Performance, nutrient utilization and meat quality traits in Bos indicus cattle: a meta-analysis examining the effect of residual feed intake.

This meta-analysis aims to investigate the effects of residual feed intake (RFI) phenotype on performance, nutrient utilization and meat quality traits in Zebu (Bos indicus) cattle. Twenty-three peer-reviewed publications with 37 treatment means were included in the dataset. Weighted mean difference analysis compared animals categorized into low RFI (more efficient) versus medium or high RFI (less efficient) groups. Data heterogeneity via meta-regression and subgroup analysis, considering variables such as animal age, sex class, experimental duration, RFI group, dietary concentrate, and estimated metabolizable energy intake were also explored. The predominant genetic group of cattle in the dataset was Nellore (89.18%), followed by Brahman (10.81%). More efficient animals (low RFI phenotype) exhibited less dry matter intake (DMI; P < 0.010) than medium or high RFI animals (-0.95 kg vs. -0.42 kg/d). Cattle dietary crude protein and fiber digestibility were consistent across RFI groups (P > 0.05), while dietary ether extract digestibility tended to decrease (P = 0.050) in low RFI animals (-13.20 g/kg DM). Low RFI animals tended to increased (P = 0.065) ribeye area (REA) compared to the high/medium RFI groups, while carcass backfat thickness (BFT) decreased (P = 0.042) compared to high/medium RFI groups. Moreover, there was an increase (P < 0.001) of 0.22 kg in Warner-Bratzler shear force (WBSF) and a reduction (P < 0.001) in the myofibrillar fragmentation index (MFI) in low RFI animals. Meat color parameters (lightness [L*] and yellowness [b*]) and visual marbling scores were consistent (P > 0.05) across RFI groups. In conclusion, Zebu cattle classified as efficient (low RFI) exhibited reduced DMI, which improves their feed efficiency. However, BFT and meat quality parameters such as tenderness (WBSF and MFI) and redness [a*] were compromised by low RFI phenotype, highlighting the challenge of enhancing feed efficiency and meat quality traits in Zebu cattle.

Environmental Impacts of High-Quality Brazilian Beef Production: A Comparative Life Cycle Assessment of Premium and Super-Premium Beef.

When individual purchasing power increases in society, there is a trend toward a quantitative and qualitative increase in the consumption of products. Considering the magnitude of beef production in Brazil, environmental impacts are important factors for the domestic and international markets. This study assessed a Brazilian feedlot system characterized by high animal welfare standards that produces high-quality beef that is more marbled than that produced in grass-fed systems. We assessed the environmental impacts and compared premium and super-premium beef produced in a feedlot system using a partial Life Cycle Assessment (LCA). Data were collected directly on the property analyzed, considering environmental inputs and outputs and economic factors associated with the production stages of each line (premium versus super-premium). The results show that high-quality beef has, beyond a greater financial cost, an environmental cost, with the super-premium line producing a 286% higher carbon footprint, 297% more eutrophication, and three times higher acidification potential and land use than the premium line. The results of the environmental impacts agree with the results of production costs, reflecting a 282.82% higher production cost in super-premium than in premium animals. Footprints of 5.0323 kg, 4.7746 kg, and 8.8858 kg CO2 eq./kg live weight gain at the feedlot were found in the three lines.

Changes in the Lipid Metabolism of the Longissimus thoracis Muscle in Bulls When Using Different Feeding Strategies during the Growing and Finishing Phases.

