Chen, L., Li, C. and Schenkel, F. 2015. An alternative computing strategy for genomic prediction using a Bayesian mixture model. Can. J. Anim. Sci. 95: 1-11. Bayesian methods for genomic prediction are commonly implemented via Markov chain Monte Carlo (MCMC) sampling schemes, which are computationally demanding in large-scale applications. An alternative computing algorithm, called right-hand side updating strategy (RHSU), was proposed by exploiting the sparsity feature of the marker effects in a Bayesian mixture model. The new algorithm was compared with the conventional Gauss-Seidel residual update (GSRU) algorithm by the number of floating point operations (FLOP) required in one round of MCMC sampling. The two algorithms were also compared in a Holstein data example with the training data size varying from 1000 to 10 000 and a marker density of 35 790 single nucleotide polymorphisms (SNP). Results showed that the proposed RHSU algorithm would outperform the traditional GSRU algorithm when the sample size exceeded a fraction of the number of the SNPs, which typically varied from 0.05 to 0.18 when the proportion of SNPs with no effect on the trait varied from 0.90 to 0.95. Results from the Holstein data example agreed very well with theoretical expectations. With adoption of a 50 k SNP panel and an increasing training data size, RHSU would be very useful if Bayesian methods are preferable for genomic prediction.

Yang, X.-q., Wang, L., Li, H.-t. and Liu, D. 2015. Immune responses of porcine airway epithelial cells to poly(I:C), a synthetic analogue of viral double-stranded RNA. Can. J. Anim. Sci. 95: 13-20. Swine respiratory disease (SRD) is one of the most economically important diseases affecting the pig industry. The main infectious agents that cause SRD are viruses, but the molecular pathogenesis of viral SRD has not been extensively studied. Here, using digital gene expression tag profiling, the global transcriptional responses to poly(I:C), a synthetic analogue of viral double-stranded RNA, was analyzed in porcine airway epithelial cells (PAECs). The profiling analysis revealed numerous differentially expressed genes (DEGs), including unknown sequences in the porcine nucleotide databases. Gene ontology enrichment analysis showed that DEGs were mainly enriched in response to stress (GO: 0006950), of which, defense response is one sub-process. Poly(I:C) challenge induced a general inflammation response as indicated by marked upregulation of a variety of pathogen recognition receptors, interferon-stimulated genes, proinflammatory cytokines, and chemokines, together with the significant downregulation of anti-inflammatory molecules. Furthermore, the antiapoptotic pathway was triggered, as demonstrated by the significant suppression of molecules involved in the induction of apoptosis, together with the significant stimulation of putative inhibitor of apoptosis. The results indicate that PAECs initiated defense against poly(I:C) challenge through the inflammation responses, whereas poly(I:C) can utilize antiapoptotic pathway to evade host defense.

Borowska, A. and Szwaczkowski, T. 2015. Pedigree analysis of Polish warmblood horses participating in riding performance tests. Can. J. Anim. Sci. 95: 21-29. The aim of this study was to describe the population structure and genetic diversity in Polish warmblood horse population participating in the performance test. The reference population consisted of 596 stallions and 866 mares that participated in stationary performance tests conducted between 2002 and 2011 in Poland. The pedigree data contained 15 452 individuals. Completeness of pedigree information was assessed by two measures: percentage of animals with both parents known and discrete generation equivalent. Individual inbreeding coefficients, coancestry coefficient, individual increase in inbreeding, founder equivalent, founder genome equivalent, effective number of non-founders and genetic diversity loss were estimated to characterize the genetic diversity of the population. The average number of discrete generation equivalents reached 4.50 for observed stallions and 5.04 for mares, which shows good pedigree completeness. Pedigree analysis showed that 34% of the stallions and 44% of mares had inbreeding coefficients above zero. The average coancestry was 0.39% in the whole tested population. Average inbreeding rate of studied populations was very low (0.46%). The effective number of founders was 560. Generally, the inbreeding rate was low; genetic diversity was observed at a constant level for mares and only a small decrease was noticed for stallion. However, further studies are needed in this area.

Hwang, J. H., Kwon, S. G., Park, D. H., Kim, T. W., Kang, D. G., Ha, J., Kim, S. W. and Kim, C. W. 2015. Molecular characterization of porcine PGM1 gene associated with meat quality traits. Can. J. Anim. Sci. 95: 31-36. The PGM1 gene from four porcine breeds (Berkshire, Duroc, Landrace, and Yorkshire) is highly expressed in liver tissue at the transcriptional level. Single nucleotide polymorphisms (SNPs) of PGM1 were examined to analyze association with increased expression of PGM1 gene in the Berkshire liver. A Leu525 synonymous SNP of Chr6:137174682A>G (c.1575A>G) was identified and showed significant (P<0.05) differences to backfat thickness, drip loss, protein content, fat content, Warner-Bratzler shear force, and post-mortem pH_24h. Therefore, it is concluded that PGM1 synonymous SNP is an important factor regulating meat quality.

