintenance requirements on the overall efficiency during two stages of growth: the early post-weaning period (EGP) and late growth period (LGP) prior to market weight. In both experiments, Select and Control line pigs were paired based on age (~65 and 132 d for EGP and LGP, respectively) and weight (23.9y4.2 and 74.8y9.9 kg, respectively) and the pairs were randomly assigned to one of four feeding level treatments: 1) ad libitum (Ad); 2) 75% of Ad (Ad75); 3) 55% of Ad (Ad55); and 4) weight stasis to maintain a constant body weight (WS). In both experiments (EGP and LGP), pigs were individually penned and on feed treatment for 6 weeks. Overall, under Ad feeding, the Select line consumed 8 to 10% (p \u3c 0.09) less feed compared to the Control, with no significant difference in weekly BW (p \u3c 0.80). In general, the Select line under the Ad treatment had less backfat and carcass fat % but no other significant differences in carcass chemical composition. Under restricted feeding, the Select line had an increase in BW (p = 0.10) while consuming the same amount of feed as the Control, in both experiments. Furthermore, no significant differences in carcass chemical composition were found. The Select line had lower visceral weights but this was only significant (p \u3c 0.01) for the LGP experiment. In the EGP experiment, the WS treatment showed no significant differences in feed intake or BW between the Select and Control line. Conversely, for the LGP experiment, the Select line required less feed than the Control by the end of the experiment to maintain static BW (p \u3c 0.08). Furthermore, there was a trend for the Select line to have reduced maintenance energy requirements (p \u3c 0.13) for the LGP experiment, as estimated by regression of consumed on retained energy. In conclusion, selection for reduced RFI has reduced feed intake, with no significant differences in growth performance but reduced backfat, reduced carcass fat%, and lower maintenance requirements. The results of this thesis show that carcass composition and energy partitioning, primarily differences in carcass fat%, and reduced estimated maintenance requirements may significantly contributed to the differences in RFI

Genome-Wide Association and Genomic Prediction for Host Response to Porcine Reproductive and Respiratory Syndrome Virus Infection

Host genetics has been shown to play a role in porcine reproductive and respiratory syndrome (PRRS), which is the most economically important disease in the swine industry. A region on Sus scrofa chromosome (SSC) 4 has been previously reported to have a strong association with serum viremia and weight gain in pigs experimentally infected with the PRRS virus (PRRSV). The objective here was to identify haplotypes associated with the favorable phenotype, investigate additional genomic regions associated with host response to PRRSV, and to determine the predictive ability of genomic estimated breeding values (GEBV) based on the SSC4 region and based on the rest of the genome. Phenotypic data and 60 K SNP genotypes from eight trials of ~200 pigs from different commercial crosses were used to address these objectives. Across the eight trials, heritability estimates were 0.44 and 0.29 for viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain to 42 days post infection (WG), respectively. Genomic regions associated with VL were identified on chromosomes 4, X, and 1. Genomic regions associated with WG were identified on chromosomes 4, 5, and 7. Apart from the SSC4 region, the regions associated with these two traits each explained less than 3% of the genetic variance. Due to the strong linkage disequilibrium in the SSC4 region, only 19 unique haplotypes were identified across all populations, of which four were associated with the favorable phenotype. Through cross-validation, accuracies of EBV based on the SSC4 region were high (0.55), while the rest of the genome had little predictive ability across populations (0.09). Traits associated with response to PRRSV infection in growing pigs are largely controlled by genomic regions with relatively small effects, with the exception of SSC4. Accuracies of EBV based on the SSC4 region were high compared to the rest of the genome. These results show that selection for the SSC4 region could potentially reduce the effects of PRRS in growing pigs, ultimately reducing the economic impact of this disease

Performance and Carcass Composition of Yorkshire Pigs Selected for Low Residual Feed Intake under Ad Libitum and Restricted Feeding