The objective was to evaluate the supplementation strategy's effect on beef cattle during the growing phase and two systems during the finishing phase. One hundred and twenty young bulls were randomly divided in a 2 × 2 factorial design to receive either mineral (ad libitum) or protein + energy (3 g/kg body weight (BW)/day) during the growing phase and pasture plus concentrate supplementation (20 g/kg BW/day) or feedlot (25:75% corn silage:concentrate) during the finishing phase. Feedlot-fed bulls had meat (Longissimus thoracis-LT) with a higher content of lipids and saturated and monounsaturated fatty acids and a greater upregulation of stearoyl-CoA desaturase and sterol regulatory element-binding protein-1c than animals that fed on pasture (p < 0.05). On the other hand, pasture-fed bulls had meat with a higher content of α-linoleic acid, linolenic acid, and n6 and a greater n6:n3 ratio compared to the feedlot-fed group (p < 0.05). In addition, meat from pasture-fed bulls during the finishing phase had 17.6% more isocitrate dehydrogenase enzyme concentration than the feedlot group (p = 0.02). Mineral-fed and pasture-finished bulls showed down-regulation of peroxisome proliferator-activated receptor gamma (p < 0.05), while the bulls fed protein + energy and finished in the feedlot had higher carnitine palmitoyltransferase 2 expression (p ≤ 0.013). In conclusion, mineral or protein + energy supplementation in the growing does not affect the fatty acid composition of intramuscular fat of LT muscle. In the finishing phase, feeding bulls in the feedlot upregulates the lipogenic genes and consequently improves the intramuscular fat content in the meat.

Early Weaning Possibly Increases the Activity of Lipogenic and Adipogenic Pathways in Intramuscular Adipose Tissue of Nellore Calves.

This study aimed to evaluate by wide-expression profile analysis how early weaning at 120 days can alter the skeletal muscle metabolism of calves supplemented with a concentrated diet until the growth phase. Longissimus thoracis muscle samples were obtained by biopsy from two groups of calves, early weaned (EW; n = 8) and conventionally weaned (CW; n = 8) at two different times (120 days of age-T1 [EW] and 205 days of age-T2 [CW]). Next, differential gene expression analysis and functional enrichment of metabolic pathways and biological processes were performed. The results showed respectively 658 and 165 differentially expressed genes when T1 and T2 were contrasted in the early weaning group and when early and conventionally weaned groups were compared at T2. The FABP4, SCD1, FASN, LDLR, ADIPOQ, ACACA, PPARD, and ACOX3 genes were prospected in both comparisons described above. Given the key role of these differentially expressed genes in lipid and fatty acid metabolism, the results demonstrate the effect of diet on the modulation of energy metabolism, particularly favoring postnatal adipogenesis and lipogenesis, as well as a consequent trend in obtaining better quality cuts, as long as an environment for the maintenance of these alterations until adulthood is provided.

Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line.

With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (FROH ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10-5 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.

Use of Biometric Images to Predict Body Weight and Hot Carcass Weight of Nellore Cattle.

The objective of this study was to evaluate different methods of predicting body weight (BW) and hot carcass weight (HCW) from biometric measurements obtained through three-dimensional images of Nellore cattle. We collected BW and HCW of 1350 male Nellore cattle (bulls and steers) from four different experiments. Three-dimensional images of each animal were obtained using the Kinect® model 1473 sensor (Microsoft Corporation, Redmond, WA, USA). Models were compared based on root mean square error estimation and concordance correlation coefficient. The predictive quality of the approaches used multiple linear regression (MLR); least absolute shrinkage and selection operator (LASSO); partial least square (PLS), and artificial neutral network (ANN) and was affected not only by the conditions (set) but also by the objective (BW vs. HCW). The most stable for BW was the ANN (Set 1: RMSEP = 19.68; CCC = 0.73; Set 2: RMSEP = 27.22; CCC = 0.66; Set 3: RMSEP = 27.23; CCC = 0.70; Set 4: RMSEP = 33.74; CCC = 0.74), which showed predictive quality regardless of the set analyzed. However, when evaluating predictive quality for HCW, the models obtained by LASSO and PLS showed greater quality over the different sets. Overall, the use of three-dimensional images was able to predict BW and HCW in Nellore cattle.

Effects of molasses supplementation on animal performance and carcass parameters of beef cattle: a meta-analysis.

