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RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured in longissimus dorsi muscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem., Competing Interests: The authors have declared that no competing interests exist.

The objective of this study was to estimate heritabilities for sensory traits and genetic correlations among sensory traits and with marbling score (MS), Warner-Bratzler shear force (WBSF), and intramuscular fat content (IMFC). Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for laboratory analysis and 1,720 steaks were analyzed by a trained sensory panel. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multitrait animal model. Estimates of heritability for MS, IMFC, WBSF, tenderness, juiciness, and connective tissue traits were 0.67, 0.38, 0.19, 0.18, 0.06, and 0.25, respectively. The genetic correlations of MS with tenderness, juiciness, and connective tissue were estimated to be 0.57 ± 0.14, 1.00 ± 0.17, and 0.49 ± 0.13, all positive and strong. Estimated genetic correlations of IMFC with tenderness, juiciness, and connective tissue were 0.56 ± 0.16, 1.00 ± 0.21, and 0.50 ± 0.15, respectively. The genetic correlations of WBSF with tenderness, juiciness, and connective tissue were all favorable and estimated to be -0.99 ± 0.08, -0.33 ± 0.30 and -0.99 ± 0.07, respectively. Strong and positive genetic correlations were estimated between tenderness and juiciness (0.54 ± 0.28) and between connective tissue and juiciness (0.58 ± 0.26). In general, genetic correlations were large and favorable, which indicated that strong relationships exist and similar gene and gene networks may control MS, IMFC, and juiciness or WBSF, panel tenderness, and connective tissue. The results from this study confirm that MS currently used in selection breeding programs has positive genetic correlations with tenderness and juiciness and, therefore, is an effective indicator trait for the improvement of tenderness and juiciness in beef. This study also indicated that a more objective measure, particularly WBSF, a trait not easy to improve through phenotypic selection, is an excellent candidate trait for genomic selection aimed at improving eating satisfaction.

The objective of this study was to characterize variation and identify SNP and chromosomal regions associated with mineral concentrations in LM of Angus beef cattle. Samples of LM from 2,285 Angus cattle were obtained, and concentrations of 7 minerals, including iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Genomic DNA extracted from the ground beef sample used for mineral composition was genotyped with the Bovine SNP50 Infinium II BeadChip, and effects of SNP on each trait were estimated using the Bayes-Cπ module of GenSel software. Pedigree-based estimates of heritabilities and corresponding genetic variances indicate iron was the only mineral concentration that could be considered a good candidate for manipulation by genomic selection. The amount of variation that could be accounted for by SNP genotypes was concordant with pedigree-based heritabilities and varied from very low for potassium and sodium (<0.09) to medium high (0.37) for iron. Although significant chromosomal regions were identified for all minerals analyzed in this study, further study focused on iron. Seven regions on 6 chromosomes (1, 2, 7, 10, 15, and 28) were identified to have a major effect on the iron content of LM in Angus cattle. The accuracy of direct genomic values (DGV) for iron concentration was estimated using a 5-fold cross-validation strategy. The accuracy of DGV estimated as the genetic correlation between DGV and the phenotype (iron concentration) adjusted for contemporary groups was 0.59. A bivariate animal model was used to estimate genetic correlations between iron concentrations and a reduced set of economically important carcass traits: HCW, rib eye area, calculated USDA yield grade, percent KPH, and marbling score. The genetic correlations between iron concentration and HCW, percentage KPH, marbling score, and rib eye area were small (-0.19 to 0.15) and nonsignificant. Although still weak (0.22), a positive significant genetic correlation was identified between iron content and USDA calculated yield grade. Beef is a major contributor of iron and zinc in the human diet, and this study found that iron content might be effectively manipulated through marker-assisted selection programs, without compromising other carcass and palatability traits.

The objective of this study was to estimate genetic parameters for concentrations of minerals in LM and to evaluate their associations with beef palatability traits. Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of mineral concentrations and for trained sensory panel assessments. Nine minerals, including calcium, copper, iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for mineral concentrations in LM varied from 0.01 to 0.54. Iron and sodium were highly and moderately heritable, respectively, whereas the other minerals were lowly heritable except for calcium, copper, and manganese, which exhibited no genetic variation. Strong positive genetic correlations existed between iron and zinc (0.49, P < 0.05), between magnesium and phosphorus (0.88, P < 0.05), between magnesium and sodium (0.68, P < 0.05), and between phosphorus and potassium (0.69, P < 0.05). Overall tenderness assessed by trained sensory panelists was positively associated with manganese, potassium, and sodium and negatively associated with phosphorus and zinc concentrations (P < 0.05). Juiciness assessed by trained sensory panelists was negatively associated with magnesium and positively associated with manganese and sodium concentrations (P < 0.05). Livery or metallic flavor was not associated with any of the minerals (P > 0.05). Beefy flavor was positively associated with calcium, iron, and zinc and negatively associated with sodium concentration, whereas a painty or fishy flavor was positively associated with sodium and negatively associated with calcium and potassium concentrations (P < 0.05). Beef is a major contributor of iron and zinc in the human diet, and these results demonstrate sufficient genetic variation for these traits to be improved through marker-assisted selection programs without compromising beef palatability.

