National Beef Quality Audit-2011: Harvest-floor assessments of targeted characteristics that affect quality and value of cattle, carcasses, and byproducts

The National Beef Quality Audit-2011 (NBQA-2011) was conducted to assess targeted characteristics on the harvest floor that affect the quality and value of cattle, carcasses, and byproducts. Survey teams evaluated approximately 18,000 cattle/carcasses between May and November 2011 in 8 beef processing facilities. Cattle identification methods were lot visual tags (85.7%), individual visual tags (50.6%), electronic tags (20.1%), metal-clip tags (15.7%), other (5.3%), none (2.5%), and wattles (0.5%). Hide colors or breed types were black (61.1%), red (12.8%), yellow (8.7%), Holstein (5.5%), brown (5.0%), gray (5.0%), white (1.4%), and brindle (1.0%). Brand frequencies were none (55.2%), 1 (40.4%), 2 (4.4%), and 3 or more (0.04%) brands, and brands were located on the butt (35.2%), side (9.0%), and shoulder (2.5%). Hide locations of mud or manure were no mud/manure (49.2%), legs (36.8%), belly (23.7%), side (14.9%), top-line (11.0%), and tail region (13.7%). There were 76.2% of cattle without horns, and the majority of those with horns (71.6%) were between 0 cm and 12.7 cm in length. Permanent incisor numbers were zero (87.3%), 1 (1.4%), 2 (8.0%), 3 (0.9%), 4 (1.9%), 5 (0.3%), 6 (0.2%), 7 (0.1%), and 8 (0.02%). Most carcasses (77.0%) were not bruised, 18.7% had 1 bruise, 3.4% had 2 bruises, 0.6% had 3 bruises, and 0.3% had more than 3 bruises. Bruise locations were loin (50.1%), rib (21.3%), chuck (13.8%), round (7.3%), and brisket/flank/plate (7.5%). Condemnation item and incidence were whole carcass (none recorded), liver (20.9%), lungs (17.3%), tongue (10.0%), viscera (9.3%), and head (7.2%). Compared with the NBQA-2005, the NBQA-2011 had an increased percentage of black-hided cattle (56.3 vs. 61.1%), more cattle with brands (38.7 vs. 44.8%), and more cattle with some form of identification (93.3 vs. 97.5%). In addition, there was a lesser percentage of carcasses with bruising in 2011 (23.0%) than in 2005 (35.2%), as well as a smaller percentage of carcasses with more than 1 bruise (2005 = 9.4% vs. 2011 = 4.2%). Compared with the 2005 audit, a similar percentage of the cattle were deemed 30 mo of age or older using dentition (2005 = 2.7% vs. 2011 = 3.3%). The information from NBQA-2011 helps the beef industry measure progress against previous NBQA assessments and provides a benchmark for future educational and research activities.

National Beef Quality Audit-2011: Survey of instrument grading assessments of beef carcass characteristics

The instrument grading assessments for the 2011 National Beef Quality Audit evaluated seasonal trends of beef carcass quality and yield attributes over the course of the year. One week of instrument grading data, HCW, gender, USDA quality grade (QG), and yield grade (YG) factors, were collected every other month (n = 2,427,074 carcasses) over a 13-mo period (November 2010 through November 2011) from 4 beef processing corporations, encompassing 17 federally inspected beef processing facilities, to create a "snapshot" of carcass quality and yield attributes and trends from carcasses representing approximately 8.5% of the U.S. fed steer and heifer population. Mean yield traits were YG (2.86), HCW (371.3 kg), fat thickness (1.19 cm.), and LM area (88.39 cm(2)). The YG distribution was YG 1, 15.7%; YG 2, 41.0%; YG 3, 33.8%; YG 4, 8.5%; and YG 5, 0.9%. Distribution of HCW was <272.2 kg, 1.6%; 272.2 to 453.6 kg, 95.1%; and ≥453.6 kg, 3.3%. Monthly HCW means were November 2010, 381.3 kg; January 2011, 375.9 kg; March 2011, 366.2 kg; May 2011, 357.9 kg; July 2011, 372.54 kg; September 2011, 376.1 kg; and November 2011, 373.5 kg. The mean fat thickness for each month was November 2010, 1.30 cm; January 2011, 1.22 cm; March 2011, 1.17 cm; May 2011, 1.12 cm; July 2011, 1.19 cm; September 2011, 1.22 cm; and November 2011, 1.22 cm. The overall average marbling score was Small(49). The USDA QG distribution was Prime, 2.7%; Top Choice, 22.9%; Commodity Choice, 38.6%; and Select, 31.5%. Interestingly, from November to May, seasonal decreases (P < 0.001) in HCW and fat thicknesses were accompanied by increases (P < 0.001) in marbling. These data present the opportunity to further investigate the entire array of factors that determine the value of beef. Data sets using the online collection of electronic data will likely be more commonly used when evaluating the U.S. fed steer and heifer population in future studies.