Glanc, D. L., Campbell, C. P., Cranfield, J., Swanson, K. C. and Mandell, I. B. 2015. Effects of production system and slaughter weight endpoint on growth performance, carcass traits, and beef quality from conventionally and naturally produced beef cattle. Can. J. Anim. Sci. 95: 37-47. Effects of production system and slaughter endpoint on performance, carcass traits, and beef quality were investigated in 64 Simmental cross steers (minimum 75% Continental breeding). Cattle were allocated to: (1) conventional production system based on use of implants and dietary ionophores or (2) natural production system in which no implants or ionophores were used. Within each production system, cattle were allocated for slaughter at 545 or 636 kg liveweight. Steers were fed an 85.5% concentrate diet based on high-moisture corn, soybean meal, and alfalfa silage. Average daily gain tended to be greater (P<0.06) in conventional production system cattle, while there was a trend (P<0.08) for production system by endpoint interactions for dry matter intake and gain to feed. Natural production system cattle tended to have greater (P<0.08) marbling and percent intramuscular fat (%IMF) with lower (P<0.09) longissimus shear force, while production system by endpoint interactions were present (P ≤ 0.03) for%IMF and carcass lean composition via rib dissection. At-home consumer evaluation of longissimus muscle steaks found tenderness, juiciness, flavour, and overall acceptability rankings were greater (P<0.01) for steaks slaughtered from heavier cattle (636 vs. 545 kg liveweight). Marketing cattle at lighter slaughter weights may have benefits for performance at the expense of eating quality.

Turner, T. D., Jensen, J., Pilfold, J. L., Prema, D., Donkor, K. K., Cinel, B., Thompson, D. J., Dugan, M. E. R. and Church, J. S. 2015. Comparison of fatty acids in beef tissues from conventional, organic and natural feeding systems in western Canada. Can. J. Anim. Sci. 95: 49-58. The effect of production system on intramuscular and associated trim fatty acid (FA) profiles of retail ribeye steaks from conventional and niche market organic and natural (grain- or grass-fed) beef were compared. Meat from organic grain- and grass-fed systems was leaner, containing greater proportions of polyunsaturated FA, i.e., 18:3n-3, 20:5n-3, 22:5n-3, 22:6n-3. Correspondingly, the n-6/n-3 ratios of organic grain- and grass-fed systems were 3:1, while conventional and natural grain systems had ratios of 8:1. High forage-to-grain ratio production systems increased proportions of desirable biohydrogenation intermediates (BI), including t11-18:1 and c9,t11-18:2, whereas conventional and natural grain systems elevated t10-18:1. Trim fat was similarly affected by production system, and was a relatively richer source of BI. Overall, proportions of desirable FAs, including n-3 and BI, were greater for organic grain- and grass-fed systems, emphasizing the importance of a high forage-to-grain ratio to enhance the healthfulness of beef, whereas conventional and natural grain-fed systems were largely equivalent.

Kalantari, A. S. and Cabrera, V. E. 2015. Stochastic economic evaluation of dairy farm reproductive performance. Can. J. Anim. Sci. 95: 59-70. The objective of this study was to assess the economic value of reproductive performance in dairy farms under uncertain and variable conditions. Consequently, the study developed methods to introduce stochasticity into transition probabilities of a Markov chain model. A robust Markov chain model with 21-d stage length and three state variables, parity, days in milk, and days in pregnancy, was developed. Uncertainty was added to all transition probabilities, milk production level, and reproductive costs. The model was run for 10 000 replications after introducing each random variable. The expected net return (US$ cow^-1 yr^-1±standard deviation) was $3192±75.0 for the baseline scenario that had 15% 21-d pregnancy rate (21-d PR). After verifying the model's behavior, it was run for 2000 replications to study the effect of changing 21-d PR from 10 to 30% with one-unit-percentage interval. The economic gain of changing 21-d PR from 10 to 30% resulted in a US$75 cow^-1 yr^-1, and this overall increase in the net return was observed mainly due to the lower reproductive and culling cost and higher calf value. The gain was even greater when milk price and milk cut-off threshold decreased.