Molasses must be one of the most used foods in the diet of ruminant animals; however, there is no consensus on the effect of including molasses on carcass parameters. In this context, the objective was to evaluate the effect of including molasses in the diet of feedlot cattle on performance and carcass parameters. Thirteen peer-reviewed publications with 45 treatment means were included in the dataset. The effect of molasses in beef cattle diets was evaluated by examining the weighted mean differences (WMD) between molasses treatment (diet with molasses) and control diet (diet without molasses). Heterogeneity was explored by meta-regression and subgroup analysis using genetic type and experimental period, molasses in diet (g/kg dry matter (DM)), molasses type, concentrate in diet (g/kg DM), and forage type. The inclusion of molasses in the diet increased dry matter digestibility, but reduced NDF digestibility, carcass weight, subcutaneous, and visceral fat. The main sources of variation for the responses with molasses inclusion on intake, digestibility, performance, and carcass parameters were the level of molasses inclusion and the experimental period. In general context, the inclusion of molasses in the diet between 100 to 150 g/kg of DM did not affect performance and carcass parameters. However, the inclusion of molasses above 200 g/kg reduces the average daily gain and carcass weight.

Post-mortem muscle proteome of crossbred bulls and steers: Relationships with carcass and meat quality.

This study investigated the skeletal muscle proteome of crossbred bulls and steers with the aim of explaining the differences in carcass and meat quality traits. Therefore, 640 post-weaning Angus-Nellore calves were fed a high-energy diet for a period of 180 days. In the feedlot trial, comparisons of steers (n = 320) and bulls (n = 320) showed lower (P < 0.01) average daily gain (1.38 vs. 1.60 ± 0.05 kg/d), final body weight (547.4 vs. 585.1 ± 9.3 kg), which resulted in lower hot carcass weight (298.4 vs. 333.7 ± 7.7 kg) and ribeye area (68.6 vs. 81.0 ± 2.56 cm2). Steers had higher (P < 0.01) carcass fatness, meat color parameters (L*, a*, b*, chroma (C*), hue (h°)) and lower ultimate pH. Moreover, lower (P < 0.01) Warner-Bratzler shear force (WBSF) were observed in steers compared to bulls (WBSF = 3.68 vs. 4.97 ± 0.08 kg; and 3.19 vs. 4.08 ± 0.08 kg). The proteomic approach using two-dimensional electrophoresis, mass spectrometry and bioinformatics procedures revealed several differentially expressed proteins between steers and bulls (P < 0.05). Interconnected pathways and substantial changes were revealed in biological processes, molecular functions, and cellular components between the post-mortem muscle proteomes of the compared animals. Steers had increased (P < 0.05) abundance of proteins related to energy metabolism (CKM, ALDOA, and GAPDH), and bulls had greater abundance of proteins associated with catabolic (glycolysis) processes (PGM1); oxidative stress (HSP60, HSPA8 and GSTP1); and muscle structure and contraction (TNNI2 and TNNT3). The better carcass (fatness and marbling degree) and meat quality traits (tenderness and color parameters) of steers were associated with higher abundance of key proteins of energy metabolism and lower abundance of enzymes related to catabolic processes, oxidative stress, and proteins of muscle contraction SIGNIFICANCE: Sexual condition of cattle is known to be an important factor affecting animal performances and growth as well as the carcass and meat quality traits. The investigation of skeletal muscle proteome help a better understanding of the origin of the differences in quality traits between bulls and steers. The inferior meat quality of bulls was found to be due to the greater expression of proteins associated with primary and catabolic processes, oxidative stress, and muscle contraction. Steers had greater expression of proteins, from which several are known biomarkers of beef quality (mainly tenderness).

Bos indicus Carcasses Suspended by the Pelvic Bone Require a Shorter Aging Time to Meet Consumer Expectations Regarding Meat Quality.