National Beef Quality Audit-2011: In-plant survey of targeted carcass characteristics related to quality, quantity, value, and marketing of fed steers and heifers

The 2011 National Beef Quality Audit (NBQA-2011) assessed the current status of quality and consistency of fed steers and heifers. Beef carcasses (n = 9,802), representing approximately 10% of each production lot in 28 beef processing facilities, were selected randomly for the survey. Carcass evaluation for the cooler assessment of this study revealed the following traits and frequencies: sex classes of steer (63.5%), heifer (36.4%), cow (0.1%), and bullock (0.03%); dark cutters (3.2%); blood splash (0.3%); yellow fat (0.1%); calloused rib eye (0.05%); overall maturities of A (92.8%), B (6.0%), and C or greater (1.2%); estimated breed types of native (88.3%), dairy type (9.9%), and Bos indicus (1.8%); and country of origin of United States (97.7%), Mexico (1.8%), and Canada (0.5%). Certified or marketing program frequencies were age and source verified (10.7%), ≤A(40) (10.0%), Certified Angus Beef (9.3%), Top Choice (4.1%), natural (0.6%), and Non-Hormone-Treated Cattle (0.5%); no organic programs were observed. Mean USDA yield grade (YG) traits were USDA YG (2.9), HCW (374.0 kg), adjusted fat thickness (1.3 cm), LM area (88.8 cm2), and KPH (2.3%). Frequencies of USDA YG distributions were YG 1, 12.4%; YG 2, 41.0%; YG 3, 36.3%; YG 4, 8.6%; and YG 5, 1.6%. Mean USDA quality grade (QG) traits were USDA quality grade (Select(93)), marbling score (Small(40)), overall maturity (A(59)), lean maturity (A(54)), and skeletal maturity (A(62)). Frequencies of USDA QG distributions were Prime, 2.1%; Choice, 58.9%; Select, 32.6%; and Standard or less, 6.3%. Marbling score distribution was Slightly Abundant or greater, 2.3%; Moderate, 5.0%; Modest, 17.3%; Small, 39.7%; Slight, 34.6%; and Traces or less, 1.1%. Carcasses with QG of Select or greater and YG 3 or less represented 85.1% of the sample. This is the fifth benchmark study measuring targeted carcass characteristics, and information from this survey will continue to help drive progress in the beef industry. Results will be used in extension and educational programs as teaching tools to inform beef producers and industry professionals of the current state of the U.S. beef industry.

Evaluation of commonly used antimicrobial interventions for fresh beef inoculated with Shiga toxin-producing Escherichia coli serotypes O26, O45, O103, O111, O121, O145, and O157:H7

Although numerous antimicrobial interventions targeting Escherichia coli O157:H7 have been developed and implemented to decontaminate meat and meat products during the harvesting process, the information on efficacy of these interventions against the so-called Big Six non-O157 Shiga toxin-producing E. coli (STEC) strains is limited. Prerigor beef flanks (160) were inoculated to determine if antimicrobial interventions currently used by the meat industry have a similar effect in reducing non-O157 STEC serogroups O26, O45, O103, O111, O121, and O145 compared with E. coli O157:H7. A high (10(4) CFU/cm(2)) or a low (10(1) CFU/cm(2)) inoculation of two cocktail mixtures was applied to surfaces of fresh beef. Cocktail mixture 1 was composed of O26, O103, O111, O145, and O157, while cocktail mixture 2 was composed of O45, O121, and O157. The inoculated fresh beef flanks were subjected to spray treatments by the following four antimicrobial compounds: acidified sodium chlorite, peroxyacetic acid, lactic acid, and hot water. High-level inoculation samples were enumerated for the remaining bacteria populations after each treatment and compared with the untreated controls, while low-level inoculation samples were chilled for 48 h at 4°C before enrichment, immunomagnetic separation, and isolation. Spray treatments with hot water were the most effective, resulting in mean pathogen reductions of 3.2 to 4.2 log CFU/cm(2), followed by lactic acid. Hot water and lactic acid also were the most effective interventions with the low-level inoculation on surfaces of fresh beef flanks after chilling. Peroxyacetic acid had an intermediate effect, while acidified sodium chlorite was the least effective in reducing STEC levels immediately after treatment. Results indicate that the reduction of non-O157 STEC by antimicrobial interventions on fresh beef surfaces were at least as great as for E. coli O157:H7. However, the recovery of these low inoculation levels of pathogens indicated that there is no single intervention to eliminate them.

Effects of breed of sire on carcass composition and sensory traits of lamb

This experiment was conducted to compare meat quality and carcass composition of a diverse sampling of sheep breeds. Finnsheep, Romanov, Dorper, White Dorper, Katahdin, Rambouillet, Suffolk, Texel, Dorset, and Composite (½ Columbia rams to 1/4; Hampshire × 1/4; Suffolk) rams were mated to mature Composite ewes. Lambs (n = 804) were reared intensively, grain finished, and serially harvested over a 63-d period. Average harvest age was 216 d and average HCW was 30.7 kg. At a common harvest age, progeny of Suffolk sires were heavier than progeny of all other breeds (P < 0.05) and their carcasses were heavier (P < 0.05) than progeny of all other breeds, except White Dorper and Dorper. Progeny of Finnsheep and Romanov sires had lighter (P < 0.05) carcasses than progeny of all other breeds. Progeny of Texel, Suffolk, White Dorper, and Dorper sires had larger (P < 0.05) LM area than all other breeds. Progeny of Finnsheep and Romanov sires had smaller (P < 0.05) LM area than all other breeds. Fat thickness at the 12th rib was greater (P < 0.05) for progeny of Dorper sires than those of all other breeds, except White Dorper and Katahdin. Fat thickness at the 4th sacral vertebrae was greater (P < 0.05) for progeny of White Dorper and Dorper sires than those of all other breeds. On a carcass weight-constant basis, progeny of Suffolk sires had a lesser (P < 0.05) percentage of ether-extractable carcass fat than progeny of all other breeds, except Texel. Regardless of harvest endpoint (age-constant or HCW-constant), LM of progeny of Finnsheep and Romanov sires contained a greater (P < 0.05) percentage of intramuscular fat and received greater (P < 0.05) marbling scores than Rambouillet, Suffolk, Texel, Dorset, or Composite. Regardless of harvest endpoint, progeny of Finnsheep, Romanov, and Katahdin sires had smaller LM slice shear force values and greater trained sensory panel tenderness ratings at 7 d postmortem than did progeny of Composite, Suffolk, and Dorset sires (P < 0.05). At an age-constant basis, small differences (P < 0.05) were observed among breeds for lamb flavor intensity scores; however, when means were adjusted to a carcass weight-constant basis, breed of sire did not affect flavor intensity or off-flavor scores. These results document that each breed has relative strengths and weaknesses across traits, and that no single breed excels for all growth, carcass, and sensory traits.

