Non-invasive metabolomics biomarkers of production efficiency and beef carcass quality traits.

The inter-cattle growth variations stem from the interaction of many metabolic processes making animal selection difficult. We hypothesized that growth could be predicted using metabolomics. Urinary biomarkers of cattle feed efficiency were explored using mass spectrometry-based untargeted and targeted metabolomics. Feed intake and weight-gain was measured in steers (n = 75) on forage-based growing rations (stage-1, 84 days) followed by high-concentrate finishing rations (stage-2, 84 days). Urine from days 0, 21, 42, 63, and 83 in each stage were analyzed from steers with the greater (n = 14) and least (n = 14) average-daily-gain (ADG) and comparable dry-matter-intake (DMI; within 0.32 SD of the mean). Steers were slaughtered after stage-2. Adjusted fat-thickness and carcass-yield-grade increased in greater-ADG-cattle selected in stage-1, but carcass traits did not differ between ADG-selected in stage-2. Overall 85 untargeted metabolites segregated greater- and least-ADG animals, with overlap across diets (both stages) and breed type, despite sampling time effects. Total 18-bile acids (BAs) and 5-steroids were quantified and associated with performance and carcass quality across ADG-classification depending on the stage. Stepwise logistic regression of urinary BA and steroids had > 90% accuracy identifying efficient-ADG-steers. Urine metabolomics provides new insight into the physiological mechanisms and potential biomarkers for feed efficiency.

Predicting aged pork quality using a portable Raman device.

The utility of Raman spectroscopic signatures of fresh pork loin (1 d & 15 d postmortem) in predicting fresh pork tenderness and slice shear force (SSF) was determined. Partial least square models showed that sensory tenderness and SSF are weakly correlated (R2 = 0.2). Raman spectral data were collected in 6 s using a portable Raman spectrometer (RS). A PLS regression model was developed to predict quantitatively the tenderness scores and SSF values from Raman spectral data, with very limited success. It was discovered that the prediction accuracies for day 15 post mortem samples are significantly greater than that for day 1 postmortem samples. Classification models were developed to predict tenderness at two ends of sensory quality as "poor" vs. "good". The accuracies of classification into different quality categories (1st to 4th percentile) are also greater for the day 15 postmortem samples for sensory tenderness (93.5% vs 76.3%) and SSF (92.8% vs 76.1%). RS has the potential to become a rapid on-line screening tool for the pork producers to quickly select meats with superior quality and/or cull poor quality to meet market demand/expectations.

Effect of packaging type during postmortem aging and degree of doneness on pork chop sensory traits of loins selected to vary in color and marbling.

The objective was to determine the interactions between packaging type and degree of doneness on sensory traits of pork loins classified based on the newly proposed USDA quality grades. A total of 144 loins were selected from 2 groups of pigs (lean growth or meat quality production focus) to represent as much variation in visual color and marbling as possible. Selection was achieved with a VQG grading camera. The ventral surface of the loins was evaluated for loin quality traits at 1 d postmortem. At 2 d postmortem loins were sliced into 28-mm-thick chops. Chop within each loin was randomly assigned to either individual vacuum packages or to individual Styrofoam trays and overwrapped in polyvinyl chloride (PVC) oxygen permeable film. Overwrapped PVC packages were then placed in bulk packages and flushed with a gas mixture that contained approximately 0.4% carbon monoxide, 30% carbon dioxide, and 80% nitrogen. Vacuum-packaged chops were aged until 14 d postmortem. Chops packaged in PVC overwrap were aged until 9 d postmortem in the bulk packages, then placed on simulated retail display until 14 d postmortem. Chops from each packaging type were cooked to an internal temperature of either 63 °C or 71 °C for the evaluation of slice shear force (SSF) or for evaluation of tenderness, juiciness, and flavor by a trained panel. Data were analyzed as split-split plot design with production focus of the pigs, proposed USDA quality grade, packaging type, and degree of doneness as fixed effects. While there were main effect differences between production focuses, there were no interactions with production focus. There were also no 3-way (P ≥ 0.19) interactions and only one 2-way interaction among quality grade, packaging type, or degree of doneness. There were no differences in sensory tenderness (P = 0.30), juiciness (P = 0.49), flavor (P = 0.89), SSF (P = 0.13), or cook loss (P = 0.06) among USDA quality grades. There were no differences in sensory tenderness (P = 0.06), juiciness (P = 0.32), flavor (P = 0.74), SSF (P = 0.99), or cook loss (P = 0.12) between chops aged in vacuum packages or PVC packages. Chops cooked to 63 °C were 4.6% more tender (P < 0.0001), 10.1% juicier (P < 0.0001), and 2.9% less flavorful (P = 0.01) than chops cooked to 71 °C. These data suggest that cooking chops to 63 °C rather than 71 °C was a more effective way to improve tenderness and juiciness than selecting chops of a certain quality grade or altering packaging postmortem.

