Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies

Maternal nutrition has the ability of influence critical processes in fetal life, including muscle development. Also, in this period, epigenetic sensitivity to external stimuli is higher and produces long-lasting effects. Thus, the aim of this study was to investigate epigenetic mechanisms, including the identification and characterization of long non-coding RNA (lncRNA) from animals that had undergone different strategies of prenatal supplementation. A group of Nellore cows (n = 126) were separated into three nutritional plans: NP (control)-Not Programmed, without protein-energy supplementation; PP-Partially Programmed, protein-energy supplementation in the final third of pregnancy; and CP-Complete Programming, protein-energy supplementation during the full period of gestation. A total of 63 male offspring were used in this study, of which 15 (5 per treatment) had Longissimus thoracis muscle at 15 (biopsy) and 22 months (slaughter). Biopsy samples were subjected to RNA extraction and sequencing. Differential expression (DE) of remodeling factors and chromatin-modifying enzyme genes were performed. For the identification and characterization of lncRNA, a series of size filters and protein coding potential tests were performed. The lncRNAs identified had their differential expression and regulatory potential tested. Regarding DE of epigenetic mechanisms, no differentially expressed gene was found (p > 0.1). Identification of potential lncRNA was successful, identifying 1823 transcripts at 15 months and 1533 at 22 months. Among these, four were considered differentially expressed between treatments at 15 months and 6 were differentially expressed at 22 months. Yet, when testing regulatory potential, 13 lncRNAs were considered key regulators in the PP group, and 17 in the CP group. PP group lncRNAs possibly regulate fat-cell differentiation, in utero embryonic development, and transforming growth factor beta receptor, whereas lncRNA in the CP group regulates in utero embryonic development, fat-cell differentiation and vasculogenesis. Maternal nutrition had no effect on differential expression of epigenetic mechanisms; however, it seems to impair lncRNA regulation of epigenetics.

Metabolomics Changes in Meat and Subcutaneous Fat of Male Cattle Submitted to Fetal Programming

This study investigated changes in meat and subcutaneous fat metabolomes and possible metabolic pathways related to prenatal nutrition in beef cattle. For this purpose, 18 Nellore bulls were used for meat sampling and 15 for fat sampling. The nutritional treatments during the gestation were: NP-not programmed or control, without protein-energy supplementation; PP-partially programmed, with protein-energy supplementation (0.3% of body weight (BW)) only in the final third of pregnancy; and FP-full programming, with protein-energy supplementation (0.3% of BW) during the entire pregnancy. The meat and fat samples were collected individually 24 h after slaughter, and the metabolites were extracted using a combination of chemical reagents and mechanical processes and subsequently quantified using liquid chromatography or flow injection coupled to mass spectrometry. The data obtained were submitted to principal component analysis (PCA), analysis of variance (ANOVA), and functional enrichment analysis, with a significance level of 5%. The PCA showed an overlap between the treatments for both meat and fat. In meat, 25 metabolites were statistically different between treatments (p ≤ 0.05), belonging to four classes (glycerophospholipids, amino acids, sphingolipids, and biogenic amine). In fat, 10 significant metabolites (p ≤ 0.05) were obtained in two classes (phosphatidylcholine and lysophosphatidylcholine). The functional enrichment analysis showed alterations in the aminoacyl-tRNA pathway in meat (p = 0.030); however, there was no pathway enriched for fat. Fetal programming influenced the meat and fat metabolomes and the aminoacyl-tRNA metabolic pathway, which is an important candidate for the biological process linked to meat quality and related to fetal programming in beef cattle.

Fetal Programming and Its Effects on Meat Quality of Nellore Bulls

This work aimed to evaluate the effects of prenatal nutritional stimulation at different pregnancy stages on carcass traits and meat quality in bovine progeny. For this purpose, 63 Nellore bulls, born from cows submitted to three nutritional plans, were used: not programmed (NP), which did not receive protein supplementation; partially programmed (PP), which had protein-energy supplementation (0.3% of mean body weight of each batch) only in the final third of pregnancy; and full programming (FP), which received supplementation (0.3% of mean body weight of each batch) throughout pregnancy. The averages of parameters were submitted to the ANOVA, and the supplementation periods, which were different when p value < 0.05, were compared. Carcass weights and rib eye area (REA) did not differ between treatments (p > 0.05), but subcutaneous fat thickness (SFT) showed a tendency (p = 0.08) between groups. For lipids and marbling, no differences were found (p > 0.05). In the analyses of maturation time and shelf life, no difference was observed between treatments. However, there was a tendency between treatments at 14 days of maturation time for cooking loss (CL) (p = 0.08). Treatments did not affect shear force in the progenies (p > 0.05). Fetal programming had no effect on the meat quality of Nellore bulls.