Prevalence, enumeration, serotypes, and antimicrobial resistance phenotypes of salmonella enterica isolates from carcasses at two large United States pork processing plants

The objective of this study was to characterize Salmonella enterica contamination on carcasses in two large U.S. commercial pork processing plants. The carcasses were sampled at three points, before scalding (prescald), after dehairing/polishing but before evisceration (preevisceration), and after chilling (chilled final). The overall prevalences of Salmonella on carcasses at these three sampling points, prescald, preevisceration, and after chilling, were 91.2%, 19.1%, and 3.7%, respectively. At one of the two plants, the prevalence of Salmonella was significantly higher (P < 0.01) for each of the carcass sampling points. The prevalences of carcasses with enumerable Salmonella at prescald, preevisceration, and after chilling were 37.7%, 4.8%, and 0.6%, respectively. A total of 294 prescald carcasses had Salmonella loads of >1.9 log CFU/100 cm(2), but these carcasses were not equally distributed between the two plants, as 234 occurred at the plant with higher Salmonella prevalences. Forty-one serotypes were identified on prescald carcasses with Salmonella enterica serotypes Derby, Typhimurium, and Anatum predominating. S. enterica serotypes Typhimurium and London were the most common of the 24 serotypes isolated from preevisceration carcasses. The Salmonella serotypes Johannesburg and Typhimurium were the most frequently isolated serotypes of the 9 serotypes identified from chilled final carcasses. Antimicrobial susceptibility was determined for selected isolates from each carcass sampling point. Multiple drug resistance (MDR), defined as resistance to three or more classes of antimicrobial agents, was identified for 71.2%, 47.8%, and 77.5% of the tested isolates from prescald, preevisceration, and chilled final carcasses, respectively. The results of this study indicate that the interventions used by pork processing plants greatly reduce the prevalence of Salmonella on carcasses, but MDR Salmonella was isolated from 3.2% of the final carcasses sampled.

Evaluation of Bovine chemerin (RARRES2) Gene Variation on Beef Cattle Production Traits

A previous study in cattle based on >48,000 markers identified markers on chromosome 4 near the chemerin gene associated with average daily feed intake (ADFI) in steers (P < 0.008). Chemerin is an adipokine associated with obesity and metabolic syndrome in humans, representing a strong candidate gene potentially underlying the observed association. To evaluate whether the bovine chemerin gene is involved in feed intake, 16 markers within and around the gene were tested for association in the same resource population. Eleven were nominally significant for ADFI (P < 0.05) and two were significant after Bonferroni correction. Two and five SNP in this region were nominally significant for the related traits of average daily gain (ADG) and residual feed intake (RFI), respectively. All markers were evaluated for effects on meat quality and carcass phenotypes. Many of the markers associated with ADFI were associated with hot carcass weight (HCW), adjusted fat thickness (AFT), and marbling (P < 0.05). Marker alleles that were associated with lower ADFI were also associated with lower HCW, AFT, and marbling. Markers associated with ADFI were genotyped in a validation population of steers representing 14 breeds to determine predictive merit across populations. No consistent relationships for ADFI were detected. To determine whether cattle feed intake or growth phenotypes might be related to chemerin transcript abundance, the expression of chemerin was evaluated in adipose of 114 heifers that were siblings of the steers in the discovery population. Relative chemerin transcript abundance was not correlated with ADFI, ADG, or RFI, but associations with body condition score and yearling weight were observed. We conclude that variation in the chemerin gene may underlie observed association in the resource population, but that additional research is required to determine if this variation is widespread among breeds and to develop robust markers with predictive merit across breeds.

Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits

With the high cost of feed for animal production, genetic selection for animals that metabolize feed more efficiently could result in substantial cost savings for cattle producers. The purpose of this study was to identify DNA markers predictive for differences among cattle for traits associated with feed efficiency. Crossbred steers were fed a high-corn diet for 140 days and average daily feed intake (ADFI), average daily gain (ADG), and residual feed intake (RFI) phenotypes were obtained. A region on chromosome 14 was previously associated with RFI in this population of animals. To develop markers with the highest utility for predicting an animal's genetic potential for RFI, we genotyped additional markers within this chromosomal region. These polymorphisms were genotyped on the same animals (n = 1066) and tested for association with ADFI, ADG and RFI. Six markers within this region were associated with RFI (P ≤ 0.05). After conservative correction for multiple testing, one marker at 25.09 Mb remained significant (P = 0.02) and is responsible for 3.6% of the RFI phenotypic variation in this population of animals. Several of these markers were also significant for ADG, although none were significant after correction. Marker alleles with positive effects on ADG corresponded to lower RFI, suggesting an effect increasing growth without increasing feed intake. All markers were also assessed for their effects on meat quality and carcass traits. All of the markers associated with RFI were associated with adjusted fat thickness (AFT, P ≤ 0.009) and three were also associated with hot carcass weight (HCW, P ≤ 0.003). Marker alleles associated with lower RFI were also associated with reduced AFT, and if they were associated for HCW, the effect was an increase in weight. These markers may be useful as prediction tools for animals that utilize feed more efficiently; however, validation with additional populations of cattle is required.