Growth performance and carcass composition of 40 Yorkshire pigs (74.8±9.9 kg or 164.9±21.8 lbs), 20 pigs from a line selected for low residual feed intake for 5 generations and 20 pigs from a control line, was observed while fed on either an ad libitum or NRC maintenance (weight-stasis) basis over a 6 week period. The aim of the latter diet treatment was to keep pigs at a constant weight for six weeks. In the ad libitum treatment, there was no difference in initial (p \u3c 0.49) or final body weights (p \u3c 0.65) but the low residual feed intake line consumed 9% less feed compared to the control (p \u3c 0.08). Similarly, there was no difference in LEA (p \u3c 0.57) but the low residual feed intake line had slightly less backfat compared to the control (p \u3c 0.21). These same results were found from chemical analysis of the carcass, as there was no difference in protein percentage (p \u3c 0.60), but the ad libitum low residual feed intake pigs had a slightly lower fat percentage (p \u3c 0.21). For the weight stasis treatment, the low residual feed intake pigs weighed 3.5% more than the control (p \u3c 0.08), despite attempts to maintain a static body weight, and consumed 7.6% less feed overall (p \u3c 0.09). Both lines had a decrease in backfat; however, the low residual feed intake line had an increase in loin eye area while the control line had a decrease. No differences were observed in chemical carcass composition between the two lines on the weight stasis treatment. These data show that the low residual feed intake line is more efficient, with only slight differences in carcass composition

Quantitative Trait Locus on Sus scrofa Chromosome 4 Associated with Host Response to Experimental Infection with Porcine Reproductive and Respiratory Syndrome Virus

The objective of this study was to conduct a genomewide association study to discover the genetic basis of host response to PRRS virus using data from the PRRS Host Genetics Consortium NPB and PRRS-CAP project. Approximately 1,600 commercial crossbred piglets were experimentally infected with the Porcine Reproductive and Respiratory Syndrome (PRRS) virus. Blood samples and body weights were collected up to 42 days post infection (dpi). Experimental pigs and their parents were genotyped with Illumina’s Porcine 60k BeadChip. Phenotypes analyzed were viral load (VL = area under the curve for log-transformed qRT-PCR based serum virus from 0-21 dpi) and weight gain from 0-42 dpi (WG). Heritabilities estimated using pedigree information were moderate at 0.41 for VL and 0.29 for WG. A 1 Mb region on Sus scrofa chromosome (SSC) 4 was found to be associated with VL and WG and explained a substantial amount of genetic variation. The frequency of the favorable allele for the most significant single nucleotide polymorphism (SNP) was 0.15. These results show that there is a host genetic component to PRRS virus infection and that there is room for genetic improvement

A Comparison of the Genetic Factors Influencing Host Response to Infection with One of Two Isolates of Porcine Reproductive and Respiratory Syndrome Virus

Host genetic differences in viral load (VL) and weight gain (WG) during porcine reproductive and respiratory syndrome virus (PRRSV) challenge were assessed for thirteen trials of ~200 commercial crossbred piglets each, from several different commercial suppliers. Piglets were experimentally infected with PRRSV isolates NVSL-97-7895 (NVSL) or KS-2006-72109 (KS06). VL and WG were moderately heritable and were antagonistically related for both virus isolates. The genetic correlation of host response to NVSL with host response to KS06 was high for both VL and WG. Consistent with previous findings, animals that were heterozygous (AB) for the WUR10000125 (WUR) marker on Chromosome 4 (SSC4) had significantly lower VL than their AA counterparts when infected with either virus isolate; however, a significant increase in WG was only observed when piglets were infected with the NVSL isolate. These results suggest that selecting for increased resistance or reduced susceptibility to PRRSV may be effective across virus isolates. Selecting for the AB genotype for WUR is expected to reduce VL across PRRSV isolates but its effect on WG during infection may differ between virus isolates

Validation of the Effects of a SNP on SSC4 Associated with Viral Load and Weight Gain in Piglets Experimentally Infected with a 2006 PRRS Virus Isolate