This study evaluated the effects of hanging the carcass by the Achilles tendon (AS) versus pelvic suspension (PS) on meat quality traits. Bos indicus carcasses of two distinct biological types/sex categories comprised 10 young Brangus heifers and 10 Nellore bulls which were finished in a feedlot. Half-carcasses of each biological type/sex category were randomly hung using Achilles suspension (n = 20, AS) or pelvic suspension (n = 20, PS) for 48 h. At boning, longissimus samples were collected for evaluation by untrained consumers for tenderness, liking of flavor, juiciness and overall acceptability, after aging for 5 or 15 days. Objective samples were also tested for shear force (SF), Minolta meat colour, ultimate pH, cooking loss (CL) and purge loss (PL). There was a positive effect (p < 0.01) of PS on the sensory tenderness of Nellore bulls and Brangus heifers aged for 5 days compared to the AS method. At 15 days of aging, difference in sensory tenderness was observed (p < 0.05) in either group. Additionally, an interaction occurred between the suspension method and the aging of Nellore beef (p < 0.05) on liking of flavor, juiciness and overall acceptance, while the same effects were not observed for Brangus beef (p > 0.05). Nellore carcasses submitted to PS tended (p = 0.06) to produce more tender meat than those submitted to AS (SF = 44.62 ± 6.96 vs. 50.41 ± 8.04 N), and lower CL (p < 0.05) were found (27.7 vs. 30.9%). Carcass-suspension methods did not influence meat color, pH or PL in either group (p > 0.05). The PS contributes to improve the quality of Bos indicus bulls loins; in addition, this method allows a reduction in the aging time from 15 to 5 days, and it can be used to supply meat consumer markets which accept a certain level of eating quality.

Effect of Cow-Calf Supplementation on Gene Expression, Processes, and Pathways Related to Adipogenesis and Lipogenesis in Longissimus thoracis Muscle of F1 Angus × Nellore Cattle at Weaning.

The aim of this study was to identify differentially expressed genes, biological processes, and metabolic pathways related to adipogenesis and lipogenesis in calves receiving different diets during the cow-calf phase. Forty-eight uncastrated F1 Angus × Nellore males were randomly assigned to two treatments from thirty days of age to weaning: no creep feeding (G1) or creep feeding (G2). The creep feed offered contained ground corn (44.8%), soybean meal (40.4%), and mineral core (14.8%), with 22% crude protein and 65% total digestible nutrients in dry matter. After weaning, the animals were feedlot finished for 180 days and fed a single diet containing 12.6% forage and 87.4% corn-based concentrate. Longissimus thoracis muscle samples were collected by biopsy at weaning for transcriptome analysis and at slaughter for the measurement of intramuscular fat content (IMF) and marbling score (MS). Animals of G2 had 17.2% and 14.0% higher IMF and MS, respectively (p < 0.05). We identified 947 differentially expressed genes (log2 fold change 0.5, FDR 5%); of these, 504 were upregulated and 443 were downregulated in G2. Part of the genes upregulated in G2 were related to PPAR signaling (PPARA, SLC27A1, FABP3, and DBI), unsaturated fatty acid synthesis (FADS1, FADS2, SCD, and SCD5), and fatty acid metabolism (FASN, FADS1, FADS2, SCD, and SCD5). Regarding biological processes, the genes upregulated in G2 were related to cholesterol biosynthesis (EBP, CYP51A1, DHCR24, and LSS), unsaturated fatty acid biosynthesis (FADS2, SCD, SCD5, and FADS1), and insulin sensitivity (INSIG1 and LPIN2). Cow-calf supplementation G2 positively affected energy metabolism and lipid biosynthesis, and thus favored the deposition of marbling fat during the postweaning period, which was shown here in an unprecedented way, by analyzing the transcriptome, genes, pathways, and enriched processes due to the use of creep feeding.

Proteomics Unveils Post-Mortem Changes in Beef Muscle Proteins and Provides Insight into Variations in Meat Quality Traits of Crossbred Young Steers and Heifers Raised in Feedlot.

