Investigation of the efficacy of albumin removal procedures on porcine serum proteome profile.

Improving the ability to predict livestock performance using biomarkers will provide a benefit for livestock genetic evaluation and improvement. The most practical biological sample to screen for development of biomarkers is serum due to the ease of collection. However, protein profiles in serum are complex and dynamic. Strategies are needed to manage variation in serum proteins used for biomarker identification. Albumin is the most abundant protein in serum, comprising over 50% of the overall protein content, and has historically been depleted from serum before biomarker identification. The objective of this study was to investigate the use of gel-based proteomic techniques to evaluate the need for porcine albumin depletion in biomarker identification. Albumin is known to bind many proteins in the blood, thus potential biomarkers could be removed during albumin depletion. Using two-dimensional difference in gel electrophoresis (2D-DIGE), we show whole serum can be used for biomarker discovery. The data obtained show that albumin removal methods are effective for porcine sera. Over 85% of the protein spots resolved on at least half of the gels were changed in abundance between whole and albumin depleted sera. Of the 204 protein spots significantly altered in abundance, 59 were changed over 400%. However, albumin removal also altered the serum proteome in an unpredictable manner; in the depleted sera, 86 protein spots were increased in abundance and 118 were decreased. Furthermore, the abundance of 59.4% of the protein spots in the albumin depleted samples had a larger standard error than whole sera. However, the resolution of albumin in 2D-DIGE analysis of whole sera permitted the detection and quantification of substantial numbers of proteins. Thus, it is proposed that whole serum can be used in a gel-based proteomics system for the identification of porcine biomarkers.

Validation and further characterization of a major quantitative trait locus associated with host response to experimental infection with porcine reproductive and respiratory syndrome virus.

Infectious diseases are costly to the swine industry; porcine reproductive and respiratory syndrome (PRRS) is the most devastating. In earlier work, a quantitative trait locus associated with resistance/susceptibility to PRRS virus was identified on Sus scrofa chromosome 4 using approximately 560 experimentally infected animals from a commercial cross. The favorable genotype was associated with decreased virus load and increased weight gain (WG). The objective here was to validate and further characterize the association of the chromosome 4 region with PRRS resistance using data from two unrelated commercial crossbred populations. The validation populations consisted of two trials each of approximately 200 pigs sourced from different breeding companies that were infected with PRRS virus and followed for 42 days post-infection. Across all five trials, heritability estimates were 0.39 and 0.34 for viral load (VL; area under the curve of log-transformed viremia from 0 to 21 days post-infection) and WG to 42 days post-infection respectively. Effect estimates of SNP WUR10000125 in the chromosome 4 region were in the same directions and of similar magnitudes in the two new trials as had been observed in the first three trials. Across all five trials, the 1-Mb region on chromosome 4 explained 15 percent of genetic variance for VL and 11 percent for WG. The effect of the favorable minor allele at SNP WUR10000125 was dominant. Ordered genotypes for SNP WUR10000125 showed that the effect was present irrespective of whether the favorable allele was paternally or maternally inherited. These results demonstrate that selection for host response to PRRS virus infection could reduce the economic impact of PRRS.

Evidence for a major QTL associated with host response to porcine reproductive and respiratory syndrome virus challenge.

Porcine reproductive and respiratory syndrome (PRRS) causes decreased reproductive performance in breeding animals and increased respiratory problems in growing animals, which result in significant economic losses in the swine industry. Vaccination has generally not been effective in the prevention of PRRS, partially because of the rapid mutation rate and evolution of the virus. The objective of the current study was to discover the genetic basis of host resistance or susceptibility to the PRRS virus through a genome-wide association study using data from the PRRS Host Genetics Consortium PRRS-CAP project. Three groups of approximately 190 commercial crossbred pigs from 1 breeding company were infected with PRRS virus between 18 and 28 d of age. Blood samples and BW were collected up to 42 d post infection (DPI). Pigs were genotyped with the Illumina Porcine 60k Beadchip. Whole-genome analysis focused on viremia at each day blood was collected and BW gains from 0 to 21 DPI (WG21) or 42 DPI (WG42). Viral load (VL) was quantified as area under the curve from 0 to 21 DPI. Heritabilities for WG42 and VL were moderate at 0.30 and litter accounted for an additional 14% of phenotypic variation. Genomic regions associated with VL were found on chromosomes 4 and X and on 1, 4, 7, and 17 for WG42. The 1-Mb region identified on chromosome 4 influenced both WG and VL, exhibited strong linkage disequilibrium, and explained 15.7% of the genetic variance for VL and 11.2% for WG42. Despite a genetic correlation of -0.46 between VL and WG42, genomic EBV for this region were favorably and nearly perfectly correlated. The favorable allele for the most significant SNP in this region had a frequency of 0.16 and estimated allele substitution effects were significant (P < 0.01) for each group when the SNP was fitted as a fixed covariate in a model that included random polygenic effects with overall estimates of -4.1 units for VL (phenotypic SD = 6.9) and 2.0 kg (phenotypic SD = 3 kg) for WG42. Candidate genes in this region on SSC4 include the interferon induced guanylate-binding protein gene family. In conclusion, host response to experimental PRRS virus challenge has a strong genetic component, and a QTL on chromosome 4 explains a substantial proportion of the genetic variance in the studied population. These results could have a major impact in the swine industry by enabling marker-assisted selection to reduce the impact of PRRS but need to be validated in additional populations.