Characterization of variability in pork carcass composition and primal quality,.

The objective was to characterize the factors and production practices that contribute to variation in pork composition and quality. It is possible the variation in pork quality traits, such as color, marbling, and tenderness, contributes to reduced customer confidence in the predictability of finished product quality and, therefore, pork products becoming less competitive for consumer dollars. Pigs raised in 8 different barns representing 2 seasons (hot and cold) and 2 production focuses (lean and quality) were used in this study. Pigs were marketed in 3 groups from each barn and marketing procedures followed commercial marketing procedures. Data were collected on a total of 7,684 pigs. The mivque0 option of the VARCOMP procedure in SAS was used to evaluate the proportion of variation each independent variable (season, production focus, marketing group, sex, and random variation) contributed to total variance. Random variation including inherent biological differences, as well as factors not controlled in this study, contributed the greatest proportion to total variation for each carcass composition and quality trait. Pig and other factors contributed to 93.5% of the variation in HCW, and marketing group, sex, season, and production focus accounted for 4.1, 1.4, 0.8, and 0.3%, respectively. Variation in percent carcass lean was attributed to production focus (36.4%), sex (15.8%), and season (10.2%). Pig and other factors contributed the greatest percentage of total variation (39.4%). Loin weight variation was attributed to production focus (21.4%), sex (5.4%), season (2.7%), marketing group (1.8%), and pig (68.7%). Belly weight variation was attributed to pig (88.9%), sex (4.1%), marketing group (3.8%), production focus (3.0%), and season (0.1%). Variation in ham weight was attributed to pig and other factors (93.9%), marketing group (2.8%), production focus (2.2%), and season (1.1%). Ultimate pH variation was attributed to pig (88.5%), season (6.2%), production focus (2.4%), marketing group (2.2%), and sex (0.7%). Aside from pig (71.9%), production focus (14.0%) was the next largest contributor to variation in iodine value followed by sex (13.2%) and marketing group (0.9%). Variation in carcass quality and composition could be accounted for, but the greatest percentage of variation was due to factors not accounted for in normal marketing practices.

Effect of hot carcass weight on loin, ham, and belly quality from pigs sourced from a commercial processing facility,.

The objective was to determine the predictive abilities of HCW for loin, ham, and belly quality of 7,684 pigs with carcass weights ranging from 53.2 to 129.6 kg. Carcass composition, subjective loin quality, and ham face color were targeted on all carcasses, whereas in-plant instrumental loin color and belly quality were assessed on 52.0 and 47.5% of carcasses, respectively. Loin chop slice shear force (SSF), cured ham quality, and adipose iodine value (IV) were evaluated on at least 10% of the population. The slope of regression lines and coefficients of determination between HCW and quality traits were computed using PROC REG of SAS and considered significant at ≤ 0.05. As HCW increased, boneless loins became darker and redder, evidenced by lower L* (ß = -0.0243, < 0.001) and greater a* values (ß = 0.0106, < 0.001); however, HCW accounted for only ≤0.80% of the variability in loin L* and a* values. Similarly, subjective loin color score (ß = 0.0024, < 0.001) increased with increasing carcass weight, but subjective marbling score was not affected by HCW (ß = -0.0022, = 0.06). After 20 d of aging, HCW explained only 0.98% of the variability in loin L* values (ß = -0.0287, < 0.01). Heavier carcasses had lower SSF values (ß = -0.1269, < 0.001) of LM chops, although HCW explained only 4.46% of the variability in SSF. Although heavier carcasses produced loins that exhibited lower ultimate pH values (ß = -0.0018, < 0.001), HCW explained only 1.23% of the variability in ultimate loin pH. Interestingly, cook loss decreased (ß = -0.0521, < 0.001) as HCW increased, with HCW accounting for 5.60% of the variability in cook loss. Heavier carcasses resulted in darker, redder ham face color ( < 0.001), but HCW accounted for only ≤2.87% of the variability in ham face L* values and 0.47% of the variability in a* values. Heavier carcasses produced thicker and firmer bellies, with HCW accounting for 37.81% of the variability in belly thickness (ß = 0.0272, < 0.001), 20.35% of the variability in subjective flop score (ß = 0.0406, < 0.001), and 10.35% of the variability in IV (ß = -0.1263, < 0.001). Overall, the proportion of variability in loin and ham quality explained by HCW was poor (≤5.60%), suggesting that HCW is a poor predictor of the primal quality of pigs within this weight range. Nonetheless, HCW was a moderate predictor of belly quality traits. The findings of this study suggest that increasing HCW did not compromise loin, ham, or belly quality attributes.

The effects of backgrounding system on growing and finishing performance and carcass characteristics of beef steers.