Fatty acid profiles and intramuscular expression of genes involved in fatty acid metabolism were characterized in concentrate- (CO) and forage- (FO) based finishing systems. Intramuscular samples from the adductor were taken at slaughter from 99 heifers finished on a CO diet and 58 heifers finished on a FO diet. Strip loins were obtained at fabrication to evaluate fatty acid profiles of LM muscle for all 157 heifers by using gas chromatography fatty acid methyl ester analysis. Composition was analyzed for differences by using the General Linear Model (GLM) procedure in SAS. Differences in fatty acid profile included a greater atherogenic index, greater percentage total MUFA, decreased omega-3 to omega-6 ratio, decreased percentage total PUFA, and decreased percentage omega-3 fatty acids in CO- compared with FO-finished heifers (P<0.05). Fatty acid profiles from intramuscular samples were ranked by the atherogenic index, and 20 heifers with either a high (HAI; n=10) or low (LAI; n=10) atherogenic index were selected for gene expression analysis using real-time PCR (RT-PCR). Gene expression data for the 20 individuals were analyzed as a 2 by 2 factorial arrangement of treatments using the GLM procedure in SAS. There was no significant diet × atherogenic index interaction identified for any gene (P>0.05). Upregulation was observed for PPARγ, fatty acid synthase (FASN), and fatty acid binding protein 4 (FABP4) in FO-finished compared with CO-finished heifers in both atherogenic index categories (P<0.05). Upregulation of diglyceride acyl transferase 2 (DGAT2) was observed in FO-finished heifers with a HAI (P<0.05). Expression of steroyl Co-A desaturase (SCD) was upregulated in CO-finished heifers with a LAI, and downregulated in FO-finished heifers with a HAI (P<0.05). Expression of adiponectin (ADIPOQ) was significantly downregulated in CO-finished heifers with a HAI compared with all other categories (P<0.05). The genes identified in this study which exhibit differential regulation in response to diet or in animals with extreme fatty acid profiles may provide genetic markers for selecting desirable fatty acid profiles in future selection programs.

Thirty-three steer calves were used to determine the effect of sire breed (Angus or Charolais), time of weaning [normal weaned at approximately 210 d of age (NW) or late weaned at approximately 300 d of age (LW)], and muscle type [LM and semitendinosus muscle (STN)] on fatty acid composition. The whole plot consisted of a 2 (sire breed) × 2 (time of weaning) treatment arrangement, and the subplot treatment was muscle type. Body weights were recorded at 28-d intervals to determine animal performance. Muscle biopsies were collected on d 127 and 128 of finishing. All calves were slaughtered on d 138, and carcass data were collected. Angus-sired steers had lighter initial BW (271 vs. 298 kg; P = 0.02), and LW steers were heavier (351 vs. 323 kg; P = 0.03) on d 28, but no other differences in BW were noted. Charolais-sired steers had larger LM area (P = 0.03), reduced yield grades (P = 0.01), less 12th-rib fat (P < 0.01), and less marbling (P < 0.01) than Angus-sired steers. Carcass measures overall indicate Angus-sired steers were fatter. Hot carcass weight was heavier (348 vs. 324 kg; P = 0.04) in LW steers than NW steers. No other differences (P > 0.05) were observed for feedlot performance or carcass characteristics. Total lipids were extracted from muscle biopsies, derivatized to their methyl esters, and analyzed using gas chromatography. The LM had greater SFA (43.94 vs. 35.76%; P < 0.01) and decreased unsaturated fatty acids (UFA; 56.90 vs. 66.19%; P < 0.01) compared with the STN. Percent total MUFA was greater in STN than LM (51.05 vs. 41.98%; P < 0.01). Total SFA, UFA, and MUFA did not differ due to sire breed or time of weaning. Total PUFA differed (P = 0.04) due to a sire breed × time of weaning interaction but did not differ due to muscle type, with greater PUFA in NW Charolais than any other sire breed × time of weaning combination. Observed changes in percent MUFA may be a result of greater Δ(9)-desaturase activity. The calculated desaturase index suggests STN has a greater Δ(9)-desaturase activity than LM, but no differences (P > 0.05) between sire breed or time of weaning were observed. These results indicate that sire breed, time of weaning, and muscle type all affect fatty acid composition in beef. This information provides insight into factors for manipulation of beef fatty acids. More research is needed to identify beef cuts based on fatty acid profile and healthfulness.