Evaluation of Maternal Nutrition Effects in the Lifelong Performance of Male Beef Cattle Offspring

This study aimed to evaluate the effects of different prenatal nutrition treatments on pregnant cows and their progeny. One hundred and twenty-six pregnant Nellore cows (455.3 ± 8.1 kg) were allocated in three different nutritional treatments during pregnancy: NP-control, PP-protein-energy supplementation in the last 3 months of pregnancy, and FP-the same supplementation throughout pregnancy. After parturition, all cows and calves received the same environmental and nutrition condition. The body condition score (BCS), body weight (BW), ribeye area (REA), backfat thickness (BFT), and rumpfat thickness (RFT) were collected on four occasions during pregnancy in the cows and from birth to finishing in calves. All data (cows and calves) were submitted to an analysis of variance (p < 0.05) using a linear model (MIXED procedure; SAS software). The BW, RFT, and BCS from the cows showed significant differences in the middle third of pregnancy and pre-delivery and RFT postpartum (p < 0.05). For the offspring, the weaning weight showed a tendency (NP lighter than others). In terms of gain, the PP group tended to be higher in RFT at calving (p = 0.06), in REA at finishing (p = 0.09), and in ADG in the same period (p = 0.09). The prenatal nutrition strategies had little or no effect on the beef cattle postnatal performance.

Impacts of Different Prenatal Supplementation Strategies on the Plasma Metabolome of Bulls in the Rearing and Finishing Phase

This study investigated the effects of maternal nutrition on the plasma metabolome of Nellore bulls in the rearing and finishing phases, and metabolic differences between these phases. For this study, three nutritional approaches were used in 126 cows during pregnancy: NP-(control) mineral supplementation; PP-protein-energy supplementation in the final third; and FP-protein-energy supplementation during the entire pregnancy. We collected blood samples from male offspring in the rearing (450 ± 28 days old) and finishing phases (660 ± 28 days old). The blood was processed, and from plasma samples, we performed the targeted metabolome analysis (AbsoluteIDQ® p180 Kit). Multiple linear regression, principal component analysis (PCA), repeated measures analysis over time, and an enrichment analysis were performed. PCA showed an overlap of treatments and time clusters in the analyses. We identified significant metabolites among the treatments (rearing phase = six metabolites; finishing phase = three metabolites) and over time (21 metabolites). No significant metabolic pathways were found in the finishing phase, however, we found significant pathways in the rearing phase (Arginine biosynthesis and Histidine metabolism). Thus, prenatal nutrition impacted on plasma metabolome of bulls during the rearing and finishing phase and the different production stages showed an effect on the metabolic levels of bulls.

Effects of early weaning on the reproductive performance of suckled Nelore cows in the subsequent breeding season

This study aimed to evaluate the effects of early weaning (EW) on body composition, hormone concentrations and metabolites, and reproductive performance of Nelore cows in the subsequent breeding season (BS). Suckled cows that became pregnant by timed-AI (TAI) in the 2020-BS were exposed in 2021 to early weaning at 150 d (27 primiparous [PRI] and 74 multiparous [MUL]) or conventional weaning (CW) at 240 d postpartum (30 PRI and 77 MUL). Body weight (BW) and body condition score (BCS) were determined at 2020-BS, EW, CW, prepartum, and 2021-BS. Blood samples were collected at EW, CW, prepartum (54.75 ± 0.56 d prepartum), and 2021-TAI and assayed for insulin-like growth factor-1 (IGF-I), non-esterified fatty acid (NEFA), and β-hydroxybutyrate (BHB) concentrations. In 2021-BS, cows were exposed to a P4/E2-based protocol for TAI at day 0 (D0), and a second TAI was performed at D22 in females detected with luteolysis (D20) by Doppler ultrasound. The presence of corpus luteum (CL) on D10, estrous expression, and dominant follicle (DF) diameter, and blood perfusion (BP) on D2 and D0 were determined. Data were analyzed by ANOVA or logistic regression of SAS as a 2 × 2 factorial with main factors of parity (PRI or MUL) and weaning strategy (EW or CW). An interaction of parity and weaning strategy was not observed (P > 0.1), but the weight (kg) and BCS were greater (P < 0.05) in MUL cows at the five timepoints, and EW cows were heavier than CW at the moment of CW (541 vs. 493 kg; and 5.3 vs. 4.3), prepartum (551 vs. 506 kg; and 5.2 vs. 4.4) and 2021-BS (475 vs. 450 kg; and 4.5 vs. 3.7). Plasma urea concentration at 2021-BS was greater (P = 0.01) for PRI than for MUL. A parity-by-time interaction was observed (P ≤ 0.05) for concentrations of IGF-I, NEFA, and BHB. PRI cows had greater (P ≤ 0.05) concentrations of IGF-I at EW and greater (P ≤ 0.05) prepartum concentrations of NEFA and BHB than MUL cows. The proportion of cows with CL at D10 was not affected (P > 0.1) by weaning but was greater (P < 0.05) in MUL than in PRI cows (40.4 vs. 15.7%). The diameter of DF and proportion of BP on D0 were greater (P < 0.05) in EW cows than in CW cows. The pregnancy rate (P/AI, %) at the first TAI was greater (P < 0.05) in EW cows (60% vs. 45%), whereas no difference (P > 0.1) was observed at the second TAI. Cumulative P/AI (first and second TAIs) was greater (P < 0.05) in EW cows (81% vs. 63%). In conclusion, weaning at 150 d in Nelore cattle is a strategy to successfully recover the parous cow's body condition and to improve pregnancy success in the next BS, regardless of the cow's parity order.