Chilling rate effects on pork loin tenderness in commercial processing plants

The present experiment was conducted to provide a large-scale objective comparison of pork LM tenderness and other meat quality traits among packing plants that differ in stunning method and carcass chilling rate. For each of 2 replicates, pigs were sourced from a single barn of a commercial finishing operation that fed pigs from a single terminal crossbred line. On each day, 3 trucks were loaded, with each of those trucks delivering the pigs to a different plant. Plant A used CO(2) stunning and conventional spray chilling; Plant B used CO(2) stunning and blast chilling; and Plant C used electrical stunning and blast chilling. The boneless, vacuum-packaged loin was obtained from the left side of each carcass (n = 597; 100 · plant(-1) · replicate(-1)). As designed, HCW, LM depth, and LM intramuscular fat percentage did not differ among plants (P > 0.05). By 1.67 h postmortem (1 h after the carcasses exited the harvest floor), the average deep LM temperature was >10°C warmer for Plant A than Plants B and C (32.1°C, 21.6°C, and 19.3°C, for Plants A, B, and C, respectively) and deep LM temperature continued to be >10°C warmer for Plant A until 4.17 h or 6.33 h postmortem than for Plants C and B, respectively. Both plants that used blast chilling produced loins with greater LM slice shear force at 15 d postmortem than did the plant that used conventional spray chilling (P < 0.0001). The frequency of loins with excessively high (>25 kg) LM slice shear force values was greater for Plant B than Plant A (14.7% vs. 1%; P < 0.01). Among all the traits studied, including visual and instrumental evaluations of LM color, ultimate pH, marbling score, and lean color stability, the only other difference between Plants A and B was that purge loss during 13 d (from d 1 to 14) of vacuum-packaged storage was greater for Plant B (P < 0.05). That is, with this sample of pigs and CO(2) stunning, no loin quality advantages were detected for blast chilling. Regardless of chilling method, CO(2) stunning resulted in darker LM lean color and greater LM water-holding capacity than did electrical stunning (P < 0.05). This research shows that differences in chilling systems among pork packing plants can have a strong influence on loin chop tenderness.

Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle

BACKGROUND

In a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (P ≤ 0.003) with average daily gain (ADG) and 3 of these were also associated (P ≤ 0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle. The SNP were clustered in a 570 kb region around 38 Mb on the draft sequence of bovine chromosome 6 (BTA6), an interval containing several positional and functional candidate genes including the bovine LAP3, NCAPG, and LCORL genes. The goal of the present study was to develop and examine additional markers in this region to optimize the ability to distinguish favorable alleles, with potential to identify functional variation.

RESULTS

Animals from the original study were genotyped for 47 SNP within or near the gene boundaries of the three candidate genes. Sixteen markers in the NCAPG-LCORL locus displayed significant association with both ADFI and ADG even after stringent correction for multiple testing (P ≤ 005). These markers were evaluated for their effects on meat and carcass traits. The alleles associated with higher ADFI and ADG were also associated with higher hot carcass weight (HCW) and ribeye area (REA), and lower adjusted fat thickness (AFT). A reduced set of markers was genotyped on a separate, crossbred population including genetic contributions from 14 beef cattle breeds. Two of the markers located within the LCORL gene locus remained significant for ADG (P ≤ 0.04).

CONCLUSIONS

Several markers within the NCAPG-LCORL locus were significantly associated with feed intake and body weight gain phenotypes. These markers were also associated with HCW, REA and AFT suggesting that they are involved with lean growth and reduced fat deposition. Additionally, the two markers significant for ADG in the validation population of animals may be more robust for the prediction of ADG and possibly the correlated trait ADFI, across multiple breeds and populations of cattle.

Impact of reducing the level of wet distillers grains fed to cattle prior to harvest on prevalence and levels of Escherichia coli O157:H7 in feces and on hides

Cattle fed finishing diets with wet distillers grains with solubles (WDGS) have been shown to harbor increased Escherichia coli O157:H7 populations in the feces and on the hides. To determine if feeding a lower level of WDGS at the end of the feeding period reduces E. coli O157:H7 load at harvest, 608 heifers were sorted into one of five treatments and fed 0, 40, or 70% WDGS (dry matter basis). For three of the treatments, WDGS was reduced midway through the study. Treatment 0W0W heifers (positive control) were fed a corn grain-based diet continuously, and 40W40W heifers (negative control) were fed 40% WDGS continuously. Heifers subjected to treatments 40W0W, 40W15W, and 70W15W were fed either 40 or 70% WDGS for the first 56 days and switched to 0 or 15% WDGS, respectively, for the last 56 days. Prior to the switch in diets, animals fed diets with 40 or 70% had higher prevalence and percent enumerable fecal samples for E. coli O157:H7. After the dietary switch, animals fed 40W0W, 40W15W, and 70W15W diets had fecal prevalence and percent enumerable samples (33.4 and 6.3%, 31.0 and 9.7%, and 34.9 and 8.4%, respectively) similar to those of animals fed 0W0W diets (10.2 and 3.2%, respectively; P > 0.05), whereas animals fed 40W40W had the highest fecal prevalence and percent enumerable samples (70.1 and 29.2%, respectively; P < 0.05). Similar relationships between the treatments were observed for hide samples. Time after dietary switch was important, as animals fed lower levels had significantly lower fecal prevalence and percent enumerable samples after 56 days, but not after 28 days. The study indicates that cattle can be switched to lower levels of dietary WDGS (15% or less) 56 days prior to harvest to significantly reduce E. coli O157:H7 in feces and on hides.