The objective of this 2-yr study was to evaluate growing and finishing performance as well as carcass characteristics of spring-born steers backgrounded on 3 different systems, using feedstuffs readily available in the Midwest: 1) grazing corn residue and being supplemented with dried distillers plus solubles at 2.68 kg DM/steer 6 d/wk (RESIDUE), 2) grazing a late summer-planted oat-brassica forage mix (CCROP), or 3) being fed a corn silage-based diet in a drylot (DRYLOT). Steers ( = 715) were stratified by BW (278 kg ± 23 in yr 1 and 291 kg ± 91 in yr 2) and assigned to treatment and replicate (4 replications per treatment per yr). Steers assigned to DRYLOT were fed a corn silage-based diet for 54 d in yr 1 and 52 d in yr 2 before being transitioned to the finishing diet. Steers assigned to RESIDUE and those assigned to CCROP grazed 65 d in yr 1 and 66 d in yr 2 and then were fed a corn silage-based diet for 21 d in yr 1 and 33 d in yr 2 before being transitioned to the finishing diet. During backgrounding, the ADG (SEM 0.022) of steers assigned to DRYLOT (1.48 kg/d) was greater ( < 0.01) than that of steers assigned to both CCROP (1.05 kg/d) and RESIDUE (0.87 kg/d) and ADG of steers assigned to CCROP was greater ( < 0.01) than that of steers assigned to RESIDUE. At the start of the finishing period, BW of steers assigned to CCROP (381 kg) was greater ( < 0.01, SEM 2.5) than that of steers assigned to DRYLOT (361 kg) and RESIDUE (366 kg). The finishing period lasted 160 d for all treatments. Both 12th-rib fat ( = 0.89) and calculated yield grade ( = 0.39) did not differ among treatments. Finishing G:F of steers assigned to DRYLOT (0.162 kg/kg) was greater ( < 0.01, SEM 0.0015) than that of steers assigned to RESIDUE (0.153 kg/kg) and CCROP (0.153 kg/kg), which did not differ ( = 0.79). In yr 1, HCW of steers assigned to CCROP (402 kg) was greater ( < 0.01, SEM 2.1) than that of steers assigned to both RESIDUE (389 kg) and DRYLOT (391 kg), which did not differ ( = 0.40). This difference in HCW is most likely a result of differences in BW at the start of the finishing phase in yr 1. However in yr 2, HCW of steers assigned to CCROP (400 kg) and RESIDUE (397 kg) did not differ ( = 0.26, SEM 2.1) but were greater ( < 0.01) than that of steers assigned to DRYLOT (367 kg), despite the fact that steers assigned to RESIDUE entered the finishing phase at a lighter BW than steers assigned to CCROP. Marbling was greater ( = 0.01, SEM 3.9) for steers assigned to DRYLOT (429) than for steers assigned to RESIDUE (414), although steers assigned to CCROP (424) were not different ( ≥ 0.10) from steers assigned to DRYLOT or RESIDUE. When cost and price scenarios from the last 5 yr were conducted, no treatment appeared to be consistently superior in terms of cost of gain or net return. Therefore, all 3 systems appear to be viable options for producers.

Comparison of variability in pork carcass composition and quality between barrows and gilts.

Pigs ( = 8,042) raised in 8 different barns representing 2 seasons (cold and hot) and 2 production focuses (lean growth and meat quality) were used to characterize variability of carcass composition and quality traits between barrows and gilts. Data were collected on 7,684 pigs at the abattoir. Carcass characteristics, subjective loin quality, and fresh ham face color (muscles) were measured on a targeted 100% of carcasses. Fresh belly characteristics, boneless loin weight, instrumental loin color, and ultimate loin pH measurements were collected from 50% of the carcasses each slaughter day. Adipose tissue iodine value (IV), 30-min loin pH, LM slice shear force, and fresh ham muscle characteristic measurements were recorded on 10% of carcasses each slaughter day. Data were analyzed using the MIXED procedure of SAS as a 1-way ANOVA in a randomized complete block design with 2 levels (barrows and gilts). Barn (block), marketing group, production focus, and season were random variables. A 2-variance model was fit using the REPEATED statement of the MIXED procedure, grouped by sex for analysis of least squares means. Homogeneity of variance was tested on raw data using Levene's test of the GLM procedure. Hot carcass weight of pigs (94.6 kg) in this study was similar to U.S. industry average HCW (93.1 kg). Therefore, these data are representative of typical U.S. pork carcasses. There was no difference ( ≥ 0.09) in variability of HCW or loin depth between barrow and gilt carcasses. Back fat depth and estimated carcass lean were more variable ( ≤ 0.0001) and IV was less variable ( = 0.05) in carcasses from barrows than in carcasses from gilts. Fresh belly weight and thickness were more variable ( ≤ 0.01) for bellies of barrows than bellies of gilts, but there was no difference in variability for belly length, width, or flop distance ( ≥ 0.06). Fresh loin subjective color was less variable ( < 0.01) and subjective marbling was more variable ( < 0.0001) in loins from barrows than in those from gilts, but there were no differences ( ≥ 0.08) in variability for any other loin traits or fresh ham traits. Overall, traits associated with carcass fatness, including back fat depth, belly thickness, and marbling, but not IV, were more variable in carcasses from barrows than in carcasses from gilts, whereas minimal differences in variability existed between carcasses of barrows and carcasses of gilts for traits associated with carcass muscling and lean quality.