Opapeju, F. O., Rodriguez-Lecompte, J. C., Rademacher, M., Krause, D. O. and Nyachoti, C. M. 2015. Low crude protein diets modulate intestinal responses in weaned pigs challenged with Escherichia coli K88. Can. J. Anim. Sci. 95: 71-78. Effects of dietary crude protein (CP) content on intestinal indicators of infection and diarrhea in pigs challenged with enterotoxigenic Escherichia coli (ETEC) K88 were investigated. Forty piglets [body weight (BW)=6.96±0.45, mean±SD], housed four per pen, were randomly allotted to two diets (five pens per diet): a 22.2% CP or a 17.3% CP supplemented with amino acids. Diets contained the same amount of standardized ileal digestible Lys, Met Cys, Thr, Trp based on the ideal amino acid ratio. Isoleucine and Val were added to the 17.3% CP diet up to the level in the 22.2% CP diet. All other nutrients were as per National Research Council (1998) specification. Three piglets per pen were serially slaughtered on days 3, 5, and 7 after weaning for evaluation of intestinal hydrolases (data reported elsewhere). On day 8 post-weaning, the remaining pigs were inoculated with 6 mL of ETEC suspension (10¹⁰ CFU mL^-1) and slaughtered 20 h later. Mucosal-associated ETEC was detected in higher counts (3.17±0.63 log₁₀ CFU g^-1 digesta) in 80% of pigs fed the 22.2% CP diet compared with 20% of those fed the 17.3% CP diet in which the counts were also lower (2.00±log₁₀ CFU g^-1 digesta). Pigs fed the 22.2% CP diet tended (P=0.09) to have fewer goblet cells with sialomucins in jejunal villi compared with those fed the 17.3% CP diet. The expression of toll-like receptors 4 and 5 was unaffected by diet but the expression of sodium-coupled glucose transporter 1 was higher (P=0.04) in the jejunum of pigs fed the 22.2% CP diet compared with those fed the 17.3% CP diet. The results suggest that feeding a low-CP diet decreases ETEC proliferation and attachment in the intestinal mucosa and this is accompanied by a reduced expression of sodium-coupled glucose transporter 1.

Saez, P. J., Abdel-Aal, E. M. and Bureau, D. P. 2015. Reduction of carotenoids in corn gluten meal: Effects on growth performance and muscle pigmentation of rainbow trout (Oncorhynchus mykiss). Can. J. Anim. Sci. 95: 79-92. Corn gluten meal (CGM) is an ingredient widely included in aquaculture feeds. The use of significant levels of CGM in diet formulation has been anecdotally related to the suboptimal pigmentation of the muscle of salmonid fish. The results of a few scientific studies that have examined the effect of CGM on muscle pigmentation in salmonids remain inconclusive. Therefore, a bench-scale study was carried out to reduce the content of yellow xanthophyll carotenoids in CGM using white soy flake flour as a bleaching agent. A 12-wk growth trial was then conducted to assess the effects of treated CGM on growth and muscle pigmentation of rainbow trout (Oncorhynchus mykiss) in comparison with regular CGM. Results of the pigment reduction study indicated that the concentration of lutein, zeaxanthin, β-cryptoxanthin and β-carotene was reduced by 86, 97, 100 and 100%, respectively, in the treated CGM. Results of the growth trial showed that the inclusion of treated or regular CGM in the diet did not significantly affect growth performance. However a significant (P<0.05) reduction in astaxanthin deposition was observed in the muscle of fish fed the diet supplemented with 190 g kg^-1 of regular CGM when compared with the fish fed the control diet (0 g kg^-1 of CGM). The muscle of fish fed the diet containing 190 g kg ^-1 of treated CGM showed the lowest astaxanthin deposition. This could be attributed to the presence of reactive peroxy radicals produced during the reduction of carotenoids in the treated CGM. Further research is underway to improve the processing method for the reduction of carotenoids in CGM.

Kenney, N. M., Vanzant, E. S., Harmon, D. L. and McLeod, K. R. 2015. Effect of direct-fed microbials on utilization of degradable intake protein in receiving steers. Can. J. Anim. Sci. 95: 93-102. One hundred ninety-two crossbred beef steers (280±25 kg) were assigned to a 5×2 factorial; degradable intake protein (DIP; 80, 90, 100, 110, 120% of requirement) with and without a direct-fed microbial (DFM) primarily containing Lactobacillus acidophilus and Enterococcus faecium (10⁹ CFU steer^-1 d^-1). Dry matter intake, morbidity, and immune response were not affected (P≥0.11). The first 28 d, average daily gain (ADG) did not differ with DIP in control, but increased in a cubic fashion with DFM (DIP×DFM; P=0.05). No differences (P≥0.25) in ADG occurred from days 29 to 56; however, there was a tendency (P=0.08) for a cubic increase in ADG with increasing DIP with DFM over 56 d. The first 28 d, growth efficiency did not differ across DIP levels in control but increased linearly with DFM (DIP×DFM; P=0.05). No differences (P≥0.21) in efficiency were observed from days 29 to 56 or overall. Without DFM, fecal pH decreased between days 7 and 14; however, with DFM there was no change in pH (DFM×time; P<0.05). Performance response to DFM is dependent on DIP; however, DFM does not impact morbidity or humoral immune response.