Use of visible and near-infrared spectroscopy to predict pork longissimus lean color stability

This study evaluated the use of visible and near-infrared (VISNIR) spectroscopy to predict lean color stability in pork loin chops. Spectra were collected immediately after and approximately 1 h after rib removal on 1,208 loins. Loins were aged for 14 d before a 2.54-cm chop was placed in simulated retail display. Spectra were collected on aged loins immediately after removal from the vacuum package and on chops 10 min after cutting. Instrumental color measurements [L*, a*, b*, hue angle, chroma, and E (overall color change)] were determined on d 0, 1, 7, 11, and 14 of display. Principal components analysis of display d 0 and 14 values of these traits identified a factor (first principal component; PC1) explaining 67% of the variance that was related to color change. Partial least squares regression was used to develop 3 models to predict PC1 values by using VISNIR spectra collected in the plant, on aged loins, and on chops. Loins with predicted PC1 values less than 0 were classified as having a stable color, whereas values greater than 0 were classified as having a labile lean color. Loins classified as stable by the in-plant model had smaller (P < 0.05) L* values than those classified as labile. Hue angle and ΔE values were less (P < 0.05) and a* and chroma values were greater (P < 0.05) after d 7 of display in loins predicted to have a stable color than in loins predicted to have a labile lean color. Similarly, chops from loins classified as stable using the aged loin model had smaller (P < 0.05) L* values than those from loins classified as labile. Furthermore, loins predicted to be stable had smaller (P < 0.05) hue angle and ΔE values and greater (P < 0.05) a* and chroma values after d 7 of display than did loins predicted to be labile. Results for the chop model were similar to those from the 2 loin models. Chops predicted to have a stable lean color had smaller (P < 0.05) L* values than did those predicted to have a labile lean color. Chops classified as stable had smaller (P < 0.05) hue angle and ΔE values and greater (P < 0.05) a* and chroma values after d 7 of display compared with chops classified as labile. All 3 models effectively segregated chops based on color stability, particularly with regard to redness. Regardless of the model being used, d 14 display values for a*, hue angle, and ΔE in loins classified as stable were similar to the d 7 values of loins classified as labile. Thus, these results suggest that VISNIR spectroscopy would be an effective technology for sorting pork loins with regard to lean color stability.

Predictive markers in calpastatin for tenderness in commercial pig populations

The identification of predictive DNA markers for pork quality would allow US pork producers and breeders to select genetically superior animals more quickly and efficiently for the production of consistent, high-quality meat. Genome scans have identified QTL for tenderness on SSC 2, which have been fine-mapped to the calpastatin locus. The objectives of this study were to identify the sequence variation in calpastatin that likely affects tenderness in commercial-level pig populations and to develop definitive DNA markers that are predictive of pork tenderness for use in marker-assisted selection programs. We resequenced the calpastatin regulatory and transcribed regions in pigs with divergently extreme shear force values to identify possible mutations that could affect tenderness. A total of 194 SNP were identified in this sequence, and 31 SNP were found in predicted transcription factor binding sites. We tested 131 polymorphisms in our research population and a subset (40) of these in samples of industry pigs for their association with objective measures of tenderness. We identified 4 SNP that were consistently associated with pork tenderness in all the populations studied, representing 2,826 pigs from 4 distinct populations. Gel shift assays were designed for these SNP and 12 other polymorphic sites. Six sites demonstrated a gel shift when probes were incubated with nuclear extract from muscle, heart, or testis. Four of these sites, a specificity protein 1 (Sp1) site around nucleotides 12978 and 12979, a potential thyrotroph embryonic factor (Tef) site at nucleotide 25587, an unknown site at nucleotide 48699, and myocyte enhancer factor-2 (Mef-2)/TATA sites with SNP at positions 49223 and 49228 were allele specific in binding nuclear proteins. The allele frequencies for the tender alleles were similar (0.11 to 0.36) in the 4 different commercial populations. These 4 SNP were not in complete linkage disequilibrium with each other and may independently affect calpastatin expression, tenderness, or both. These markers should be predictive of pork tenderness in industry populations.

Genomic regions associated with kyphosis in swine

BACKGROUND

A back curvature defect similar to kyphosis in humans has been observed in swine herds. The defect ranges from mild to severe curvature of the thoracic vertebrate in split carcasses and has an estimated heritability of 0.3. The objective of this study was to identify genomic regions that affect this trait.

RESULTS

Single nucleotide polymorphism (SNP) associations performed with 198 SNPs and microsatellite markers in a Duroc-Landrace-Yorkshire resource population (U.S. Meat Animal Research Center, USMARC resource population) of swine provided regions of association with this trait on 15 chromosomes. Positional candidate genes, especially those involved in human skeletal development pathways, were selected for SNP identification. SNPs in 16 candidate genes were genotyped in an F2 population (n = 371) and the USMARC resource herd (n = 1,257) with kyphosis scores. SNPs in KCNN2 on SSC2, RYR1 and PLOD1 on SSC6 and MYST4 on SSC14 were significantly associated with kyphosis in the resource population of swine (P ≤ 0.05). SNPs in CER1 and CDH7 on SSC1, PSMA5 on SSC4, HOXC6 and HOXC8 on SSC5, ADAMTS18 on SSC6 and SOX9 on SSC12 were significantly associated with the kyphosis trait in the F2 population of swine (P ≤ 0.05).