The effects of zilpaterol hydrochloride and shade on blood metabolites of finishing beef steers.

The effects of feeding zilpaterol hydrochloride (ZH) and shade were evaluated on blood metabolites in finishing beef steers ( = 480). Cattle were fed 0 or 8.33 mg/kg of diet DM ZH for 21 d with a 3- or 4-d withdrawal before harvest and were housed in open or shaded pens. Blood samples were collected the day before ZH was fed and on the day the cattle were shipped to the commercial abattoir. Lactate concentration was not different between cattle fed ZH in open or shaded pens ( = 0.12). Nonetheless, a tendency for a diet × time interaction was detected for lactate concentration ( = 0.09), in which it was greater in cattle fed the control diet in open pens before being fed ZH. Cortisol concentration was less before and after ZH was fed ( = 0.01). Glucose was greater for cattle fed the control diet than cattle fed ZH for 21 d ( = 0.03). Cattle fed in open vs. shaded pens did not differ in glucose concentration ( = 0.12), whereas glucose concentrations were greater before ZH was fed than after ( = 0.02). In contrast, plasma urea nitrogen (PUN) concentration was not different in response to diet ( = 0.24), housing type ( = 0.65), or before vs. after being fed ZH ( = 0.60). Lactate concentrations were not different across diet or shade treatments before ZH was fed, whereas after ZH, lactate concentrations were greater in control cattle than cattle fed ZH. Additionally, cortisol was less after feeding ZH. Glucose was greater before than after feeding ZH.

Effects of dietary protein concentration and ractopamine hydrochloride on performance and carcass characteristics of finishing beef steers.

Ractopamine hydrochloride (RAC) is used in the feedlot industry to increase daily gain, improve feed efficiency, and increase HCW. However, little work has been done to determine whether additional protein is needed in the diet to maximize the benefit of RAC in beef cattle. Objectives of our experiment were to determine if feeding additional CP in conjunction with RAC would improve animal performance and carcass characteristics. Therefore, an experiment was conducted using finishing diets containing 13.5 or 17.5% CP with 0 or 300 mg of RAC for 30 to 33 d at the end of the finishing period. Beef steers ( = 438; 387.8 ± 1.9 kg initial BW) were randomly assigned to 1 of 4 treatments in a 2 × 2 factorial arrangement (16 pens total, 4 pens/treatment). No interactions between feeding RAC and CP level were detected ( > 0.19) for animal performance or carcass traits. Final BW did not differ among treatment ( = 0.37); however, final BW had a tendency to be 2% greater ( = 0.07) when the 13.5% CP diet was fed. Dry matter intake was not different between steers fed 0 or 300 mg/d of RAC ( = 0.20), yet DMI was 12% greater for cattle fed the 13.5% CP compared with steers fed the 17.5% CP diet ( < 0.01). Daily gain did not differ for cattle fed different levels of RAC or CP ( > 0.16). The G:F was 3.6% greater for cattle fed 300 vs. 0 mg/d of RAC ( = 0.04). The G:F was 8.7% greater for cattle fed the 17.5% diet vs. the 13.5% CP diet ( < 0.01), which can be attributed to the decreased DMI for cattle fed the 17.5% CP diet. Hot carcass weight was not different for steers fed 0 or 300 mg/d of RAC ( = 0.36) or for steers fed the 13.5% diet vs. 17.5% CP diet ( = 0.93). Dressing percentage was 1.5% greater for cattle fed 300 vs. 0 mg/d of RAC ( = 0.05) but was not different between cattle fed the different CP levels in the diet ( = 0.16). Longissimus area, adjusted 12th-rib fat, and marbling score did not differ across RAC or CP treatments ( > 0.26). Additionally, no differences in USDA yield grade or percentage of cattle grading USDA Choice were detected for RAC or CP treatments ( > 0.26), which also supports the idea that quality grade of cattle fed RAC at the same level of fatness is not impacted. Our data indicate excess protein did not enhance the response to RAC, and furthermore, the improved performance from RAC reported by others was not observed other than a small increase in G:F.

The effects of degree of dark cutting on tenderness and sensory attributes of beef.

