Influence of proportion of Brahman genetics on productivity of Brahman-Angus cows at weaning.

This study evaluated the association between the proportion of Brahman genetics and productivity of Brahman-Angus cows at weaning using a 31-yr dataset containing 6,312 cows and 5,405 pregnancies. Cows were contemporaneously reared and enrolled in yearly breeding seasons under subtropical conditions of North-Central Florida. They were evenly distributed in six-breed groups (G) according to the proportion of Brahman genetics: G0% to 19%, G21% to 34%, G38% (Brangus), G41% to 59%, G63% to 78%, and G81% to 100%. The proportion of cows calving (84.9%) did not differ across the six-breed groups. However, cows in the G81% to 100% weaned fewer calves (90.8%) than cows in the G0% to 19% and G21% to 34% (95.7%, each). The weaning rate of cows in the G38% (94.3%), G41% to 59% (94.2%), and G63% to 78% (93.0%) was intermediate between these three breed groups. The preweaning calf mortality was greater for cows in the G81% to 100% (9.2%) than cows in the G0% to 19% and G21% to 34% (4.3%, each), but intermediate for cows in the G38% (5.7%), G41% to 59% (5.8%), and G63% to 78% (7.0%). Cows in the G81% to 100% also weaned lighter calves (220.6 kg) than cows in the G0% to 19% (245.2 kg), G21% to 34% (250.2 kg), G38% (247.9 kg), G41% to 59% (252.5 kg), and G63% to 78% (245.2 kg). Cows in the G0% to 19% weaned lighter calves than cows with 21% to 78% of Brahman genetics. The 205-d adjusted weaning weight evidenced the less productive results of cows in G0% to 19% and G81% to 100% compared with other genetic groups, as they calved at the fastest and slowest rate, respectively. Thus, the 205-d adjusted weaning weight eliminated this bias. Additionally, younger cows weaned lighter calves; and male calves were heavier at weaning than female calves. Both parity order of cow and calf sex altered the magnitude of the described association between breed group of cows and calf weaning weights. Overall, after adjusting for weaning rate and age of calves at weaning, the number of kilograms produced per cow submitted to reproduction was less for cows in the G0% to 19% (191.1 kg) and G81% to 100 (181.8 kg) compared with cows in the G21% to 34 (197.0 kg), G38 (195.9 kg), G41% to 59 (199.7), and G63% to 78 (196.2). Cows in the G81% to 100% were the least productive. Thus, a proportion of Brahman genetics between 21% and 78% ensured superior productivity of Brahman-Angus cows subjected to subtropical conditions.

Genetic factors influencing milk and fat yields in tropically adapted dairy cattle: insights from quantitative trait loci analysis and gene associations.

OBJECTIVE: The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions. METHODS: A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-yearseason, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis. RESULTS: A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease. CONCLUSION: Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.

A comparison of five sets of overlapping and non-overlapping sliding windows for semen production traits in the Thai multibreed dairy population.

OBJECTIVE: This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population. METHODS: The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows. RESULTS: Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population. CONCLUSION: This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.

Estimation of heritabilities and additive genetic correlations for reproduction traits in swine: insights for tropical commercial production systems using multiple trait animal models.

