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Consumer interest in grass-fed beef has been steadily rising due to consumer perception of its potential benefits. This interest has led to a growing demand for niche market beef, particularly in the western United States. Therefore, the objective of this study was to assess the impact of feeding systems on the change in microbial counts, color, and lipid oxidation of steaks during retail display, and on their sensory attributes. The systems included: conventional grain-fed (CON), 20 months-grass-fed (20GF), 25-months-grass-fed (25GF) and 20-months-grass-fed + 45-day-grain-fed (45GR). The results indicate that steaks in the 20GF group displayed a darker lean and fat color, and a lower oxidation state than those in the 25GF group. However, the feeding system did not have an impact on pH or objective tenderness of beef steaks. In addition, consumers and trained panelist did not detect a difference in taste or flavor between the 20GF or 25GF steaks but expressed a preference for the CON and 45GR steaks, indicating that an increased grazing period may improve the color and oxidative stability of beef, while a short supplementation with grain may improve eating quality.

Mitochondrial DNA copy number (mtDNA CN) is heritable and easily obtained from low-pass sequencing (LPS). This study investigated the genetic correlation of mtDNA CN with growth and carcass traits in a multi-breed and crossbred beef cattle population. Blood, leucocyte, and semen samples were obtained from 2,371 animals and subjected to LPS that resulted in nuclear DNA (nuDNA) and mtDNA sequence reads. Mitochondrial DNA CN was estimated as the ratio of mtDNA to nuDNA coverages. Variant calling was performed from mtDNA, and 11 single nucleotide polymorphisms (SNP) were identified in the population. Samples were classified in taurine haplogroups. Haplogroup and mtDNA type were further classified based on the 11 segregating SNP. Growth and carcass traits were available for between 7,249 and 60,989 individuals. Associations of mtDNA CN, mtDNA haplogroups, mtDNA types, and mtDNA SNP with growth and carcass traits were estimated with univariate animal models, and genetic correlations were estimated with a bivariate animal model based on pedigree. Mitochondrial DNA CN tended (P -value ≤0.08) to be associated with birth weight and weaning weight. There was no association (P -value >0.10) between mtDNA SNP, haplogroups, or types with growth and carcass traits. Genetic correlation estimates of mtDNA CN were −0.30 ± 0.16 with birth weight, −0.31 ± 0.16 with weaning weight, −0.15 ± 0.14 with post-weaning gain, −0.11 ± 0.19 with average daily dry-matter intake, −0.04 ± 0.22 with average daily gain, −0.29 ± 0.13 with mature cow weight, −0.11 ± 0.13 with slaughter weight, −0.14 ± 0.13 with carcass weight, −0.07 ± 0.14 with carcass backfat, 0.14 ± 0.14 with carcass marbling, and −0.06 ± 0.14 with ribeye area. In conclusion, mtDNA CN was negatively correlated with most traits investigated, and the genetic correlation was stronger with growth traits than with carcass traits. [ABSTRACT FROM AUTHOR]

Beginning with a large push from consumers to improve meat and carcass quality in the 1990s, through selection, the beef industry has successfully made significant genetic gains towards achieving these improvements. For producers looking to increase the genetic potential of their own herds for carcass quality there are multiple considerations that will inform the time it takes to see improvement. Some of the primary factors influencing the rate of genetic gain for carcass quality phenotypes include: 1) available selection candidates, 2) trait heritability, 3) selection accuracy, and 4) selection intensity. Using the Germplasm Evaluation beef herd at the US Meat Animal Research Center, many of the possible factors influencing this timeline have been evaluated. Collection of carcass quality phenotypes has been an ongoing, long-term objective of the project and has allowed for the estimation of trait heritabilities, breed differences, heterosis effects, and genetic trends over time for this trait complex. Additionally, this herd facilitated the development of decision support tools for creating selection indices and breeding programs, representing the culmination of many of these research outcomes. There are multiple ways to achieve genetic improvement for carcass quality, and our primary objective is to equip producers and other stakeholders with the necessary information to make informed selection decisions. The USDA is an equal opportunity provider and employer [ABSTRACT FROM AUTHOR]

Abstract 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.

Abstract 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.