The objective of this study was to determine the effect of degree of dark cutting (DC) on the tenderness, juiciness, and flavor attributes of beef. During carcass grading at a large U.S. commercial beef harvesting facility, DC carcasses ( = 160) and matching normal control (NC) carcasses ( = 160) were selected. Longissimus lumborum (LL) pH was determined and DC carcasses were classified as severe (severe dark cutter [SEDC]; mean pH = 6.9; = 40), moderate (moderate dark cutter [MODC]; mean pH = 6.6; n = 40), mild (mild dark cutter [MIDC]; mean pH = 6.4; = 40), or shady (shady dark cutter [SHDC]; mean pH = 6.1; = 40). Strip loins were obtained from the left carcass sides, vacuum-packaged, and aged at 1°C. Slice shear force (SSF) was measured (14 d postmortem) fresh (never frozen), and trained descriptive sensory analysis of tenderness, juiciness, and flavor was measured (13 d postmortem) on frozen/thawed LL steaks. Cooked SSF pieces were frozen and used for western blotting of desmin to determine extent of postmortem proteolysis. Thaw and cook loss decreased as intensity of DC increased, with SEDC having the lowest loss (1.83 and 10.1%, respectively) compared with NC (3.37 and 14.9%, respectively). Slice shear force was higher (P < 0.05) for SHDC (25.6 kg) and MIDC (22.9 kg) compared with SEDC (16.8 kg), MODC (19.4 kg), and NC (17.8 kg). Sarcomere length was shorter ( < 0.05) between DC class (1.66, 1.67, 1.71, and 1.73 µm for SEDC, MODC, MIDC, and SHDC, respectively) and NC (1.86 µm). Postmortem proteolysis of desmin was greater ( < 0.05) for NC compared with all DC classes (59.83% vs. 49.20, 40.31, 42.07, and 43.30% for SEDC, MODC, MIDC, and SHDC, respectively). Trained sensory panel ratings for tenderness differed ( < 0.05) among DC class with SEDC (6.51) the most tender followed by MODC (6.04) and then MIDC (5.19), whereas SHDC (4.66) and NC (4.93) were the toughest. Juiciness ratings differed ( < 0.05) among each DC class (5.9, 5.7, 5.4, and 5.2 for SEDC, MODC, MIDC, and SHDC, respectively), with no difference between MIDC or SHDC compared with NC (5.23). Fat-like, rancid, heated oil, chemical, and musty/earthy/hummus flavors increased ( < 0.05) whereas metallic, sour, and salty flavors decreased as severity of DC increased. This study showed DC and NC differed in LL tenderness, juiciness, and flavor. The direction and/or magnitude of those differences were greatly dependent on severity of DC. Steaks with intermediate pH (SHDC and MIDC) are most likely to be tough and are regularly included in U.S. Select and U.S. Choice product lines.

Meta-analysis of genome-wide association from genomic prediction models.

Genome-wide association (GWA) studies based on GBLUP models are a common practice in animal breeding. However, effect sizes of GWA tests are small, requiring larger sample sizes to enhance power of detection of rare variants. Because of difficulties in increasing sample size in animal populations, one alternative is to implement a meta-analysis (MA), combining information and results from independent GWA studies. Although this methodology has been used widely in human genetics, implementation in animal breeding has been limited. Thus, we present methods to implement a MA of GWA, describing the proper approach to compute weights derived from multiple genomic evaluations based on animal-centric GBLUP models. Application to real datasets shows that MA increases power of detection of associations in comparison with population-level GWA, allowing for population structure and heterogeneity of variance components across populations to be accounted for. Another advantage of MA is that it does not require access to genotype data that is required for a joint analysis. Scripts related to the implementation of this approach, which consider the strength of association as well as the sign, are distributed and thus account for heterogeneity in association phase between QTL and SNPs. Thus, MA of GWA is an attractive alternative to summarizing results from multiple genomic studies, avoiding restrictions with genotype data sharing, definition of fixed effects and different scales of measurement of evaluated traits.

Endocannabinoids concentrations in plasma associated with feed efficiency and carcass composition of beef steers.

Endocannabinoids, including anandamide (AEA) and 2-arachidonoylglycerol (2-AG), are a class of endogenous lipid mediators that activate cannabinoids receptors and may be involved in the control of feed intake and energy metabolism. The objective of this study was to quantify AEA and 2-AG in plasma and identify possible associations with production traits and carcass composition in finishing beef steers. Individual DMI and BW gain were measured on 140 Angus-sired steers for 105 d on a finishing ration. Blood samples were collected on d 84 of the experiment, which was 40 d before slaughter. Variables were analyzed using Pearson CORR procedure of SAS. Mean endocannabinoid concentrations in plasma were 4.48 ± 1.82 ng/mL and 0.44 ± 0.24 ng/mL for AEA and 2-AG, respectively. The AEA concentration was positively correlated with G:F ratio ( = 0.20; = 0.02), indicating that more efficient animals had greater AEA plasma concentrations. In addition, AEA concentration tended to be negatively correlated with the 12th rib fat thickness ( = -0.17; = 0.07); but no correlation was found with USDA-calculated yield grade ( = -0.14; = 0.11), or marbling score ( = 0.05; = 0.54). The concentration of 2-AG was positively correlated with AEA ( = 0.21; = 0.01); however, 2-AG concentration was not correlated with parameters of feed efficiency or carcass composition. To our knowledge, this study is the first to report plasma concentration of endocannabinoids in steers. These results provide evidence that plasma concentration of a key endocannabinoid, AEA, was favorably correlated with feed efficiency and fat thickness in finishing steers.