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 < 0.01) at the end of the test period. Calpastatin activity was greater (P < 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 < 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 < 0.05) loin depth, and greater (P < 0.05) fat free lean. Loin chops from the select line had less (P < 0.01) intramuscular lipid content than loin chops from control line. Significant residual correlations between RFI and both tenderness (r = 0.24, P < 0.01) and star probe (r = -0.26, P < 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.

Effects of ad libitum and restricted feed intake on growth performance and body composition of Yorkshire pigs selected for reduced residual feed intake.

Residual feed intake (RFI), defined as the difference in the observed and expected feed intake while accounting for growth and backfat, has gained much attention, but little is known about why pigs selected for reduced RFI are more efficient. To this end, a line of Yorkshire pigs selected for reduced RFI was developed. The objective of this study was to evaluate the 5th generation of this select line against a randomly selected control line for performance, carcass and chemical carcass composition, and overall efficiency toward the later part of the growth phase. Eighty barrows, 40 from each line, were paired by age (~132 d, P < 0.60) and BW (74.8 ± 9.9 kg, P < 0.49) and randomly assigned to 1 of 4 feeding treatments in 10 replicates: 1) ad libitum, 2) 75% of ad libitum, 55% of ad libitum, and BW stasis, with weekly adjustments in intake to keep BW constant for each pig. Pigs were individually penned (group housing was used for selection) and on treatment for 6 wk. Initial BW did not differ between the lines (P < 0.49). The ad libitum select pigs consumed 10% less feed (P < 0.09) than the ad libitum control with no significant difference in BW (P < 0.80) and slight differences in carcass fat composition (P < 0.20) and backfat (P < 0.11), which resulted in significantly less carcass energy (P < 0.03). Under restricted feeding, the select line had an increase in BW (P = 0.10) while consuming the same ration of feed as the control line with no significant difference in chemical carcass composition and lighter visceral weights, which was significant for the 75% of ad libitum treatment (P < 0.01). Under BW stasis feeding the select line consumed 7.6% less feed overall (P = 0.21) and 18% less feed at the end of the 6 wk (P < 0.08), to maintain static BW with no significant difference in chemical carcass composition compared with the control line. Overall, the select line had lighter visceral weight (P < 0.02) and a greater dressing percentage (P < 0.03) compared with the control line. Using regression, the select line had reduced energy retention (P < 0.04) and feed energy utilization (P < 0.34); however, the select line appeared to have reduced maintenance requirements (P < 0.13). In conclusion, selection for reduced RFI decreases feed intake with no significant difference (P > 0.05) in growth performance, reduced backfat, increased dressing percentage, and reduced maintenance requirements. All of these traits are appealing to the producer and result in increased profits in the production setting.

Effects of ad libitum and restricted feeding on early production performance and body composition of Yorkshire pigs selected for reduced residual feed intake.

Residual feed intake (RFI), defined as the difference between observed and expected feed intake based on growth and backfat, has been used to investigate genetic variation in feed efficiency in cattle, poultry and pigs. However, little is known about the biological basis of differences in RFI in pigs. To this end, the objective of this study was to evaluate the fifth generation of a line of pigs selected for reduced RFI against a randomly selected Control line for performance, carcass and chemical carcass composition and overall efficiency. Here, emphasis was on the early grower phase. A total of 100 barrows, 50 from each line, were paired by age and weight (22.6 ± 3.9 kg) and randomly assigned to one of four feeding treatments in 11 replicates: ad libitum (Ad), 75% of Ad (Ad75), 55% of Ad (Ad55) and weight stasis (WS), which involved weekly adjustments in intake to keep body weight (BW) constant for each pig. Pigs were individually penned (group housing was used for selection) and were on treatment for 6 weeks. Initial BW did not significantly differ between the lines (P > 0.17). Under Ad feeding, the low RFI pigs consumed 8% less feed compared with Control line pigs (P < 0.06), had less carcass fat (P < 0.05), but with no significant difference in growth rate (P > 0.85). Under restricted feeding, low RFI pigs under the Ad75 treatment had a greater rate of gain while consuming the same amount of feed as Control pigs. Despite the greater gain, no significant line differences in carcass composition or carcass traits were observed. For the WS treatment, low RFI pigs had similar BW (P > 0.37) with no significant difference in feed consumption (P > 0.32). Overall, selection for reduced RFI has decreased feed intake, with limited differences in growth rate but reduced carcass fat, as seen under Ad feeding. Collectively, results indicate that the effects of selection for low RFI are evident during the early grower stage, which allows for greater savings to the producer.