Abstract Background In 2006, an atypical U.S. case of bovine spongiform encephalopathy (BSE) was discovered in Alabama and later reported to be polymorphic for glutamate (E) and lysine (K) codons at position 211 in the bovine prion protein gene (Prnp) coding sequence. A bovine E211K mutation is important because it is analogous to the most common pathogenic mutation in humans (E200K) which causes hereditary Creutzfeldt – Jakob disease, an autosomal dominant form of prion disease. The present report describes a high-throughput matrix-associated laser desorption/ionization-time-of-flight mass spectrometry assay for scoring the Prnp E211K variant and its use to determine an upper limit for the K211 allele frequency in U.S. cattle. Results The K211 allele was not detected in 6062 cattle, including those from five commercial beef processing plants (3892 carcasses) and 2170 registered cattle from 42 breeds. Multiple nearby polymorphisms in Prnp coding sequence of 1456 diverse purebred cattle (42 breeds) did not interfere with scoring E211 or K211 alleles. Based on these results, the upper bounds for prevalence of the E211K variant was estimated to be extremely low, less than 1 in 2000 cattle (Bayesian analysis based on 95% quantile of the posterior distribution with a uniform prior). Conclusion No groups or breeds of U.S. cattle are presently known to harbor the Prnp K211 allele. Because a carrier was not detected, the number of additional atypical BSE cases with K211 will also be vanishingly low.

A study was conducted to examine the dynamics of Escherichia coli O157:H7 fecal and hide prevalence over a 9-month period in a feedlot setting and also determine the animals shedding E. coli O157:H7 at high levels that affect the prevalence and levels of E. coli O157:H7 on the hides of other animals in the same pen. The detected large and unpredictable fluctuations within and between pens in both fecal and hide prevalence of E. coli O157:H7 could be minimized by keeping the levels of shedding below 200 CFU/g and could be used as guideline for preharvest intervention studies.

The hide and carcass hygiene of cull cattle at slaughter in the United States is examined by measuring the aerobic plate counts (APC) and the prevalences and the loads of Salmonella and Escherichia coli O157:H7. The pathogen prevalence on hides and carcasses is not affected by the season, whereas differences are observed between plants with respect to the incoming pathogen load and the ability to mitigate hide-to-carcass transfer.

The aerobic plate counts (APC) and the prevalences and loads of Salmonella and Escherichia coli 0157:H7 is measured to examine the hide and carcass hygiene of cull cattle at slaughter in four geographically distant regions of the United States. The pathogen prevalence on hides and carcasses is not affected by the season, however postintervention carcass contamination is significantly reduced due to the use of one or more intervention processes employed at each of the four processing plants examined.

The objective of this study was to enhance estimates of additive, dominance, and epistatic effects of marker polymorphisms on beef carcass and quality traits. Myostatin (MSTN) F94L SNP and the µ-calpain (CAPN1) 316 and 4751 SNP haplotype have previously been associated with fat and muscle traits in beef cattle. Multiyear selection in a composite population segregating these polymorphisms increased minor allele (F94L L) and chosen haplotype (CAPN1 CC and GT) frequencies to intermediate levels resulting in more precise estimates of additive and nonadditive genetic effects. During the 3 yr after selection, 176 steers were evaluated for growth, carcass, meat quality, tenderness (n = 103), and meat color traits. The statistical model included year, age of dam, age of the steer, and genotype in a random animal model. The 9 genotypes (3 CAPN1 diplotypes × 3 F94L genotypes) affected marbling score, ribeye area, adjusted fat thickness, vision yield grade (all P < 0.001), slice shear force (P = 0.03), and CIE L* reflectance (P = 0.01). Linear contrasts of the 9 genotypes estimated additive, recessive, and epistatic genetic effects. Significant additive effects of the F94L L allele decreased marbling score, adjusted fat thickness, vision yield grade, and slice shear force; and increased ribeye area and CIE L* reflectance. The homozygous F94L FF and LL genotypes differed by 1.3 to 1.9 phenotypic SD for most carcass traits and by 0.8 to 0.9 SD for slice shear force and CIE L * reflectance but carcass weight differed by only 3 kg (0.1 SD). The L allele was partially recessive to F for ribeye area (P = 0.02) and the heterozygous FL means tended to be closer to the FF genotype than the LL genotype for other carcass traits but differences from additive were not significant. The CAPN1 additive × F94L additive effect on slice shear force was the only significant epistatic estimate. The F94L L allele is prevalent in Limousin but nearly absent in other U.S. purebreds. This allele had about half of the effects on birth weight, muscle, and fat traits reported for severe MSTN mutations in Belgian Blue and Piedmontese breeds. The interaction between MSTN and CAPN1 genotypes may reflect the strong additive effects of MSTN F94L L allele on fat and muscle traits interfering with the phenotypic effect of CAPN1 genotype on meat tenderness. [ABSTRACT FROM AUTHOR]