0891 Genome-wide efficient mixed-model study for meat quality in Nellore cattle

Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (FPed), the genomic relationship matrix (FGRM), runs of homozygosity (FROH) of different lengths (> 1Mb (genome), between 1 and 2Mb - FROH 1-2; 2-4 Mb FROH 2-4 or > 8 Mb FROH >8) and excess homozygosity (FSNP). The correlation between FPed and FROH was lower when the latter was based on shorter segments (r = 0.15 with FROH 1-2, r = 0.20 with FROH 2-4 and r = 0.28 with FROH 4-8). Meanwhile, the FPed had a moderate correlation withFSNP (r = 0.47) and high correlation withFROH >8 (r = 0.58)and FROH-genome (r = 0.60). The FROH-genome was highly correlated with inbreeding based on FROH>8 (r = 0.93) and FSNP (r = 0.88). The FGRM exhibited a high correlation with FROH-genome (r = 0.55)and FROH >8 (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for FROH 2-4 to 0.37 for FROH 1-2. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traitsranged from 0.12 to 0.51 for FPed, 0.19-0.59 for FGRM, 0.21-0.58 for FROH-genome, and 0.19-0.54 for FSNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for FPed, 0.49-1.97% for FGRM, 0.34-2.2% for FROH-genome, and 0.50-1.62% for FSNP per 1% of inbreeding.The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits. The low correlation observed between FPed and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait.

Understanding the biological factors that influence carcass and meat quality traits in Nellore cattle requires a clear interpretation of molecular complexity and its variations at different levels of expression. Hence, this study aimed to elucidate the biological control of carcass and meat quality traits in Nellore cattle by integrating genome-wide association study (GWAS), transcriptomic, and proteomic data, focusing on identifying key genes and pathways. GWAS analysis was performed using weighted single-step GBLUP with two iterations. RNA-Seq and proteomic analyses were performed on 24 muscle samples from animals with divergent adjusted phenotypic values (12 for high and 12 for low), for meat tenderness, ribeye area (REA), marbling, and backfat thickness (BFT). The phenotypic values were adjusted for the systematic effects of contemporary groups and age. Differential expression analyses indicated that genes associated with the promotion of growth processes, such as FRZB, IGFBP5 and SEMA6C, exhibited overexpression within the group characterized by higher meat tenderness that inhibits cellular cycles and growth (RTN4 and RB1) were downregulated. Proteins related to heat shock, structural functions, and metabolic regulation also affected the higher meat tenderness group. For marbling, actin-binding proteins, microtubule-forming proteins, and structural proteins were downregulated, while genes involved in fatty acid composition and synthesis were upregulated, with the key genes and transcripts CAND1, ACTN4, FGFR2, and NCOR2 identified. For BFT, neuronal genes, transcripts, and proteins associated with actin cytoskeleton organization and microtubule formation were found. Key genes related to ubiquitination, regulation of energy metabolism, and tissue remodeling were also identified. These findings provide a better understanding of genes, transcripts, proteins, and metabolic pathways involved in carcass and meat quality traits in Nellore cattle.

Genome-enabled prediction of meat and carcass traits using Bayesian regression, single-step genomic best linear unbiased prediction and blending methods in Nelore cattle

Investigating potential causal relationships among carcass and meat quality traits using structural equation model 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.

This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner-Bratzler shear force (WBSF), respectively, from the Nellore Brazil Breeding Program. The animals have been genotyped using low-density SNP panel (30 k), and subsequently imputed for arrays with 777 k SNPs. Four Bayesian specifications of genomic regression models, namely Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression methods were compared in terms of prediction accuracy using a five folds cross-validation. Prediction accuracy for REA, BF and RF was all similar using the Bayesian Alphabet models, ranging from 0.75 to 0.95. For WBSF, the predictive ability was higher using Bayes B (0.47) than other methods (0.39 to 0.42). Although the prediction accuracies using Markov blanket of SNP markers were lower than those using all SNPs, for WBSF the relative gain was lower than 13%. With a subset of informative SNPs markers, identified using Markov blanket, probably, is possible to capture a large proportion of the genetic variance for WBSF. The development of low-density and customized arrays using Markov blanket might be cost-effective to perform a genomic selection for this trait, increasing the number of evaluated animals, improving the management decisions based on genomic information and applying genomic selection on a large scale.