Proteomics has been widely used to study muscle biology and meat quality traits from different species including beef. Beef proteomics studies allow a better understanding of the biological processes related to meat quality trait determination. This study aimed to decipher by means of two-dimensional electrophoresis (2D-PAGE), mass spectrometry and bioinformatics the changes in post-mortem muscle with a focus on proteins differentially expressed in the Longissimus thoracis (LT) muscle of immunocastrated young heifers and steers. Carcass traits, chemical composition, pH, instrumental color (L*, a*, b*), cooking loss and Warner-Bratzler shear force (WBSF) of meat from F1 Montana-Nellore cattle were also evaluated. Backfat thickness (BFT) and intramuscular fat content (IMF) were 46.8% and 63.6% higher in heifers (p < 0.05), respectively, while evaporation losses (EL) were 10.22% lower compared to steers. No differences (p > 0.05) were observed for tenderness evaluated by WBSF (3, 10, and 17 days post-mortem), pH, and color traits (L*, a* and b*) between the experimental groups. The study revealed several proteins to be differentially expressed proteins in heifers compared steers (p < 0.05). In heifers, proteins involved in nutrient transport (TF, ALB, and MB), energy metabolism (ALDOA, GAPDH, and PKM), and oxidative stress and response to stress (HSPA8 and CA3) were associated with a greater BFT and IMF deposition. The higher expression of these proteins indicated greater oxidative capacity and lower glycolytic activity in the LT muscle of heifers. In steers, there was greater abundance of protein expression related to muscle contraction and proteins of structure (ACTA1, TPM2 and TNNT3), energy metabolism (ENO1, ENO3, PYGM, PGM1 and TPI1) and ATP metabolism (ATP5F1B, PEBP1 and AK1), indicating greater glycogenolysis in LT muscle, suggesting a shift in the glycolytic/oxidative fibers of steers.

Assessment of corn wet distillers grains fed to crossbred bulls on feeding behavior, rumen morphology, liver abscesses and blood parameters.

Corn ethanol production has been growing in Brazil in the last ten years, generating by-products to feedlot diets. This study evaluates the effects of the inclusion of low-fat corn wet distillers grains (LF-WDG) on feeding behavior, ruminal health, liver abscesses and blood parameters of F1 Angus-Nellore bulls feedlot finished. Our hypothesis is that evaluation of data from feeding behavior, rumen and liver health would help to explain animal performance. In this trail, one-hundred animals were fed for 129 days with diets containing amounts of 0 (control), 15, 30 and 45% of LF-WDG replacing corn grain and soybean meal. Evaluations of fluctuation of dry matter intake (DMI) were carried out. Additionally, feeding behavior data were assessed by monitoring (24-h period) the feeding, rumination, time spent eating (TSE), and time expended on other activities (resting and number of meals per day). Blood variables such as pH, bicarbonate, total CO2 content, and base excess in extracellular fluid (Beecf) were determined. After slaughter, rumen epithelium was classified according to the incidence of lesions (rumenitis) and abnormalities (papillae clumped), and samples were collected for morphology and histology evaluations. Moreover, livers were scored for severity of abscesses as follow: as unabscessed (0), one or two small abscesses (A-), two to four small active abscesses (A) or one or more large, active abscesses (A+). The DMI (kg/day) differed (P = 0.03) among treatments and there is a tendency of 15 and 30 LF-WDG (% DM) had lower %DMI fluctuation compared to 0 or 45%. The TSE increased linearly (P < 0.01) as the amounts of inclusion of LF-WDG increased. Moreover, neutral detergent fiber (NDF) intake, NDF consumption rate and NDF rumination efficiency increased linearly (P < 0.01) in response to LF-WDG feeding. The incidence of rumenitis tended (P = 0.08) to be greater at 45% LF-WDG, while keratin thickness decreased linearly in bulls fed LF-WDG (P < 0.01). The severity of liver abscesses (score A+) increased linearly (P = 0.02). Regarding blood parameters, only Beecf decreased linearly (P < 0.01) in response to LF-WDG feeding. Therefore, the hypothesis of the current study was confirmed. We previous reported that F1 Angus-Nellore bulls fed LF-WDG show greater weight gain (1.94 ± 0.09 kg/day) and final body weight (620 ± 18.8 kg) when compare to control (1.8 ± 0.09 kg/day and 602 ± 18.8 kg, respectively). Here, we conclude that inclusion of 15 to 30% LF-WDG in feedlot diets improved feeding behavior without impairing ruminal health and blood parameters, driving performance and weigh gain of crossbred bulls. However, bulls fed 45% LF-WDG had greater severity of liver abscesses.