CONCLUSIONS

These data suggest that this kyphosis trait may be affected by several loci and that these may differ by population. Carcass value could be improved by effectively removing this undesirable trait from pig populations.

Inoculation of beef with low concentrations of Escherichia coli O157:H7 and examination of factors that interfere with its detection by culture isolation and rapid methods

Currently used industry testing programs require the ability to detect Escherichia coli O157:H7 in samples of beef trim or ground beef at levels as low as 1 CFU/375 g. We present a reliable protocol for generating a control inoculum for verification testing at this low concentration and evaluate its use. Results show that half of all samples received no cells when 1 CFU was the target concentration and that targets greater than 3 CFU were much more reliable. Detection by culture isolation and two commercial assays, Qualicon BAX-MP and BioControl GDS, detected 94% ± 11%, 92% ± 10%, and 92% ± 7% of samples inoculated with 5.4 CFU (range 1 to 9 CFU), respectively. We also examined the effect of background aerobic plate count (APC) bacteria and fat content effects on the detection of E. coli O157:H7. At APC concentrations below 6 log CFU/g, the rapid methods detected all beef trim samples inoculated with 26 CFU of E. coli O157:H7 per 65 g. At an APC of 6.7 log CFU/g, culture, BAX-MP, and GDS detected 100, 75, and 13%, respectively, of inoculated samples. Neither commercial method detected E. coli O157:H7 in the samples when APC was 7.7 log CFU/g, whereas culture was able to detect 63% of E. coli O157:H7 in the samples when APC was at this concentration. Increased fat content correlated with decreasing recovery of immunomagnetic separation beads, but this was not observed to interfere with detection of E. coli O157:H7.

Super shedding of Escherichia coli O157:H7 by cattle and the impact on beef carcass contamination

Beef carcass contamination is a direct result of pathogen transfer from cattle hides harboring organisms such as enterohemorrhagic Escherichia coli. Hide contamination occurs from direct and indirect fecal contamination in cattle production and lairage environments. In each of these environments, individual animals shedding E. coli O157:H7 at high levels (>10(4) CFU/g of feces, hereafter referred to as "super shedders") can have a disproportionate effect on cattle hide and subsequent carcass contamination. It is not known what criteria must be met to cause an animal to shed at levels exceeding 10(4) CFU/g. Understanding the factors that play a role in super shedding will aid in minimizing or eliminating the super shedding population. Interventions that would prevent super shedding in the cattle population should reduce E. coli O157:H7 transmission in the production and lairage environments resulting in reduced risk of beef carcass contamination and a safer finished product.

Characterization of biological types of cattle (Cycle VIII): carcass, yield, and longissimus palatability traits

The objective of this experiment was to evaluate alternative sources of tropically adapted cattle germplasm and compare them with Angus- (AN) and Hereford- (HE) sired steers. Carcass, yield, and longissimus thoracis palatability traits from F(1) steers (n = 621) obtained from mating AN and MARC III cows to HE, AN, Brangus (BR), Beefmaster (BM), Bonsmara (BO), or Romosinuano (RO) sires were compared. Data were adjusted to constant age (426 d), carcass weight (340 kg), fat thickness (1.0 cm), fat trim percentage (25%), and marbling (Small(00)) endpoints. For Warner-Bratzler and slice shear force and trained and untrained sensory panel traits, data were obtained on LM from ribeye steaks stored at 2 degrees C for 14 or 15 d postmortem. The following comparisons were from the age-constant endpoint. Carcasses from BM-, AN-, and BR-sired steers (358, 355, and 351 kg, respectively) were heavier (P < 0.05) than carcasses from steers from HE (343 kg) and BO (331 kg) sires; RO-sired steers (318 kg) had the lightest (P < 0.05) carcasses. Adjusted fat thicknesses for AN- and BM-sired steers (1.3 and 1.2 cm, respectively) were greater (P < 0.05) than for steers from BR (1.0 cm) and BO (0.9 cm) sires; RO-sired steers (0.8 cm) had the least fat thickness. Longissimus areas were larger (P < 0.05) for BO- and BR-sired steers (84.4 and 84.1 cm(2), respectively) than for BM- and HE-sired steers (80.8 and 80.2 cm(2), respectively). A greater (P < 0.05) percentage of carcasses from AN-sired steers graded USDA Choice (69%) than other sire breeds (17 to 47%) except HE (52%). Carcass yield of boneless, totally trimmed retail product was least (P < 0.05) for AN-sired steers (60.1%) and greatest (P < 0.05) for RO- and BO-sired steers (64.4 to 63.5%). Considering all measurements, AN LM tended to be more tender and BM LM tended to be least tender. American composite breeds BM and BR were heavier, fatter, lesser yielding, with similar marbling scores but less tender LM than BO and RO. Angus carcasses were similar in size, fatter, lesser yielding, with more marbling and more tender LM compared with BM and BR. Bonsmara and RO provide tropically adapted germplasm and produce carcasses that are lighter, leaner, greater yielding, with similar marbling and LM that tend to be more tender than carcasses from BM and BR.