Genomic selection for meat quality traits in Nelore cattle

The effects of substituting ~50% of the soybeans in the diet of finishing Nellore steers with either urea (U) and/or slow-release urea (SRU) on the steer performance and meat quality were assessed in two experiments. In the first experiment, 46 Nellore steers in a 104-day experiment (Exp. 1) were fed a Control diet with U or SRU or U+SRU. In Experiment 2 (Exp. 2), digestibility and microbial protein (MCP) synthesis were assessed in four steers by using a 4 × 4 Latin square design with 21-day periods. Four corn-based diets were used in both Exp. 1 and 2. (1) Control (CTL): 0% of non-protein nitrogen (NPN). (2) U: 1.66% of NPN. (3) SRU: 1.8% of NPN. (4) U+SRU: 1.72% of NPN. In Exp. 1, final bodyweight, average daily gain, dry matter intake, Gain to Feed ratio, carcass traits and steer meat quality were not influenced by the experimental diets. In Exp. 2, the apparent digestibility was similar for all diets, and the MCP synthesis was affected by dietary treatments (P = 0.065). The NPN treatments showed 25.5% more (P = 0.03) MCP efficiency (g microbial protein/kg of total digestible nutrient content consumed) than the CTL. We conclude that the partial replacement of SBM with U, SRU or U+SRU will provide similar animal performance without negatively impacting carcass and meat quality and improve the efficiency of microbial protein synthesis in Nellore cattle.

Performance, carcass characteristics and meat quality of Nellore cattle supplemented with supranutritional doses of sodium selenite or selenium-enriched yeast

Com o presente trabalho objetivou-se avaliar as alterações físico-químicas na carne maturada de bovinos Charolês x Nelore. Para isso foram utilizados 38 bovinos inteiros, abatidos com peso médio de 437,08 (± 15,06 kg). Após 24 horas de resfriamento, as meias carcaças direita foram seccionadas na altura da 13ª costela para retirada de uma amostra de 35 cm do músculo longissimus dorsi (contra-filé), em sentido caudal – cranial. As amostras foram fatiadas, embaladas a vácuo e maturadas por zero, sete e quatorze dias. Após o término do período de maturação as carnes foram congeladas para posterior realização das análises de: perda de água por exsudato, força de cisalhamento, perda de água por pressão, pH, cor (valor de L*, a*, b*, croma e tonalidade), análise sensorial, microbiologia e índice de fragmentação miofibrilar. Todas as análises foram realizadas no Laboratório de Análise de Produtos de Origem Animal, da Universidade Estadual de Londrina. O delineamento experimental foi completamente casualizado e os dados foram submetidos à análise de variância e as médias comparadas pelo teste de Tukey a 5%. A Análise microbiológica revelou que todas as bactérias avaliadas tiveram crescimento até o dia sete de maturação, porém diminuíram no tempo 14 dias de maturação. O pH diminuiu com o aumento do período de maturação. A perda de água por pressão e o índice de fragmentação miofibrilar, não foram alterados com o tempo de maturação. A força de cisalhamento e os componentes da cor (L, a*, b*, croma e tonalidade) foram influenciados pelos tempos de maturação, sendo o tempo 14 dias o melhor deles. A análise sensorial só apresentou diferença para maciez. A carne bovina maturada embalada a vácuo não perdeu suas características de carne, entretanto melhorou a maciez.

