Feeding behavior of grow-finish swine and the impacts of heat stress.

Heat stress has negative impacts on pork production, particularly in the grow-finish phase. During heat stress events, the feeding behavior of pigs is altered to reduce heat production. Several different systems have been developed to study feeding behavior. Most systems are not accurate representations of grow-finish commercial production as feed intake is monitored for only one pig at a time. The objective of this study was to utilize a feed monitoring system, representative of commercial conditions, to determine feeding behavior patterns of grow-finish pigs throughout the year and to identify changes that occurred during heat stress events. Feeder visit data were collected on barrows and gilts (n = 932) from three different sire breeds, Landrace, Yorkshire, and Duroc, between May 2014 and April 2016. Days in the study were partitioned into groups based on their maximum temperature-humidity index (THI), where a THI less than 23.33 °C was classified as "Normal", a THI between 23.33 and 26.11 °C was classified as "Alert", a THI between 26.11 and 28.88 °C was classified as "Danger", and a THI greater than 28.88 °C was classified as "Emergency". Feeding behavioral differences among breeds and sex were observed across all THI categories. Landrace-sired pigs had fewer feeder visits compared to Duroc- and Yorkshire-sired pigs. Gilts had fewer feeder visits than barrows in all THI categories. Differences in feeding behavior patterns between THI categories demonstrated that heat stress reduced the feeding duration of Landrace-sired pigs without any dramatic effects on the other pigs in the study. During elevated temperatures, all pigs tended to increase feeding events during the early (03:00-05:59) and late (18:00-20:59) periods of the day. Utilizing a feed monitoring system that is a more accurate representation of commercial conditions will lead to a greater understanding of feeding behavior among breed types and sexes during heat stress, allowing producers to enhance their ability to properly care for their pigs during both normal and heat stress events.

Genome-wide association of changes in swine feeding behaviour due to heat stress.

BACKGROUND: Heat stress has a negative impact on pork production, particularly during the grow-finish phase. As temperature increases, feeding behaviour changes in order for pigs to decrease heat production. The objective of this study was to identify genetic markers associated with changes in feeding behaviour due to heat stress. Feeding data were collected on 1154 grow-finish pigs using an electronic feeding system from July 2011 to March 2016. In this study, days were classified based on the maximum temperature humidity index (THI) during the day as "Normal" (< 23.33 °C), "Alert" (23.33 °C ≤ × < 26.11 °C), "Danger" (26.11 °C ≤ × < 28.88 °C), and "Emergency" (≥ 28.88 °C). Six hundred and eighty-one pigs that experienced more than one THI category were genotyped using a variety of SNP platforms, with final genotypes imputed to approximately 60,000 markers. RESULTS: A genome-wide association study (GWAS) for change in feeding behaviour between each pair of THI categories (six pairs) was conducted. Estimates of heritability for differences in feeding activity between each of the THI categories were low (0.02 ± 0.03) to moderate (0.21 ± 0.04). Sixty-six associations which explained more than 1% of the genomic variation for a trait were detected across the six GWAS, with the smallest number of associations detected in comparisons with Emergency THI. Gene ontology enrichment analysis showed that biological processes related to immune response and function were over-represented among the genes located in these regions. CONCLUSIONS: Genetic differences exist for changes in feeding behaviour induced by elevated ambient temperatures in grow-finish pigs. Selection for heat-tolerant grow-finish pigs should improve production efficiency during warm months in commercial production. Genetic variation in heat shock, stress response and immune function genes may be responsible for the observed differences in performance during heat stress events.

Changes in chondrocyte gene expression following in vitro impaction of porcine articular cartilage in an impact injury model.

Our objective was to monitor chondrocyte gene expression at 0, 3, 7, and 14 days following in vitro impaction to the articular surface of porcine patellae. Patellar facets were either axially impacted with a cylindrical impactor (25 mm/s loading rate) to a load level of 2,000 N or not impacted to serve as controls. After being placed in organ culture for 0, 3, 7, or 14 days, total RNA was isolated from full thickness cartilage slices and gene expression measured for 17 genes by quantitative real-time RT-PCR. Targeted genes included those encoding proteins involved with biological stress, inflammation, or anabolism and catabolism of cartilage extracellular matrix. Some gene expression changes were detected on the day of impaction, but most significant changes occurred at 14 days in culture. At 14 days in culture, 10 of the 17 genes were differentially expressed with col1a1 most significantly up-regulated in the impacted samples, suggesting impacted chondrocytes may have reverted to a fibroblast-like phenotype.

Estimates of marker effects for measures of milk flow in the Italian brown Swiss dairy cattle population.

