Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality.

Transcript data obtained by RNA-Seq were used to identify differentially expressed alternatively spliced genes in ribeye muscle tissue between Nelore cattle that differed in their ribeye area (REA) or intramuscular fat content (IF). A total of 166 alternatively spliced transcripts from 125 genes were significantly differentially expressed in ribeye muscle between the highest and lowest REA groups (p ≤ 0.05). For animals selected on their IF content, 269 alternatively spliced transcripts from 219 genes were differentially expressed in ribeye muscle between the highest and lowest IF animals. Cassette exons and alternative 3' splice sites were the most frequently found alternatively spliced transcripts for REA and IF content. For both traits, some differentially expressed alternatively spliced transcripts belonged to myosin and myotilin gene families. The hub transcripts were identified for REA (LRRFIP1, RCAN1 and RHOBTB1) and IF (TRIP12, HSPE1 and MAP2K6) have an important role to play in muscle cell degradation, development and motility. In general, transcripts were found for both traits with biological process GO terms that were involved in pathways related to protein ubiquitination, muscle differentiation, lipids and hormonal systems. Our results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the whole cell muscle mRNA of Nelore cattle.

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.

Genome-Wide Association Study of Meat Quality Traits in Nellore Cattle.

The objective of this study was to identify genomic regions that are associated with meat quality traits in the Nellore breed. Nellore steers were finished in feedlots and slaughtered at a commercial slaughterhouse. This analysis included 1,822 phenotypic records of tenderness and 1,873 marbling records. After quality control, 1,630 animals genotyped for tenderness, 1,633 animals genotyped for marbling, and 369,722 SNPs remained. The results are reported as the proportion of variance explained by windows of 150 adjacent SNPs. Only windows with largest effects were considered. The genomic regions were located on chromosomes 5, 15, 16 and 25 for marbling and on chromosomes 5, 7, 10, 14 and 21 for tenderness. These windows explained 3,89% and 3,80% of the additive genetic variance for marbling and tenderness, respectively. The genes associated with the traits are related to growth, muscle development and lipid metabolism. The study of these genes in Nellore cattle is the first step in the identification of causal mutations that will contribute to the genetic evaluation of the breed.

Genomic prediction of breeding values for carcass traits in Nellore cattle.

BACKGROUND: The objective of this study was to evaluate the accuracy of genomic predictions for rib eye area (REA), backfat thickness (BFT), and hot carcass weight (HCW) in Nellore beef cattle from Brazilian commercial herds using different prediction models. METHODS: Phenotypic data from 1756 Nellore steers from ten commercial herds in Brazil were used. Animals were offspring of 294 sires and 1546 dams, reared on pasture, feedlot finished, and slaughtered at approximately 2 years of age. All animals were genotyped using a 777k Illumina Bovine HD SNP chip. Accuracy of genomic predictions of breeding values was evaluated by using a 5-fold cross-validation scheme and considering three models: Bayesian ridge regression (BRR), Bayes C (BC) and Bayesian Lasso (BL), and two types of response variables: traditional estimated breeding value (EBV), and phenotype adjusted for fixed effects (Y*). RESULTS: The prediction accuracies achieved with the BRR model were equal to 0.25 (BFT), 0.33 (HCW) and 0.36 (REA) when EBV was used as response variable, and 0.21 (BFT), 0.37 (HCW) and 0.46 (REA) when using Y*. Results obtained with the BC and BL models were similar. Accuracies increased for traits with a higher heritability, and using Y* instead of EBV as response variable resulted in higher accuracy when heritability was higher. CONCLUSIONS: Our results indicate that the accuracy of genomic prediction of carcass traits in Nellore cattle is moderate to high. Prediction of genomic breeding values from adjusted phenotypes Y* was more accurate than from EBV, especially for highly heritable traits. The three models considered (BRR, BC and BL) led to similar predictive abilities and, thus, either one could be used to implement genomic prediction for carcass traits in Nellore cattle.