High body energy reserve influences extracellular vesicles miRNA contents within the ovarian follicle

Aiming to evaluate the effects of increased body energy reserve (BER) in Nellore cows' reproductive efficiency, cows were fed with different nutritional plans to obtain animals with high BER (HBER; Ad libitum diet) and moderate BER (MBER: cows fed 70% of HBER group ingestion). To evaluate the BER, cows were weekly weighted and evaluated for subcutaneous fat thickness and insulin serum concentration along the experimental period. At the end of the experimental period, animals were submitted to estrous synchronization and artificial insemination. Animals were slaughtered approximately 120 h after ovulation induction and the reproductive tracts were collected for embryo recovery and samples collection. Cumulus-oocyte-complexes (COC) and follicular fluid were collected from 3-6 mm in diameter ovarian follicles to perform miRNA analysis of cumulus cells (CC) and extracellular vesicles from follicular fluid (EV FF). As expected, differences were observed among MBER and HBER groups for body weight, fat thickness, and insulin serum concentration. HBER animals showed lower ovulation and embryo recovery rates compared to MBER animals. Different miRNAs were found among CC and EV FF within groups, suggesting that the BER may influence follicular communication. This suggests that small follicles (3-6 mm diameter) are already under BER effects, which may be greater on later stages of follicular development.

Prenatal Supplementation in Beef Cattle and Its Effects on Plasma Metabolome of Dams and Calves

This study investigated the effect of different prenatal nutrition on the plasma metabolome of Nellore dams and their offspring. For that purpose, three nutritional treatments were used in 126 cows during pregnancy: NP—(control) only mineral supplementation; PP—protein-energy supplementation in the final third; and FP—protein-energy supplementation during the entire pregnancy. Targeted metabolomics were analyzed in plasma at the beginning of pregnancy and in pre-delivery of cows (n = 27) as well as in calves (n = 27, 30 ± 9.6 days of age). Data were analyzed by the analysis of variance, partial least squares discriminant analysis, and the principal component analysis (PCA). The PCA showed a clear clustering in the periods investigated only in cows (early gestation and pre-delivery). We found significant metabolites in both supervised analyses (p < 0.05 and VIP score > 1) for cows (Taurine, Glutamic acid, Histidine, and PC aa C42:2) and for calves (Carnosine, Alanine, and PC aa C26:0). The enrichment analysis revealed biological processes (p < 0.1) common among cows and calves (histidine metabolism and beta-alanine metabolism), which may be indicative of transgenerational epigenetic changes. In general, fetal programming affected mainly the metabolism of amino acids.