OBJECTIVE: This study was to estimate heritabilities, additive genetic correlations, and phenotypic correlations between number of piglets born alive (NBA), litter birth weight (LTBW), number of piglets weaned (NPW) and litter weaning weight (LTWW) in different parities of Landrace (L), Yorkshire (Y), Landrace×Yorkshire (LY), and Yorkshire×Landrace (YL) sows in a commercial swine operation in Northern Thailand. METHODS: Two models were utilized, a single trait repeatability model (RM) and a multiple trait animal model (MTM). The RM assumed reproductive records from different parities to be repeated values of the same trait, whereas the MTM assumed these records to be different traits. The two models accounted for the fixed effects of farrowing year-season, genetic group of the sow, heterosis, and age at first farrowing, and the random effects of sow, boar, and residual. RESULTS: Heritability estimates from RM were 0.02±0.01 for NBA, 0.10±0.01 for LTBW, 0.04±0.01 for NPW, and 0.11±0.01 for LTWW. Heritability estimates from MTM fluctuated across parities, ranging from 0.04±0.01 in parity 2 to 0.09±0.02 in parity 4 for NBA, 0.07±0.02 in parity 2 to 0.16±0.02 in parity 3 for LTBW, 0.04±0.02 in parity 4 to 0.08±0.01 in parity 1 for NPW, and 0.16±0.02 in parity 1 to 0.20±0.02 in parity 2 for LTWW. Additive genetic correlation estimates from MTM were also variable, ranging from 0.29±0.24 between NBA in parity 1 and NBA in parity 2 to 0.99±0.05 between LTWW in parity 3 and LTWW in parity 4. CONCLUSION: The findings of this study highlight the advantage of using MTM for the genetic improvement of reproductive traits in swine and contribute to the development of sustainable swine breeding programs in Thailand.

What a 31-yr multibreed herd taught us about the influence of B. indicus genetics on reproductive performance of cows.

Bos taurus × Bos indicus crosses are widespread in tropical and subtropical regions, nonetheless, quantitative information about the influence of B. indicus genetics on the reproductive performance of beef cattle is lacking. Herein, we determined the association between level of B. indicus genetics and reproduction from a 31-yr dataset comprising sequential breeding seasons of the University of Florida multibreed herd (n = 6,503 Angus × Brahman cows). The proportion of B. indicus genetics in this herd is evenly distributed by each 1/32nd or approximately 3-percentage points. From 1989 to 2020, the estrous cycle of cows was synchronized for artificial insemination (AI) based on detected estrus or timed-AI (TAI) using programs based on gonadotropin-releasing hormone and prostaglandin, and progestin/progesterone. All cows were exposed to natural service after AI and approximately 90-d breeding seasons, considering the day of AI as day 0. The proportion of B. indicus genetics of cows was associated negatively with pregnancy per AI, ranging from 51.6% for cows with 0%-19% of B. indicus genetics to 37.4% for cows with 81%-100% of B. indicus genetics. Similar association was found for estrous response at the end of the synchronization protocol, ranging from 66.3% to 38.4%, respectively. This reduced estrous response helped to explain the pregnancy results, once the pregnancy to AI of cows showing estrus was 2.3-fold greater than for those not showing estrus and submitted to TAI. Despite reduced pregnancy per AI, the increase in the proportion of B. indicus genetics of cows was not associated with a reduction in the proportion of pregnant cows at the end of the breeding season. Nevertheless, the interval from entering the breeding season to pregnancy was lengthened as the proportion of B. indicus genetics of cows increased. The median days to pregnancy was extended by 25 when the proportion of B. indicus genetics surpassed 78% compared with less than 20%. Thus, the increase in the proportion of B. indicus genetics of cows was related to a reduction in pregnancy per AI and lengthening the interval to attain pregnancy during the breeding season, but not with the final proportion of pregnant cows. As a result, reproductive management strategies directed specifically to cows with a greater proportion of B. indicus genetics are needed to improve the rate of pregnancy in beef herds.

Cow­calf operations in the tropics and sub-tropics have benefited from the environmental adaptation provided by Bos indicus genetics. However, reproductive performance has been a cause of concern, although poorly quantified. This study characterized how much the B. indicus genetics in crossbred cows influence herd reproduction. We analyzed data from cows with known proportions of Angus and Brahman genetics, from the same crossbred herd, for 31 sequential breeding seasons. The increase in the proportion of B. indicus genetics reduced estrous response and pregnancy per artificial insemination after estrous synchronization, but not the proportion of pregnant cows at the end of the breeding season. Interval from the beginning of the breeding season to pregnancy was extended by 25 d when the proportion of B. indicus genetics surpassed 78%. In conclusion, reproductive management strategies directed specifically to cows with a greater proportion of B. indicus genetics are needed to improve the rate of pregnancy in beef herds.