Effects of marketing group on the quality of fresh and cured hams sourced from a commercial processing facility.

The objective was: 1) to characterize the effect of marketing group on fresh and cured ham quality, and 2) to determine which fresh ham traits correlated to cured ham quality traits. Pigs raised in 8 barns representing 2 seasons (hot and cold) and 2 production focuses (lean and quality) were used. Three groups were marketed from each barn. A total of 7,684 carcasses were used for data collection at the abattoir. Every tenth carcass was noted as a select carcass for in-depth ham quality analyses. Leg primal weight and instrumental color were measured on 100% of the population. On the select 10% of the population, hams were fabricated into sub-primal pieces, and 3-piece hams were manufactured to evaluate cured ham quality and processing yield. Data were analyzed as a split-plot design in the MIXED procedure of SAS with production focus as the whole-plot factor, and marketing group as the split-plot factor. Pearson correlation coefficients between fresh and cured ham traits were computed. There were no differences ( ≥ 0.15) in instrumental color or ultimate pH ( ≥ 0.14) among fresh ham muscles from any marketing group. The only exception was the semimembranosus of marketing group 2 was lighter than marketing group 1 ( = 0.03) and the dark portion of the semitendinosus muscle from group 1 was lighter than from group 3 ( = 0.01). There were no differences ( ≥ 0.33) in ultimate pH of fresh ham muscles between production focuses, but several muscles from quality focus pigs were lighter in color than ham muscles from lean focus pigs. The lack of differences in fresh ham quality lead to few differences in cured ham quality. Cured hams from the quality focus pigs had greater lipid content ( < 0.01) than hams from lean focus pigs. Cured lightness values of hams from marketing group 1 and 2 were 1.52 units lighter than hams from marketing group 3 ( 0.01). Overall, marketing group did not impact ham quality. Fresh ham quality was not strongly related to cured ham quality. Some correlations were present between fresh and cured ham traits, but those relationships were likely not strong enough to be used as a sorting tool for fresh hams to generate high quality cured hams.

Effects of marketing group and production focus on quality and variability of adipose tissue and bellies sourced from a commercial processing facility.

Objectives were to determine the effects of marketing group on quality and variability of belly and adipose tissue quality traits of pigs sourced from differing production focuses (lean vs. quality). Pigs ( = 8,042) raised in 8 barns representing 2 seasons (cold and hot) were used. Three groups were marketed from each barn with 2 barns per production focus marketed per season. Data were collected on 7,684 carcasses at a commercial abattoir. Fresh belly characteristics, American Oil Chemists' Society iodine value (AOCS-IV), and near-infrared iodine value were measured on a targeted 50, 10, and 100% of carcasses, respectively. Data were analyzed as a split-plot design in the MIXED procedure of SAS 9.4 with production focus as the whole-plot factor and marketing group as the split-plot factor. Barn (block), season, and sex were random variables. A multivariance model was fit using the REPEATED statement with the marketing group × production focus interaction as the grouping variable. Variances for production focus and marketing groups were calculated using the MEANS procedure. Homogeneity of variance was tested on raw data using the Levene's test of the GLM procedure. Among quality focus carcasses, marketing group 3 bellies weighed less ( ≤ 0.03) than those from either marketing group 1 or 2, but there was no difference ( ≥ 0.99) among marketing groups of the lean focus carcasses. There was no effect ( ≥ 0.11) of production focus on fresh belly measures, SFA, or iodine value (IV), but lean focus carcasses had decreased ( = 0.04) total MUFA and increased ( < 0.01) total PUFA compared with quality focus carcasses. Marketing group did not affect ( ≥ 0.10) fresh belly dimensions, total SFA, total MUFA, total PUFA, or IV. Belly weight, flop score, width, and all depth measurements were less variable ( ≤ 0.01); whereas, belly length, total SFA, and total MUFA were more variable ( < 0.0001) in lean focus carcasses than in quality focus carcasses. There was no difference ( ≥ 0.17) in total PUFA or AOCS-IV variability between production focuses. Variance of flop score, total MUFA, and total PUFA were not equal ( ≤ 0.01) among marketing groups. Belly weight, length, width, and depth measurements; SFA; or IV variance did not differ ( ≥ 0.06) among marketing groups. Although a multiple-marketing strategy was effective at minimizing differences in belly characteristics, differences in the variability of these traits exist among marketing groups and are likely dependent on the production system used.

Pork loin quality is not indicative of fresh belly or fresh and cured ham quality.