Effects of Maternal Nutrition on Female Offspring Weight Gain and Sexual Development

Maternal nutrition during pregnancy influences postnatal life of animals; nevertheless, few studies have investigated its effects on the productive performance and reproductive development of heifers. This study evaluated the performance, reproductive development, and correlation between reproduction × fat thickness and performance × ribeye area (REA) traits of heifers. We also performed an exploratory genomic association during the rearing period in heifers submitted to fetal programming. The study comprised 55 Nellore heifers born to dams exposed to one of the following nutritional planes: control, without protein-energy supplementation; PELT, protein-energy last trimester, protein-energy supplementation offered in the final third of pregnancy; and PEWG, protein-energy whole gestation, protein-energy supplementation upon pregnancy confirmation. Protein-energy supplementation occurred at the level of 0.3% live weight. After weaning, heifers were submitted to periodic evaluations of weight and body composition by ultrasonography. From 12 to 18 months, we evaluated the reproductive tract of heifers to monitor its development for sexual precocity and ovarian follicle population. The treatments had no effect (p > 0.05) on average daily gain; however, the weight of the animals showed a significant difference over time (p = 0.017). No differences were found between treatments for REA, backfat, and rump fat thickness, nor for puberty age, antral follicular count, and other traits related to reproductive tract development (p > 0.05). The correlation analysis between performance traits and REA showed high correlations (r > 0.37) between REA at weaning and year versus weight from weaning until yearling; however, no correlation was found for reproductive development traits versus fat thickness (p > 0.05). The exploratory genomic association study showed one single-nucleotide polymorphism (SNP) for each treatment on an intergenic region for control and PEWG, and the one for PELT on an intronic region of RAPGEF1 gene. Maternal nutrition affected only the weight of the animals throughout the rearing period.

Effects of different maternal nutrition approaches on weight gain and on adipose and muscle tissue development of young bulls in the rearing phase

This study evaluated the effects of prenatal nutrition on body weight (BW), average daily gain (ADG), rump fat thickness (RFT), backfat thickness (BFT), ribeye area (REA), muscle cell area (MCA), and the number of cells in REA (NCREA) of young Nellore bulls during the rearing period. After pregnancy confirmation (30 days of pregnancy), 126 Nellore cows were separated into three prenatal nutritional treatments (NP (control; 0.03% of BW), only mineral supplementation; PP (0.3% of BW), protein-energy supplementation in the final third; and FP (0.3% of BW) protein-energy supplementation during the entire pregnancy). After calving, all animals were submitted to the same environmental conditions (sanitary and nutritional) and the different supplementation protocols ceased. The males (63 bulls) were evaluated during the entire rearing phase (210 ± 28 days to 540 ± 28 days of age) to weight gain (BW and ADG), carcass characteristics (RFT, BFT, and REA), and for histological assessments (MCA and NCREA; 7 animals per treatment randomly selected). All phenotypes were subjected to an analysis of variance. The different prenatal stimuli had no effect on BFT, RFT, MCA, and NCREA (P > 0.05); however, prenatal nutrition influenced BW of the animals during the rearing phase (P < 0.01) and showed a tendency on ADG (P = 0.09) and REA (P = 0.08). In conclusion, the offspring from FP treatment showed greater BW during the rearing phase in comparison to the NP group. This is related to a greater protein offered in prenatal nutrition, increasing muscle development during the gestational period.

Genetic parameters associated with meat quality of Nellore cattle at different anatomical points of longissimus: Brazilian standards

The present study estimated genetic parameters and evaluated the genetic and phenotypic correlations between meat quality characteristics of Nellore cattle evaluated at different anatomical points of the longissimus. Data from 1329 Nellore young bulls were used to evaluate, in the 5th and 12th ribs, marbling score (MAR), shear force (SF), cooking weight losses (CWL) and intramuscular fat (IMF). In addition, the subcutaneous fat thickness was measured at the 12th rib (SFT₁₂) and between the last lumbar and the first sacral vertebrae (SFT_LR), in the separation of loin and round. Results yielded moderate heritability coefficients for evaluated characteristics, except CWL. High genetic correlations (0.61) were found between measurements of SFT₁₂ and SFT_LR. MAR, IMF and SF were evaluated at the 5th and 12th rib. Meat quality and subcutaneous fat thickness measured at different anatomical points of the longissimus are genetically correlated and can be used in genetic selection programs to improve meat quality characteristics in Nellore cattle.

Predicting the shear value and intramuscular fat in meat from Nellore cattle using Vis-NIR spectroscopy

Visible and near-infrared spectroscopy (Vis-NIRS) was tested for its effectiveness in predicting intramuscular fat (IMF) and WBSF in Nellore steers. Beef samples from longissimus thoracis, aged for either 2 or 7 days, had their spectra collected for wavelengths ranging from 400 to 1395 nm. Partial least squares regression models were developed for each trait. Determination coefficients of calibration models for WBSF ranged from 0.17 to 0.53. Considering WBSF in samples aged for 2 days, Vis-NIR correctly classified 100% of tough samples (>45 N), but wrongly classified all tender samples (≤45 N) as tough. Determination coefficients of calibration models for IMF ranged from 0.12 to 0.14. Vis-NIRS is a useful tool for identifying tough beef, but it is less effective in predicting tender samples and IMF. Additional studies are necessary to generate more robust models for the prediction of intramuscular fat in intact meat samples of Nellore cattle.