BACKGROUND: Milkability is a complex trait that is characterized by milk flow traits including average milk flow rate, maximum milk flow rate and total milking time. Milkability has long been recognized as an economically important trait that can be improved through selection. By improving milkability, management costs of milking decrease through reduced labor and improved efficiency of the automatic milking system, which has been identified as an important factor affecting net profit. The objective of this study was to identify markers associated with electronically measured milk flow traits, in the Italian Brown Swiss population that could potentially improve selection based on genomic predictions. RESULTS: Sires (n = 1351) of cows with milk flow information were genotyped for 33,074 single nucleotide polymorphism (SNP) markers distributed across 29 Bos taurus autosomes (BTA). Among the six milk flow traits collected, ascending time, time of plateau, descending time, total milking time, maximum milk flow and average milk flow, there were 6,929 (time of plateau) to 14,585 (maximum milk flow) significant SNP markers identified for each trait across all BTA. Unique regions were found for each of the 6 traits providing evidence that each individual milk flow trait offers distinct genetic information about milk flow. This study was also successful in identifying functional processes and genes associated with SNPs that influences milk flow. CONCLUSIONS: In addition to verifying the presence of previously identified milking speed quantitative trait loci (QTL) within the Italian Brown Swiss population, this study revealed a number of genomic regions associated with milk flow traits that have never been reported as milking speed QTL. While several of these regions were not associated with a known gene or QTL, a number of regions were associated with QTL that have been formerly reported as regions associated with somatic cell count, somatic cell score and udder morphometrics. This provides further evidence of the complexity of milk flow traits and the underlying relationship it has with other economically important traits for dairy cattle. Improved understanding of the overall milking pattern will aid in identification of cows with lower management costs and improved udder health.

Effectiveness of genomic prediction on milk flow traits in dairy cattle.

BACKGROUND: Milkability, primarily evaluated by measurements of milking speed and time, has an economic impact in milk production of dairy cattle. Recently the Italian Brown Swiss Breeders Association has included milking speed in genetic evaluations. The main objective of this study was to investigate the possibility of implementing genomic selection for milk flow traits in the Italian Brown Swiss population and thereby evaluate the potential of genomic selection for novel traits in medium-sized populations. Predicted breeding values and reliabilities based on genomic information were compared with those obtained from traditional breeding values. METHODS: Milk flow measures for total milking time, ascending time, time of plateau, descending time, average milk flow and maximum milk flow were collected on 37 213 Italian Brown Swiss cows. Breeding values for genotyped sires (n = 1351) were obtained from standard BLUP and genome-enhanced breeding value techniques utilizing two-stage and single-step methods. Reliabilities from a validation dataset were estimated and used to compare accuracies obtained from parental averages with genome-enhanced predictions. RESULTS: Genome-enhanced breeding values evaluated using two-stage methods had similar reliabilities with values ranging from 0.34 to 0.49 for the different traits. Across two-stage methods, the average increase in reliability from parental average was approximately 0.17 for all traits, with the exception of descending time, for which reliability increased to 0.11. Combining genomic and pedigree information in a single-step produced the largest increases in reliability over parent averages: 0.20, 0.24, 0.21, 0.14, 0.20 and 0.21 for total milking time, ascending time, time of plateau, descending time, average milk flow and maximum milk flow, respectively. CONCLUSIONS: Using genomic models increased the accuracy of prediction compared to traditional BLUP methods. Our results show that, among the methods used to predict genome-enhanced breeding values, the single-step method was the most successful at increasing the reliability for most traits. The single-step method takes advantage of all the data available, including phenotypes from non-genotyped animals, and can easily be incorporated into current breeding evaluations.

Application of multiple shrinkage methods to genomic predictions.

New challenges have arisen with the development of large marker panels for livestock species. Models easily become overparameterized when all available markers are included. Solutions have led to the development of shrinkage or regularization techniques. The objective of this study was the application and comparison of Bayesian LASSO (B-L), thick-tailed (Student-t), and semiparametric multiple shrinkage methods. The B-L and Student-t methods were also each analyzed within a single shrinkage and a multiple shrinkage framework. Simulated and real data were used to evaluate each method's performance. Real data consisted of SNP genotypes of 4,069 Holstein sires. Traits included in analysis of real data were milk, fat, protein yield, and somatic cell score. The performance of each model was compared based on correlations between true and predicted genomic predicted transmitting abilities. Model performance was also compared with the performance of routinely used methods such as Bayes-A and GBLUP through cross-validation techniques. When using simulated data regardless of shrinkage framework, shrinkage models outperformed genomic BLUP (GBLUP). The average advantage of shrinkage models ranged from 1% to approximately 8% depending on the prior specification. When analyzing real data, shrinkage models slightly outperformed GBLUP for most traits. Shrinkage models were better able to model traits for which 1 or more SNP of large effect have been identified. Overall, results suggested a relatively small advantage in multiple shrinkage models. Multiple shrinkage methods could represent a useful alternative to current methods of prediction; however, their performance in a variety of scenarios needs to be investigated further.