Current applications and perspectives of genomic selection in Bos indicus (Nellore) cattle

Two complementary methods, namely Multi-Trait Meta-Analysis and Versatile Gene-Based Test for Genome-wide Association Studies (VEGAS), were used to identify putative pleiotropic genes affecting carcass traits in Bos indicus (Nellore) cattle. The genotypic data comprised over 777,000 single-nucleotide polymorphism markers scored in 995 bulls, and the phenotypic data included deregressed breeding values (dEBV) for weight at birth, weight gain at weaning and yearling, as well visual scores taken at weaning and yearling for carcass finishing precocity, conformation and muscling. Both analyses pointed to the pleomorphic adenoma gene 1 (PLAG1) as a major pleiotropic gene. VEGAS analysis revealed 224 additional candidates. From these, 57 participated, together with PLAG1, in a network involved in the modulation of the function and expression of IGF1 (insulin like growth factor 1), IGF2 (insulin like growth factor 2), GH1 (growth hormone 1), IGF1R (insulin like growth factor 1 receptor) and GHR (growth hormone receptor) genes, suggesting that those pleiotropic genes operate as satellite regulators of the growth pathway.

Beef cattle farming faces challenges in optimizing production while meeting demands for meat quality and animal welfare. For the Nelore breed, which represents a significant portion of the Brazilian herd, accurately determining the optimal slaughter time is essential to maximize carcass yield and ensure production efficiency. However, traditional monitoring methods, such as manual weighing and visual inspection, are often imprecise, potentially resulting in slaughter outside the ideal point, compromising meat quality and increasing costs. In this research, an intelligent monitoring system based on computer vision and artificial intelligence was developed to identify the optimal slaughter time of Nelore cattle, reducing waste and improving the quality of the final product. The study employed 3D cameras and deep learning algorithms to monitor animal development in real time. For the cost-benefit analysis, initial investments in hardware and software were considered, as well as operational costs and economic gains from increased precision in slaughter decisions. The results indicated improvements in productivity and meat quality, with a return on investment (ROI) estimated at 268.42% over five years. The implementation of the system proved to be financially viable and sustainable, contributing to waste reduction and better animal welfare. These findings highlight the importance of applying advanced technologies to modernize beef cattle production in Brazil, making it more efficient and competitive.

The quality of meat, with a focus on compounds important for human health, is directly related to the rearing systems in which the animals are produced. The search for a balanced diet, with an emphasis on low cholesterol and adequate levels of vitamins, aligns with society's emphasis on healthy eating, directly correlated with the importance of the offer made by producers for the cattle's diet. The objective was to verify the impact of different rearing systems, in the Eastern Amazon, during the rainy season, on the concentrations of vitamins (A, E) and cholesterol in the muscle (Longissimus lumborum) of crossbred Nelore cattle, castrated, aged between 24 and 36 months, and weighing between 410 and 628 kg. Twelve animals, from each of the three pasture rearing systems: native pasture in flooded areas of Monte Alegre; native pasture in a flooded area of Santa Cruz do Arari; and pasture cultivated on dry land in São Miguel do Guamá, all located in Pará, Brazil-were sampled in commercial slaughterhouses. A notable influence was observed in the concentrations of β-carotene (p < 0.01), α-Tocopherol (p = 0.02), β-Tocopherol (p < 0.01) and the combined sum of β-Tocotrienol and γ-Tocopherol (p < 0.01), as well as δ-Tocopherol (p < 0.01) when contrasting extensive with intensive systems (confinement). However, there was a difference in the content of vitamins and cholesterol between the isolated extensive systems, or between the four rearing systems (p > 0.05). Extensive systems, mainly in Monte Alegre, demonstrated greater amounts of α-Tocopherol and δ-Tocopherol. On the other hand, the intensive system exhibited higher levels of other investigated compounds, clarifying the nutritional variations generated by different livestock rearing practices in the region. Therefore, the results obtained are innovative in the Eastern Amazon, Brazil, in addition to inspiring the development of new research to meet other demands in this field, and achieve additional results, such as determining which meat, coming from cattle in production systems in the country, presents the better compositional quality of vitamins and lipids.

Carcass traits and meat quality of Nellore cattle fed different non-fiber carbohydrates sources associated with crude glycerin