Ribeiro Jr., G. A., Teixeira, A. M., Velasco, F. O., Faria Jr., W. G., Jayme, D. G., Maurício, R. M., Gonçalves, L. C. and McAllister, T. A. 2015. Methane production and energy partitioning in sheep fed Andropogon gayanus grass ensiled at three regrowth stages. Can. J. Anim. Sci. 95: 103-110. This study was undertaken to evaluate the effect of harvesting Andropogon gayanus at different regrowth stages (56, 84 and 112 d) on the nutritional value of silage and CH₄ emissions from sheep. Rams (n=18) were adapted to silages for 21 d after which intake and digestibility were measured over 5 d in a completely randomized design (six rams/treatment). Heat production and methane emissions from each ram were measured in a respiration chamber over 24 h. Silage dry matter (DM; 54.4 g kg^-1 BW^0.75 d^-1) intake was not influenced (P>0.05) by silage regrowth stage, but apparent DM digestibility linearly decreased (P<0.05) from 526 to 380 g kg^-1 with increasing regrowth. Energy lost as a percent of gross energy intake (GEI) linearly increased with longer regrowth, yet no effect on CH₄ losses (as% GEI; g kg^-1 DM; g kg^-1 digestible DM) or heat production were observed. Ensiling A. gayanus grass at an earlier regrowth stage (56 d) will improve silage quality, but improvements in the energetic value are not due to a reduction in enteric CH₄ emissions as a% GEI.

Awawdeh, M. S., Talafha, A. Q. and Obeidat, B. S. 2015. Postpartum injection with vitamin E and selenium failed to improve the performance of Awassi ewes and their lambs. Can. J. Anim. Sci. 95: 111-115. The objective of this study was to investigate the effect of vitamin E and Se injection of nursing Awassi ewes on the performance of ewes (body weight change, milk yield, and composition) and their lambs (growth rate and weaning weight). Twenty-eight Awassi ewes were randomly assigned upon lambing to one of two groups; Control (n=13) and Inject (n=15), where ewes received 0 (control) or 15 plus 0.05 mg kg^-1 BW of vitamin E and Se, respectively (inject). Intramuscular injections were given at 1 and 4 wk postpartum. Body weight (BW) of ewes and their lambs were recorded at lambing and at 2, 4, 6, and 8 wk postpartum. Milk yield and composition were measured at 2, 4, and 6 wk postpartum and somatic cell count (SCC) was evaluated weekly (from lambing through 8 wk). Injecting nursing ewes with vitamin E and Se had no effects (P≥0.10) on BW change of ewes, milk yield and composition, composition yields, or milk SCC. Injecting nursing ewes with vitamin E and Se had no significant effects (P≥0.29) on weaning weight, BW gain, or growth rate of their lambs. Under conditions similar to the current study, injecting nursing Awassi ewes with vitamin E and Se at 1 and 4 wk postpartum was not effective in improving the performance of ewes and their suckling lambs. Such observations could be attributed to the time of supplementation (pre- or post-partum) and/or the adequate basal vitamin E status in ewes.

Lascano, G. J., Heinrichs, A. J. and Tricarico, J. M. 2015. Saccharomyces cerevisiae live culture affects rapidly fermentable carbohydrates fermentation profile in precision-fed dairy heifers. Can. J. Anim. Sci. 95: 117-127. The experimental objective was to determine the dose effect of live yeast culture (YC) on rumen fermentation profiles and microbial total cell concentrations in precision-fed dairy heifers exposed to different rapidly fermented carbohydrates diets. A split-plot design with starch level as the whole plot and YC dose as sub-plot was administered in a four-period (21 d) 4×4 Latin square balanced for carryover effects. Eight Holstein heifers were allocated to two starch treatments (28% starch: HS; 17% starch: LS) and to a sequence of YC doses (0, 10, 30, and 50 g d^-1). Total volatile fatty acid concentration was not different among YC doses or starch level, but molar proportions of propionate, isobutyrate, and isovalerate were higher for HS than for LS. Mean ruminal ammonia concentration was increased in HS-fed heifers. Heifers fed HS had an increased number of viable, non-viable, and total fluid-associated bacteria, particle-associated bacteria, and total bacteria. Increasing YC dose linearly beyond 10 g d^-1 decreased viable and total fluid-associated bacteria. The effects of various YC doses on ruminal fermentation products, pH, and microbial total cell concentrations indicate diet dependency between source of readily available carbohydrates and YC addition in dairy heifers.