Does distillers' grains supplementation affect beef cattle performance, carcass characteristics, and meat quality? A meta-analysis study.

This study evaluated, through meta-analysis, the effect of distillers' grains (DG) supplementation to beef cattle on their performance, carcass parameters, and meat fatty acid profile. Eighty-one peer-reviewed publications with 439 treatments means were included in the data set. The effects of DG supplementation to beef cattle were evaluated using weighted mean differences (WMD) between the control group (diets with no DG) and DG group (diets with DG). Heterogeneity was explored by meta-regression and subgroup analysis using genetic type, treatment period, DG type, amount of DG in diet (g DG/kg DM), sulfur in diet (g S/kg DM), ether extract in diet (g EE/kg DM), feed systems (pasture or total mixed ration), and concentrate level in the diet (g/kg DM). Meat fatty acid profile was more affected when DG was fed to crossbreed animals. In Angus animals, DG inclusion to the diets had little effect on meat fatty acid profile whereas, a pronounced reduction was reported in meat omega-6/omega-3 ratio. In response to DG inclusion to the diets, an increase in diet sulfur content up to 6.0 g/kg and ether extract content up to 110 g/kg had no adverse effects on performance, carcass parameters, and meat physicochemical characteristics. Distillers' grains inclusions in amounts between 500 and 600 g DG/kg provided the greatest responses when evaluating carcass parameters and meat fatty acid profile. Increased CLA c9 t11, linolenic acid, and total PUFA and reduced myristic acid concentration in meat were reported when animals were fed diets containing DG.

Meat Quality and Muscle Tissue Proteome of Crossbred Bulls Finished under Feedlot Using Wet Distiller Grains By-Product.

Wet distiller grains (WDG) are a corn by-product rich in protein and fiber that can be used in feedlot diets. This study evaluated F1 Angus-Nellore bulls fed on a control diet vs. WDG (n = 25/treatment). After a period of 129 days on these feeds, the animals were slaughtered and Longissimusthoracis samples were collected for both a meat quality evaluation and gel-based proteomic analyses. A greater ribeye area (99.47 cm²) and higher carcass weight (333.6 kg) (p < 0.05) were observed in the WDG-finished cattle compared to the control (80.7 cm²; 306.3 kg). Furthermore, there were differences (p < 0.05) in the intramuscular fat between the WDG and control animals (IMF = 2.77 vs. 4.19%), which led to a significant decrease (p < 0.05) in saturated fatty acids (FA). However, no differences (p > 0.10) were observed in terms of tenderness, evaluated using Warner-Bratzler shear force (WBSF). The proteomic and bioinformatic analyses revealed substantial changes in the biological processes, molecular functions, and cellular components of the WDG-finished cattle compared to the control. Proteins related to a myriad of interconnected pathways, such as contractile and structural pathways, energy metabolism, oxidative stress and cell redox homeostasis, and transport and signaling. In this experiment, the use of WDG supplementation influenced the protein expression of several proteins, some of which are known biomarkers of beef quality (tenderness and color), as well as the protein-protein interactions that can act as the origins of increases in muscle growth and reductions in IMF deposition. However, despite the effects on the proteome, the tenderness, evaluated by WBSF, and fatty acid profile were not compromised by WDG supplementation.

Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping.