Evaluation of a direct-fed microbial product effect on the prevalence and load of Escherichia coli O157:H7 in feedlot cattle

Direct-fed microbials (DFM) have been identified as potential preharvest interventions for the reduction of foodborne bacterial pathogens such as Escherichia coli O157:H7. This study evaluated the efficacy of a DFM consisting of Bacillus subtilis strain 166 as an antimicrobial intervention strategy for the reduction of prevalence and load of E. coli O157:H7 in feces and on hides of feedlot cattle. Cattle (n = 526) were divided among 16 feedlot pens. Half of the pens received the DFM, and the other half did not. Hide and fecal samples were collected from each animal on days 28, 63, and 84 of the feeding trial. Over the course of the 84-day feeding period, there were no significant differences observed between treatments for either hide or fecal prevalence of E. coli O157:H7, or for the percentage of animals that were shedding E. coli O157:H7 at high levels (> or =200 CFU/g) in their feces or harboring E. coli O157:H7 at high levels (> or =40 CFU/cm(2)) on their hides. In addition, there was no significant difference between the average daily gains for the treated and control groups, with both groups averaging 1.3 kg/day. We concluded that the DFM tested would not be an effective preharvest intervention against E. coli O157:H7.

Associations of polymorphisms in the promoter I of bovine acetyl-CoA carboxylase-alpha gene with beef fatty acid composition

The objectives of this study were to identify single nucleotide polymorphisms (SNPs) in the promoter I (PI) region of the bovine acetyl-CoA carboxylase-alpha (ACACA) gene and to evaluate the extent to which they were associated with lipid-related traits. Eight novel SNPs were identified, which were AJ276223:g.2064T>A (SNP1), g.2155C>T (SNP2), g.2203G>T (SNP3), g.2268T>C (SNP4), g.2274G>A (SNP5), g.2340A>G (SNP6), g.2350T>C (SNP7) and g.2370A>G (SNP8). Complete linkage disequilibrium was observed among SNP1, 2, 4, 5, 6 and 8. Phenotypic data were collected from 573 cross-bred steers with six sire breeds, including Hereford, Angus, Brangus, Beefmaster, Bonsmara and Romosinuano. The genotypes of SNP1/2/4/5/6/8 were significantly associated with adjusted backfat thickness. The genotypes of SNP3 were significantly associated with triacylglycerol (TAG) content and fatty acid composition of longissimus dorsi muscle (LM) in Brangus-, Romosinuano- and Bonsmara-sired cattle. Cattle with g.2203GG genotype had greater concentrations of TAG, total lipid, total saturated fatty acid and total monounsaturated fatty acid than did cattle with g.2203GT genotype. The genotypes of SNP7 were significantly associated with fatty acid composition of LM. Cattle with genotype g.2350TC had greater amounts of several fatty acids in LM than did cattle with genotype g.2350CC. Our results suggested that the SNPs in the PI region of ACACA gene are associated with variations in the fatty acid contents in LM.

Prevalence and level of Escherichia coli O157:H7 in feces and on hides of feedlot steers fed diets with or without wet distillers grains with solubles

The objective of this study was to determine if wet distillers grains with solubles (WDGS) from corn in diets affected Escherichia coli O157:H7 in growing and finishing cattle; steers (n = 603) were randomly assigned to diets with or without WDGS. Hide and fecal samples were collected monthly (October through June) from each animal for enumeration and enrichment of E. coli O157:H7. In the growing phase (0 or 13.9% WDGS diets), fecal prevalence for E. coli O157:H7 in steers fed a diet with WDGS was twice that of the prevalence in control steers (P < 0.001). In the finishing phase (0 or 40% WDGS diets), the average prevalence in feces (P < 0.001) and on hides (P < 0.001) was higher for cattle fed WDGS. The average percentage of fecal E. coli O157:H7 enumerable samples during the finishing phase for cattle fed WDGS was 2.7% compared with 0.1% for control steers (P < 0.001). The average percentage of E. coli O157:H7 enumerable hide samples was not different between diets, but the cattle fed WDGS had higher levels (P < 0.05) of the pathogen. Animals fed WDGS had higher levels of E. coli (P < 0.001), higher pH values (P < 0.001), and lower concentrations of L-lactate (P < 0.001) in feces than those values of the control steers. These results indicate that feeding 40% WDGS could increase the level and prevalence of E. coli O157:H7 in and on feedlot cattle when E. coli O157:H7 is seasonally low.

Prevalence of Mycobacterium avium subsp. paratuberculosis in ileocecal lymph nodes and on hides and carcasses from cull cows and fed cattle at commercial beef processing plants in the United States

Clinical associations between Crohn's disease in humans and Mycobacterium avium subsp. paratuberculosis (MAP) have been suggested but not confirmed. Cattle could be sources for MAP, but little information on MAP prevalence with beef has been reported. Samples of ileocecal lymph nodes and swabs of hides and carcasses from 343 animals at cull cattle slaughtering facilities and 243 animals at fed cattle slaughtering facilities across the United States were analyzed for the presence of MAP. Amplification of genetic sequences detected MAP DNA predominantly on hides and in lymph nodes of samples taken at both types of processing facilities. More than 34% of the cattle at cull cow slaughtering facilities had ileocecal lymph nodes that tested positive for MAP DNA. From these same cattle, hide prevalence was more than twofold greater than the prevalence in ileocecal lymph nodes, suggesting that cross-contamination could be occurring during transport and lairage. The prevalence of MAP DNA decreased during processing, and less than 11% of the carcasses tested positive after interventions in the cull cow processing facilities. Using standard double-decontamination and culture techniques, less than 1% of the postintervention carcasses tested positive for viable MAP at cull cow facilities. In samples from the facilities processing only fed cattle, MAP prevalence of 1% or less was detected for ileocecal lymph node, hide, and carcass samples, and viable MAP was not detected. Based on this study, fed cattle carcasses are unlikely sources of MAP, and carcasses at cull cow plants have only a slight risk for transmitting viable MAP, due to current interventions.