The objective was to characterize the relationship between fresh loin quality with fresh belly or fresh and cured ham quality. Pigs raised in 8 barns representing 2 seasons [cold ( = 4,290) and hot ( = 3,394)] and 2 production focuses [lean ( = 3,627) and quality ( = 4,057)] were used. Carcass characteristics and other meat quality data were collected on 7,684 carcasses. All of the carcasses were evaluated for HCW, LM depth, tenth rib fat depth, leg (ham primal) weight, instrumental color on the gluteus medius and gluteus profundus of the ham face, and subjective loin quality. Instrumental loin color and ultimate pH (≥ 22 h postmortem) were collected on the ventral side of loins along with dimensions and firmness scores of fresh bellies from 50% of the carcasses. Ten percent of the boneless loins and fresh hams were evaluated for slice shear force (SSF) or cured ham characteristics. Correlation coefficients between traits were computed using the CORR procedure of SAS and considered significantly different from 0 at ≤ 0.05. Temperature decline, beginning at 31 min postmortem and concluding at 22 h postmortem, for the longissimus dorsi and semimembranosus muscles were evaluated on 10% of the carcasses. Ultimate loin pH was correlated with dimensional belly characteristics ( ≥ |0.07|; < 0.0001) fresh ham instrumental color ( ≥ |0.03|; ≤ 0.05), and semimembranosus ultimate pH ( = 0.33; < 0.0001). Further, ultimate loin pH was correlated ( ≤ 0.01) with pump retention ( = 0.087) and cooked yield ( = 0.156) of cured hams. Instrumental L*on the ventral surface of the loin was related to L* on both muscles of the ham face ( ≤ 0.0001). Even though significant relationships between the loin, belly, and ham were detected, the variability in belly and ham quality explained by variability in loin quality was poor (≤ 22.09%). Compositional differences between the loin and belly may have contributed to those poor relationships. Additionally, differences in temperature declines during chilling between the loin and ham likely contributed to the weak nature of relationships. Equilibration of longissimus dorsi temperature to ambient cooler temperature occurred at 14 h postmortem ( = 0.0005), yet the semimembranosus had not equilibrated with ambient (equilibration bay) temperature ( < 0.0001) at 22 h postmortem. Using loin quality to draw conclusions about fresh belly and fresh and cured ham quality may be misleading.

Implementing meta-analysis from genome-wide association studies for pork quality traits.

Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is the limited power due to small sample sizes in animal populations. One alternative is to implement a meta-analysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implemented by combining -scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [] and calpastatin []), as well as for ultimate pH, purge loss, and cook loss (protein kinase, AMP-activated, γ 3 noncatalytic subunit []). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial []) and for the objective measure of muscle redness, CIE a* (glycogen synthase 1, muscle [] and ferritin, light polypeptide []). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.

Effects of shade and feeding zilpaterol hydrochloride to finishing steers on performance, carcass quality, heat stress, mobility, and body temperature.

Steers ( = 480; 22% with black hides and 78% with red hides) were used to study the effects of shade and feeding zilpaterol hydrochloride (ZH) on performance, carcass quality, heat stress, mobility, and body temperature (BT). A randomized block design with a 2 × 2 factorial treatment arrangement was used with 4 replicates per treatment. Factors included housing type (open or shaded pens) and the feeding of ZH (0 or 8.33 mg/kg DM) the last 21 d on feed with a 3-d withdrawal. Cattle were blocked by BW into a heavy or light block and randomly assigned to pen within each block. Rumen boluses to record BT were inserted before ZH feeding. Respiration rate and panting scores were recorded daily during the ZH feeding period. Mobility scores were collected at various time points from before ZH feeding through harvest. Interactions between ZH and housing type were not significant ( > 0.26) for animal performance, carcass characteristics, and respiration or panting score. No differences ( > 0.44) were observed for DMI, ADG, or G:F on a live basis due to ZH; however, cattle fed in open pens tended ( = 0.08) to have a greater ADG than cattle in shaded pens. Cattle fed ZH had 14 kg heavier carcasses with larger LM area ( < 0.01) than control cattle. Respiration rates for cattle fed ZH were greater ( = 0.05) with no differences ( = 0.88) due to housing. Time affected ( < 0.01) mobility scores, with observations on the morning of harvest at the abattoir being the worst for all groups of cattle. An interaction ( < 0.01) was observed between ZH and housing type for BT. Cattle fed ZH, in both shaded and open pens, had lower ( < 0.05) average, maximum, and area under the curve BT than control cattle fed in the same housing type. However, the observed reduction in BT due to ZH was greater for cattle fed ZH in open pens than for cattle fed ZH in shaded pens. From these results, we conclude that ZH improved HCW with little impact on heat stress or mobility, suggesting that animal welfare was not affected by feeding ZH for 21 d at the end of the feeding period.

Relationship of leptin concentrations with feed intake, growth, and efficiency in finishing beef steers.