The objective of this study was to determine the influence of beef LM nutrient components on beef palatability traits and evaluate the impact of USDA quality grade on beef palatability. Longissimus muscle samples from related Angus cattle (n = 1,737) were obtained and fabricated into steaks for trained sensory panel, Warner-Bratzler shear force (WBSF), lipid oxidation measured by thiobarbituric acid reactive substances (TBARS), fatty acid, and mineral composition analysis. Pearson phenotypic correlations were obtained by the correlation procedure of SAS. Beef palatability data were analyzed by the GLM procedure of SAS with USDA quality grade as the main effect. Specific mineral concentrations did not demonstrate strong correlations with WBSF or sensory traits (r = -0.14 to 0.16). However, minerals appeared to have a stronger relationship with flavor; all minerals evaluated except Ca and Mn were positively correlated (P < 0.05) with beef flavor. Stearic acid (C18:0), C18:2, C20:4, and PUFA were negatively correlated (P < 0.05) with all 3 panelist tenderness traits (r = -0.09 to -0.22) and were positively correlated (P < 0.05) with WBSF (r = 0.09 to 0.15). The MUFA were positively correlated (P < 0.05) with panelist tenderness ratings (r = 0.07 to 0.10) and negatively associated (P < 0.05) with WBSF (r = -0.11). The strongest correlations with juiciness were negative relationships (P < 0.05) with C18:2, C18:3, C20:4, and PUFA (r = -0.08 to -0.20). Correlations with beef flavor were weak, but the strongest was a positive relationship with MUFA (r = 0.13). Quality grade affected (P < 0.05) WBSF, TBARS, and all trained sensory panel traits, except livery/metallic flavor. As quality grade increased, steaks were more tender (P < 0.05), as evidenced by both WBSF and sensory panel tenderness ratings. Prime steaks were rated juiciest (P < 0.05) by panelists, whereas Select and Low Choice were similarly rated below Top Choice for sustained juiciness. Quality grade influenced (P < 0.05) beef flavor, but not in a linear fashion. Although there were significant correlations, these results indicate tenderness, juiciness, and flavor are not strongly influenced by individual nutrient components in beef LM. Furthermore, the positive linear relationships between USDA quality grade and beef palatability traits suggest quality grade is still one of the most valuable tools available to predict beef tenderness.

Testosterone is known to act differentially on skeletal muscle from different regions. Two genes likely to mediate the testosterone effect are IGF-I, an important growth regulator acting in an autocrine and paracrine way, and androgen receptor (AR), as receptor density could account for differential muscle growth. Another muscle-specific gene that may play a role in differential muscle growth is myostatin, a member of the transforming growth factor-beta superfamily, shown to be a negative regulator of skeletal muscle mass. The objective of this study was to quantify and compare the expression of these three genes in two different skeletal muscles in sheep. East Friesian x Dorset-sired ram lambs from Dorset ewes were used in a 2 x 4 factorial experiment. Eighteen sets of twins were assigned to four age groups corresponding to 77, 105, 133, and 161 d of age, and one individual from each set was castrated at birth. Total RNA was extracted from samples of splenius (SP) and semitendinosus muscles collected at the time of slaughter. Insulin-like growth factor-I mRNA was measured using competitive reverse-transcription PCR. Androgen receptor and myostatin mRNA were measured by ribonuclease protection assay with standard curves. Weight of SP was greater than semitendinosus in rams compared with wethers at 105, 133, and 161 d (P = 0.05, P = 0.04, and P = 0.02, respectively). The difference in IGF-I mRNA levels between the two muscles was greater in rams than in wethers at 133 (P = 0.001) and 161 d (P = 0.014), and the difference in AR mRNA levels was greater in rams than in wethers at 105, 133, and 161 d (P = 0.002, P < 0.001, and P < 0.001, respectively), with greater abundance in the SP. No difference was found in myostatin mRNA level between the two muscles in rams and wethers at any age. These results suggest that locally produced IGF-I and the regulation of AR expression are important for sexually dimorphic muscle growth patterns.