Trans-10, cis-12-conjugated linoleic acid alters hepatic gene expression in a polygenic obese line of mice displaying hepatic lipidosis.

The trans-10, cis-12 isomer of conjugated linoleic acid (CLA) causes a rapid reduction of body and adipose mass in mice. In addition to changes in adipose tissue, numerous studies have reported alterations in hepatic lipid metabolism. Livers of CLA-fed mice gain mass, partly due to lipid accumulation; however, the precise molecular mechanisms are unknown. To elucidate these mechanisms, we examined fatty acid composition and gene expression profiles of livers from a polygenic obese line of mice fed 1% trans-10, cis-12-CLA for 14 days. Analysis of gene expression data led to the identification of 1393 genes differentially expressed in the liver of CLA-fed male mice at a nominal P value of .01, and 775 were considered significant using a false discovery rate (FDR) threshold of .05. While surprisingly few genes in lipid metabolism were impacted, pathway analysis found that protein kinase A (PKA) and cyclic adenosine monophosphate (cAMP) pathways signaling pathways were affected by CLA treatment and 98 of the 775 genes were found to be regulated by hepatocyte nuclear factor 4alpha, a transcription factor important in controlling liver metabolic status.

Detection of transcriptional difference of porcine imprinted genes using different microarray platforms.

BACKGROUND: Presently, multiple options exist for conducting gene expression profiling studies in swine. In order to determine the performance of some of the existing microarrays, Affymetrix Porcine, Affymetrix Human U133+2.0, and the U.S. Pig Genome Coordination Program spotted glass oligonucleotide microarrays were compared for their reproducibility, coverage, platform independent and dependent sensitivity using fibroblast cell lines derived from control and parthenogenic porcine embryos. RESULTS: Array group correlations between technical replicates demonstrated comparable reproducibility in both Affymetrix arrays. Glass oligonucleotide arrays showed greater variability and, in addition, approximately 10% of probes had to be discarded due to slide printing defects. Probe level analysis of Affymetrix Human arrays revealed significant variability within probe sets due to the effects of cross-species hybridization. Affymetrix Porcine arrays identified the greatest number of differentially expressed genes amongst probes common to all arrays, a measure of platform sensitivity. Affymetrix Porcine arrays also identified the greatest number of differentially expressed known imprinted genes using all probes on each array, an ad hoc measure of realistic performance for this particular experiment. CONCLUSION: We conclude that of the platforms currently available and tested, the Affymetrix Porcine array is the most sensitive and reproducible microarray for swine genomic studies.

Functional genomic characterization of delipidation elicited by trans-10, cis-12-conjugated linoleic acid (t10c12-CLA) in a polygenic obese line of mice.

Gene expression was measured during t10c12-CLA-induced body fat reduction in a polygenic obese line of mice. Adult mice (n = 185) were allotted to a 2 x 2 factorial experiment consisting of either nonobese (ICR-control) or obese (M16-selected) mice fed a 7% fat, purified diet containing either 1% linoleic acid (LA) or 1% t10c12-CLA. Body weight (BW) by day 14 was 12% lower in CLA- compared with LA-fed mice (P < 0.0001). By day 14, t10c12-CLA reduced weights of epididymal, mesenteric, and brown adipose tissues, as a percentage of BW, in both lines by 30, 27, and 58%, respectively, and increased liver weight/BW by 34% (P < 0.0001). Total RNA was isolated and pooled (4 pools per tissue per day) from epididymal adipose (days 5 and 14) of the obese mice to analyze gene expression profiles using Agilent mouse oligo microarray slides representing > 20,000 genes. Numbers of genes differentially expressed by greater than or equal to twofold in epididymal adipose (days 5 and 14) were 29 and 125, respectively. It was concluded that, in adipose tissue, CLA increased expression of uncoupling proteins (1 and 2), carnitine palmitoyltransferase system, tumor necrosis factor-alpha (P < 0.05), and caspase-3 but decreased expression of peroxisome proliferator-activated receptor-gamma, glucose transporter-4, perilipin, caveolin-1, adiponectin, resistin, and Bcl-2 (P < 0.01). In conclusion, this experiment has revealed candidate genes that will be useful in elucidating mechanisms of adipose delipidation.