The objective of this experiment was to determine the association of serum leptin concentrations with production measures including DMI, ADG, and G:F as well as carcass characteristics in genetically diverse finishing beef steers. Three cohorts of steers ( = 473 total) were individually fed a finishing ration for 92, 64, and 84 d for cohort 1, 2, and 3, respectively. Serum was collected on d 42, 22, and 19 of the experiment for cohort 1, 2, and 3, respectively. Leptin concentrations were positively correlated to DMI ( = 0.21, < 0.01) but negatively correlated to grams DMI per kilogram initial BW ( = -0.21, < 0.01). Leptin concentrations were also negatively correlated to ADG and G:F ( < 0.01). Leptin concentrations were positively correlated to 12th-rib fat thickness, yield grade, and marbling score ( < 0.01) and negatively correlated to LM area ( < 0.01). Using a mixed model analysis (SAS 9.3; SAS Inst. Inc., Cary, NC) to account for breed effects, leptin concentrations were positively associated with DMI ( = 0.01) and accounted for 1.10% of the variance. However, if initial BW and yield grade were included as covariates to account for body size and fatness, leptin was negatively associated with DMI ( = 0.02) and accounted for 0.54% of the variance. Regardless of covariates included in the model, leptin was negatively associated with ADG ( < 0.01) and G:F ( < 0.01) and accounted for 2.62 and 7.87% of the variance for ADG and G:F, respectively. Leptin concentrations were also positively associated with 12th-rib fat thickness, yield grade, and marbling score ( < 0.01) and accounted for 14.74, 12.74, and 6.99% of the variance for 12th-rib fat, yield grade, and marbling score, respectively. Leptin concentrations could be a useful physiological marker for growth and feed efficiency of finishing beef cattle. Genetic influences on the biology of leptin also need to be considered when using leptin as physiological marker for production measures.

Genomewide association study of lung lesions in cattle using sample pooling.

Bovine respiratory disease complex (BRDC) is the most expensive disease in beef cattle in the United States costing the industry at least US$1 billion annually. Bovine respiratory disease complex causes damage to lung tissue resulting in persistent lung lesions observable at slaughter. Severe lung lesions at harvest have been associated with decreased preharvest ADG and increased clinical BRDC in the feedlot. Our objective was to identify SNP that are associated with severe lung lesions observed at harvest in feedlot cattle. We conducted a genomewide association study (GWAS) using a case-control design for severe lung lesions in fed cattle at slaughter using the Illumina Bovine HD array (approximately 770,000 SNP) and sample pooling. Lung samples were collected from 11,520 young cattle, a portion of which had not been treated with antibiotics (participating in a "natural" marketing program), at a large, commercial beef processing plant in central Nebraska. Lung samples with lesions (cases) and healthy lungs (controls) were collected when both phenotypes were in close proximity on the viscera (offal) table. We constructed 60 case and 60 control pools with 96 animals per pool. Pools were constructed by sampling sequence to ensure that case and control pool pairs were matched by proximity on the processing line. The Bovine HD array (770,000 SNP) was run on all pools. Fourteen SNP on BTA 2, 3, 4, 9, 11, 14, 15, 22, 24, and 25 were significant at the genomewide experiment-wise error rate of 5% ( ≤ 1.49 × 10). Eighty-five SNP on 28 chromosomes achieved a false discovery rate of 5% ( ≤ 5.38 × 10). Significant SNP were near (±100 kb) genes involved in tissue repair and regeneration, tumor suppression, cell proliferation, apoptosis, control of organ size, and immunity. Based on 85 significantly associated SNP in or near a collection of genes with diverse function on 28 chromosomes, we conclude that the genomic footprint of lung lesions is complex. A complex genomic footprint (genes and regulatory elements that affect the trait) is consistent with what is known about the cause of the disease: complex interactions among multiple viral and bacterial pathogens along with several environmental factors including dust, commingling, transportation, and stress. Characterization of sequence variation near significant SNP will enable accurate and cost effective genome-enhanced genetic evaluations for BRDC resistance in AI bulls and seed stock populations.

Sire breed effect on beef longissimus mineral concentrations and their relationships with carcass and palatability traits.

The objective of this study was to evaluate sire breed effect on mineral concentration in beef longissimus thoracis (LT) and investigate the correlations between beef mineral concentrations and carcass and palatability traits. Steer progeny (N=246) from the Germplasm Evaluation project-Cycle VIII were used in this study. In addition to carcass traits, LT was evaluated for mineral concentrations, Warner-Bratzler shear force, and palatability traits. A mixed linear model estimated breed effects on mineral concentrations. No significant sire breed (P≥0.43) or dam breed (P≥0.20) effects were identified for mineral concentrations. Pearson correlation coefficients were calculated among mineral concentrations, carcass, and sensory traits. Zinc concentration was positively correlated (P≤0.05) with total iron (r=0.14), heme iron (r=0.13), and magnesium (r=0.19). Significant (P<0.05) correlations were identified between non-heme or heme iron and most traits in this study. Magnesium concentration was correlated with all carcass and palatability traits.