Host genetic differences in viral load (VL) and weight gain (WG) during challenge were assessed for five trials of ~200 commercial crossbred piglets each, all from different commercial suppliers. Piglets were experimentally infected with porcine reproductive and respiratory syndrome virus (PRRSV) isolate KS-2006-72109 in order to validate the effects of a SNP previously identified on SSC4 (WUR10000125), whereby AB individuals had increased WG and reduced VL when experimentally infected with PRRSV isolate NVSL-97-7895. VL was defined as the area under the curve of logged viremia from 0-21 dpi. WG was defined as the weight gained from 0-42 dpi. The SNP effects on VL and WG were assessed. AB individuals had higher WG and lower VL than AA individuals, suggesting this marker may be useful for genetic selection of pigs for increased resistance or reduced susceptibility to PRRSV isolates that differ genetically and possibly pathogenically

Pigs Selected for Increased Feed Efficiency Are Less Affected by Experimental Infection with the PRRS Virus

Analyses of average daily gain (ADG) and viral load (VL) suggest that selection for increased feed efficiency based on residual feed intake (RFI) does not increase the impact of Porcine Reproductive and Respiratory Syndrome (PRRS) infection on these two traits. In fact, the results show that growth of the more efficient pigs was less affected by PRRS infection than that of the inefficient line. These findings provide commercial farmers with additional incentives to invest in feed-efficient pigs

Effects of selection for decreased residual feed intake on composition and quality of fresh pork

The objectives of this study were to determine the extent to which selection for decreased residual feed intake (RFI) affects pork composition and quality. Pigs from the fifth generation of selection for decreased RFI (select) and a randomly selected line (control) were utilized. Two experiments were conducted. In Exp. 1, barrows (22.6 ± 3.9 kg) from select and control lines were paired based on age and BW. The test was conducted in 8 replicates of pairs for the test period of 6 wk. Calpastatin activity and myosin isoforms profile were determined on samples from the LM. Control barrows were heavier (59.1 vs. 55.0 kg; P \u3c 0.01) at the end of the test period. Calpastatin activity was greater (P \u3c 0.01) in LM of select barrows than control barrows. In Exp. 2, composition and quality of gilts (114 kg) from control and select lines were determined. The model included fixed effects of line, slaughter date, melanocortin-4 receptor (MC4R) genotype, barn group, line × slaughter date, genotype × line interactions, a covariate of off-test BW, and sire, pen, and litter fitted as random effects. The select line (n = 80) had 0.043 kg less (P \u3c 0.05) RFI per day than the control line (n = 89). Loin quality and composition were determined at 2 d postmortem. Desmin degradation was measured at 2 and 7 d postmortem. Purge, cook loss, sensory traits, and star probe texture were measured at 7 to 10 d postmortem on cooked chops. Residual correlations between RFI and composition and quality traits were calculated. Compared with the control line, carcasses from the select line tended to have less (P = 0.09) backfat, greater (P \u3c 0.05) loin depth, and greater (P \u3c 0.05) fat free lean. Loin chops from the select line had less (P\u3c 0.01) intramuscular lipid content than loin chops from control line. Significant residual correlations between RFI and both tenderness (r = 0.24, P \u3c 0.01) and star probe (r = −0.26, P \u3c 0.01) were identified. Selection for decreased RFI has the potential to improve carcass composition with few effects on pH and water-holding capacity. However, decreased RFI could negatively affect tenderness and texture because of decreased lipid content and decreased postmortem protein degradation

Prenatal and Postnatal Dietary n-3 Fatty Acid Supplementation Alters Buffy Coat DNA Methylation Profile in Pigs

The objective of this study was to determine the effect of maternal long chain n-3 fatty acid supplementation on the DNA methylation profile of offspring buffy coats. We demonstrated several methylated regions across the genome were influenced by maternal n-3 dietary treatment. Therefore, feeding n-3 fatty acids to sows during gestation and lactation may result in a DNA methylation imprint on offspring buffy coats that persists beyond the nursery phase and may alter the phenotype of the growing pig