Prevalence rates of Escherichia coli O157:H7 and Salmonella at different sampling sites on cattle hides at a feedlot and processing plant

The prevalence rates of Escherichia coli O157:H7 and Salmonella at different sampling sites on cattle hides were determined at a feedlot and a processing plant. Sponge samples were collected from six hide surface sites at the feedlot (left and right shoulders, left and right ribs, back, and belly) and four sites at the processing plant (left and right shoulders, back, and belly). The prevalence of E. coli O157:H7 was approximately 80% for left and right shoulder and rib samples, 68% for back samples, and 92% for belly samples collected at the feedlot. At the processing plant, the prevalences of E. coli O157:H7 at all four sites were between 76 and 79%. Salmonella prevalence in feedlot samples was too low to allow for accurate analysis. The prevalence of Salmonella at processing was 49% for left shoulder samples, 48% for right shoulder samples, 40% for back samples, and 68% for belly samples. The results of this study indicate that the site most likely to be naturally contaminated with E. coli O157:H7 and Salmonella simultaneously was the belly.

Relationships among calpastatin single nucleotide polymorphisms, calpastatin expression and tenderness in pork longissimus

Genome scans in the pig have identified a region on chromosome 2 (SSC2) associated with tenderness. Calpastatin is a likely positional candidate gene in this region because of its inhibitory role in the calpain system that is involved in postmortem tenderization. Novel single nucleotide polymorphisms (SNP) in calpastatin were identified and used to genotype a population (n = 1042) of Duroc-Landrace-Yorkshire swine for association with longissimus lumborum slice shear force (SSF) measured at days 7 and 14 postmortem. Three genetic markers residing in the calpastatin gene were significantly associated with SSF (P < 0.0005). Haplotypes constructed from markers in the calpastatin gene were significantly associated with SSF (F-ratio = 3.93; P-value = 0.002). The levels of normalized mRNA expression of calpastatin in the longissimus lumborum of 162 animals also were evaluated by real-time RT-PCR and were associated with the genotype of the most significant marker for SSF (P < 0.02). This evidence suggests that the causative variation alters expression of calpastatin, thus affecting tenderness. In summary, these data provide evidence of several significant, publicly available SNP markers associated with SSF that may be useful to the swine industry for marker assisted selection of animals that have more tender meat.

Effectiveness of 1,3-dibromo-5,5 dimethylhydantoin on reduction of Escherichia coli O157:H7- and Salmonella-inoculated fresh meat

1,3-Dibromo-5,5-dimethylhydantoin (DBDMH; 25 degrees C) and hot water (85 degrees C) spray treatments were evaluated for efficacy in decontamination of pathogenic bacteria attached to beef carcass surfaces represented by cutaneous trunci (CT) muscle sections and beef hearts. Treatments were evaluated using two different systems, a commercial carcass wash cabinet and a model carcass washer. The effects were measured immediately after treatment and again after 48 h of storage at 4 degrees C. Section of CT and beef hearts were inoculated with bovine fecal solution containing approximately 6 log CFU/cm2 of Escherichia coli O157:H7 and Salmonella. After DBDMH or hot water spray treatments, bacterial populations were enumerated immediately and after storage for 48 h at 4 degrees C. DBDMH treatments reduced aerobic plate counts, Enterobacteriaceae, E. coli O157: H7, and Salmonella by the same or slightly lower amounts relative to hot water treatment. DBDMH reduced aerobic plate counts and Enterobacteriaceae by 2.8 to 3.6 log CFU/cm2, E. coli O157:H7 by 1.6 to 2.1 log CFU/cm2, and Salmonella by 0.7 to 2.3 log CFU/cm2 on CT sections and beef hearts. Hot water treatment reduced aerobic plate counts and Enterobacteriaceae by 3.0 to 4.1 log CFU/cm2, E. coli O157:H7 by 1.8 to 2.3 log CFU/cm2, and Salmonella by 2.5 to 2.8 log CFU/cm2. After 48 h of storage, the reductions of organisms by DBDMH and hot water treatments were not different. This study demonstrated that DBDMH spray washing could be effective as an antimicrobial intervention for beef carcasses and variety meats.

Comparison of effects of antimicrobial interventions on multidrug-resistant Salmonella, susceptible Salmonella, and Escherichia coli O157:H7

Several strains of Salmonella have been identified as resistant to multiple antibiotics. What is not known is whether strains possessing multidrug resistance properties also have the ability to resist the killing effects of the antimicrobial interventions used in beef processing. The research project described herein was designed to determine whether antimicrobial interventions currently in place in beef processing facilities are adequate for reducing the foodborne pathogen loads on beef carcass surfaces contaminated with multidrug-resistant (MDR) Salmonella. The data presented here indicate that MDR Salmonella is reduced at least as effectively as are Escherichia coli O157:H7 and susceptible Salmonella when treated with antimicrobial interventions currently in use at most U.S. beef processing plants. The E. coli O157:H7 strains used in this study were divided into two groups, strains that have a genetic polymorphism associated with human disease and strains not typically found to cause human disease. No differences were detected in the abilities of these two strain types to survive antimicrobial interventions. These results indicate that neither the drug resistance status of a particular Salmonella strain nor the likelihood that a particular E. coli O157:H7 strain will cause human illness influences the antimicrobial efficacy of the interventions utilized by the modern beef processing plants.