BACKGROUND: The detection of signatures of selection in genomic regions provides insights into the evolutionary process, enabling discoveries regarding complex phenotypic traits. In this research, we focused on identifying genomic regions affected by different selection pressures, mainly highlighting the recent positive selection, as well as understanding the candidate genes and functional pathways associated with the signatures of selection in the Mangalarga Marchador genome. Besides, we seek to direct the discussion about genes and traits of importance in this breed, especially traits related to the type and quality of gait, temperament, conformation, and locomotor system. RESULTS: Three different methods were used to search for signals of selection: Tajima's D (TD), the integrated haplotype score (iHS), and runs of homozygosity (ROH). The samples were composed of males (n = 62) and females (n = 130) that were initially chosen considering well-defined phenotypes for gait: picada (n = 86) and batida (n = 106). All horses were genotyped using a 670 k Axiom® Equine Genotyping Array​ (Axiom MNEC670). In total, 27, 104 (chosen), and 38 candidate genes were observed within the signatures of selection identified in TD, iHS, and ROH analyses, respectively. The genes are acting in essential biological processes. The enrichment analysis highlighted the following functions: anterior/posterior pattern for the set of genes (GLI3, HOXC9, HOXC6, HOXC5, HOXC4, HOXC13, HOXC11, and HOXC10); limb morphogenesis, skeletal system, proximal/distal pattern formation, JUN kinase activity (CCL19 and MAP3K6); and muscle stretch response (MAPK14). Other candidate genes were associated with energy metabolism, bronchodilator response, NADH regeneration, reproduction, keratinization, and the immunological system. CONCLUSIONS: Our findings revealed evidence of signatures of selection in the MM breed that encompass genes acting on athletic performance, limb development, and energy to muscle activity, with the particular involvement of the HOX family genes. The genome of MM is marked by recent positive selection. However, Tajima's D and iHS results point also to the presence of balancing selection in specific regions of the genome.

Testing different devices to assess the meat tenderness: preliminary results.

Meat tenderness is one of the principal attribute associated with consumer preferences. This study describes tenderness measurements at three final endpoint cooking temperatures (51, 61 and 71 °C) using a mechanical Warner-Bratzler (WBSF) as the standard instrument versus digital texturometer (CT3) and penetrometer (FHT) devices. Thirty-six cross-breed heifers (Bos indicus) with initial body weight 330 ± 40 kg, 20-24 months of age, were slaughtered after 100 days on feed. Subsequently, 48 h post-slaughter, Longissimus thoracis (LT) samples were collected between the 10th and 13th ribs. Six LT samples from each animal were used to evaluate tenderness and cooking losses through analysis of variance and regression analyses. No interaction between device × temperature was observed (p = 0.57). Shear force values were greater (p < 0.05) as endpoint cooking increased and the results from CT3 were close to the ones using the WBSF (R2 = 0.76; p < 0.0001). In conclusion, the digital CT3 can replace the mechanical WBSF because these devices were strongly correlated (r = 0.85; p < 0.00). However, the results from FHT were underestimated (R2 = 0.19; p < 0.006), indicating that FHT device should not be used for the evaluation of meat tenderness.

Comparison of Dental Carcass Maturity in Non-Castrated Male F1 Angus-Nellore Cattle Finished in Feedlot.

Dental classification of carcasses is used as a parameter of cattle maturity at slaughter, and it can influence carcass and meat quality traits. Brazilian beef-packing companies use the number of permanent incisor (PI) teeth as a parameter for bonus and certification of carcasses with superior quality. However, when non-castrated male such as F1 Angus-Nellore (Bos taurus×Bos indicus) are slaughtered, only animals without PI teeth are subsidized by the breed association. We evaluated these animals finished in feedlot for 180 days with zero versus two PI teeth on the carcass and meat quality traits. At the time of slaughter, 88 carcasses were selected, forming two treatments according to dental carcass maturity (0 versus 2 PI teeth; 44 animals per category). It was demonstrated that the number of PI teeth (0 versus 2 PI) did not influence (p>0.05) carcass (weights, yield, cooling loss, ribeye area and the backfat thickness) and meat quality traits (Longissimus thoracis chemical composition, color, cooking losses, shear force and pH). Thus, dental carcass maturity (zero versus two PI teeth) does not influence non-castrated male F1 Angus-Nellore finished in feedlot for 180 days. This is the first study to demonstrate that carcasses of non-castrated male F1 Angus-Nellore with two PI teeth should be subsidized in a similar way to those with zero PI teeth. Moreover, Brazilian beef-packing companies could produce heavier and leaner carcasses of acceptable quality though the use of crossbred cattle such as non-castrated F1 Angus Nellore.

Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed.

With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array-670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (FROH ) = 0.16; pedigree-based (FPED ) = 0.008; and a method based on excess homozygosity (FHOM ) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0-2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0-2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg2+ /Mn2+ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.

Application of the principal component analysis, cluster analysis, and partial least square regression on crossbreed Angus-Nellore bulls feedlot finished.

Principal component analysis (PCA) and the non-hierarchical clustering analysis (K-means) were used to characterize the most important variables from carcass and meat quality traits of crossbred cattle. Additionally, partial least square (PLS) regression analysis was applied between the carcass measurements and meat quality traits on the classes defined by the cluster analysis. Ninety-seven non-castrated F1 Angus-Nellore bulls feedlot finished were used. After slaughter, hot carcass weight, carcass yield, cold carcass weight, carcass weight losses, pH, and backfat thickness (BFT) were measured. Subsequently, samples of the longissimus thoracis were collected to analyze shear force (SF), cooking loss (CL), meat color (L*, chroma, and hue), intramuscular fat, protein, collagen, moisture, and ashes. Principal component 1 (PC1) was correlated with colorimetric variables, while PC2 was correlated with carcass weights. Afterwards, three clusters (k = 3) were formed and projected in the gradient defined by PC1 and PC2 and allowed distinguishing groups with divergent values for collagen, protein, moisture, CL, SF, and BFT. Animals from high chroma group presented meat with more attractive colors and tenderness (SF = 1.97 to 4.84 kg). Subsequently, the PLS regression on the three chroma groups revealed a good fitness and the coefficients are used to predict the chroma variable from the explanatory variables, which may have practical importance in attempts to predict meat color from carcass and meat quality traits. Thus, PCA, K-means, and PLS regression confirmed the relationship between meat color and tenderness.

The inclusion of de-oiled wet distillers grains in feedlot diets reduces the expression of lipogenic genes and fat content in Longissimus muscle from F1 Angus-Nellore cattle.

The inclusion of agro-industry by-products originated from corn ethanol production has increased in animal nutrition in Brazil, reducing formulation costs. In the literature, there is no consensus on how the high inclusion of de-oiled wet distillers grains can affect beef quality and the expression of lipogenic genes in Longissimus muscle. The aim of this study was to evaluate the effects of WDG in the diet of F1 Angus-Nellore cattle on meat quality characteristics, chemical composition and expression of genes involved in lipid metabolism. A hundred F1 Angus-Nellore bulls, with average initial body weight (BW) of 369.5 ± 49 kg were used. The experiment was carried out in a randomized block design, and the animals were divided into two blocks (light and heavy) according to the initial body weight. The animals were fed diets containing levels of 0 (control), 15, 30 and 45% of WDG replacing dry corn and soybean meal. After 129 days of feedlot, the animals were slaughtered and samples of the longissimus thoracis (LT) muscle were collected for quality analyzes such as shear force (3, 10 and 17 aging days), color (luminosity, red, Chroma and Hue), cooking losses, pH and chemical composition (moisture, protein, lipids and ash contents). In addition, the expression of the PPARα, PPARγ, SREBP-1c, SCD1, LPL, FABP4, FASN, ACOX, CPT2, GPX1 and ACACA genes was investigated in the LT muscle by real-time reverse transcription polymerase chain reaction (RT-PCR). Data were analyzed using polynomial contrasts (linear, quadratic and control vs. WDG). There was no interaction (P > 0.05) between aging times and the inclusion of WDG in the diets on the meat quality (pH, cooking losses, coloration and tenderness). However, diets with increasing levels of WDG caused a linear reduction (P = 0.01) in the intramuscular fat of LT. The lipogenic genes SCD1, PPARγ, FASN and CPT2 were less expressed (P < 0.05) in response to the inclusion of WDG. These results suggest that the inclusion of WDG reduced the expression of lipogenic genes and consequently the marbling of LT muscle without affecting tenderness (shear force) and meat color traits.