Effects of fibre digestibility and level of roughage on performance and rumen fermentation of finishing beef cattle

The objective was to evaluate effects of neutral detergent fibre (NDF) digestibility and level of fresh sugarcane on intake, body fatness, carcass characteristics, and rumen kinetics and fermentation of beef cattle. Forty-eight Nellore young bulls were used in a complete randomized block design with a 2 × 2 factorial arrangement of treatments. Eight rumen-cannulated Nellore steers were used in a replicated 4 × 4 Latin square design. Two sugarcane genotypes divergent for stalk NDF digestibility (NDFD) were used. Experimental diets were formulated with 20 or 40% of sugarcane on a dry matter (DM) basis. High-NDFD genotype associated with the lower level of roughage in the diet promoted greater DM intake, resulting in greater body gain. Sugarcane with high-NDFD increased final body weight, hot carcass weight, and back-fat thickness. Animals receiving the genotype with high NDFD had greater rump-fat thickness only with 40% sugarcane in the diet. Animals receiving the low-NDFD genotype at 20% of the diet had lower NDF passage rate. Rumen pH was greater for diets with greater NDF content. There was greater proportion of butyrate in the rumen of animals receiving diets with greater NDF content. In conclusion, high-NDFD sugarcane increased final body and carcass weight, HCW, and fat thickness. When associated with lower inclusion of roughage in the diet, it can also increase DM intake and body weight gain of beef cattle.

Using a system of differential equations that models cattle growth to uncover the genetic basis of complex traits

The interplay between dynamic models of biological systems and genomics is based on the assumption that genetic variation of the complex trait (i.e., outcome of model behavior) arises from component traits (i.e., model parameters) in lower hierarchical levels. In order to provide a proof of concept of this statement for a cattle growth model, we ask whether model parameters map genomic regions that harbor quantitative trait loci (QTLs) already described for the complex trait. We conducted a genome-wide association study (GWAS) with a Bayesian hierarchical LASSO method in two parameters of the Davis Growth Model, a system of three ordinary differential equations describing DNA accretion, protein synthesis and degradation, and fat synthesis. Phenotypic and genotypic data were available for 893 Nellore (Bos indicus) cattle. Computed values for parameter k₁ (DNA accretion rate) ranged from 0.005 ± 0.003 and for α (constant for energy for maintenance requirement) 0.134 ± 0.024. The expected biological interpretation of the parameters is confirmed by QTLs mapped for k₁ and α. QTLs within genomic regions mapped for k₁ are expected to be correlated with the DNA pool: body size and weight. Single nucleotide polymorphisms (SNPs) which were significant for α mapped QTLs that had already been associated with residual feed intake, feed conversion ratio, average daily gain (ADG), body weight, and also dry matter intake. SNPs identified for k₁ were able to additionally explain 2.2% of the phenotypic variability of the complex ADG, even when SNPs for k₁ did not match the genomic regions associated with ADG. Although improvements are needed, our findings suggest that genomic analysis on component traits may help to uncover the genetic basis of more complex traits, particularly when lower biological hierarchies are mechanistically described by mathematical simulation models.

Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle

The use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR.

Blood cell and metabolic profile of Nellore bulls and their correlations with residual feed intake and feed conversion ratio

Due to the potential metabolic changes related to the residual feed intake (RFI), this study investigated the correlation of traditional RFI (RFI1), RFI adjusted for final rump fat thickness (RFI2) and feed conversion ratio (FCR) with the metabolic and blood profiles, as well as determined the possible different classes of RFI1 and RFI2. For this purpose, 46 Nellore bulls, 22 month-old and 411kg of weight at the beginning of the study were used. The animals were fed with the same diet for 84 days, and blood samples were collected every 21 days for evaluation of serum metabolites and blood cell profiles. No significant correlations were found between FCR and metabolic or blood traits, although there was a significant correlation between RFI1 and urea serum concentration. There were also differences between the RFI classes for creatinine, in which more efficient animals showed higher values. The RFI2 did not correlate with any metabolic and blood cell variable, but young bulls with smaller RFI2 had a smaller number of eosinophils when compared to animals with higher RFI2. These results suggest that animals with a high RFI can have greater energy expenditure due to protein synthesis and degradation process, resulting in a larger blood urea level.