Molecular Profiling of DNA Methylation and Alternative Splicing of Genes in Skeletal Muscle of Obese Rabbits.

DNA methylation and the alternative splicing of precursor messenger RNAs (pre-mRNAs) are two important genetic modification mechanisms. However, both are currently uncharacterized in the muscle metabolism of rabbits. Thus, we constructed the Tianfu black rabbit obesity model (obese rabbits fed with a 10% high-fat diet and control rabbits from 35 days to 70 days) and collected the skeletal muscle samples from the two groups for Genome methylation sequencing and RNA sequencing. DNA methylation data showed that the promoter regions of 599 genes and gene body region of 2522 genes had significantly differential methylation rates between the two groups, of which 288 genes had differential methylation rates in promoter and gene body regions. Analysis of alternative splicing showed 555 genes involved in exon skipping (ES) patterns, and 15 genes existed in differential methylation regions. Network analysis showed that 20 hub genes were associated with ubiquitinated protein degradation, muscle development pathways, and skeletal muscle energy metabolism. Our findings suggest that the two types of genetic modification have potential regulatory effects on skeletal muscle development and provide a basis for further mechanistic studies in the rabbit.

Untargeted Metabolomics Analysis Revealed Lipometabolic Disorders in Perirenal Adipose Tissue of Rabbits Subject to a High-Fat Diet.

A high-fat diet (HFD) is widely recognized as a significant modifiable risk for insulin resistance, inflammation, Type 2 diabetes, atherosclerosis and other metabolic diseases. However, the biological mechanism responsible for key metabolic disorders in the PAT of rabbits subject to HFD remains unclear. Here, untargeted metabolomics (LC-MS/MS) combined with liquid chromatography (LC) and high-resolution mass spectrometry (MS) were used to evaluate PAT metabolic changes. Histological observations showed that the adipocytes cells and density of PAT were significantly increased in HFD rabbits. Our study revealed 206 differential metabolites (21 up-regulated and 185 down-regulated); 47 differential metabolites (13 up-regulated and 34 down-regulated), comprising mainly phospholipids, fatty acids, steroid hormones and amino acids, were chosen as potential biomarkers to help explain metabolic disorders caused by HFD. These metabolites were mainly associated with the biosynthesis of unsaturated fatty acids, the arachidonic acid metabolic pathway, the ovarian steroidogenesis pathway, and the platelet activation pathway. Our study revealed that a HFD caused significant lipometabolic disorders. These metabolites may inhibit oxygen respiration by increasing the adipocytes cells and density, cause mitochondrial and endoplasmic reticulum dysfunction, produce inflammation, and finally lead to insulin resistance, thus increasing the risk of Type 2 diabetes, atherosclerosis, and other metabolic syndromes.

Intramuscular adipocyte and fatty acid differences between high-fat and control rabbit groups subject to a restricted diet.

Fatty acids of intramuscular fat (IMF) in rabbits can influence meat quality, but it is unclear which fatty acids benefit to human health. A rabbit model of weight gain and weight loss was constructed using two rabbit groups and two growth stages. Stage 1 included control group1 fed a commercial diet(CG1) and experimental group1 fed a high fat diet (EG1). Stage 2 include control group2(CG2) and experimental group2 (EG2) both fed a restricted commercial diet. We detected differences in blood biochemical indicators as well as changes in intramuscular adipose cells and intramuscular fatty acid content in control and experiment groups at two stages. High fat induction can make rabbits become obese, have higher concentrations of glucose (GLU), total cholesterol (TC), triglyceride (TG), low density lipoprotein-cholesterol (LDL-C) and free fatty acid (FFA), and lower concentrations of insulin (INS). In addition, a high-fat diet promotes hypertrophy of precursor adipocytes in femoral muscles. Conversely, a restricted diet causes weight loss, decreases the concentration of TG, FFA, and INS in CG2 and EG2, and increases the deposition of unsaturated fatty acids in the femoral muscle. The content of monounsaturated trans oleic acid (C18:1n-9T) in EG2 was significantly higher than in CG2, whereas oleic acid (C18:1n-9C) was significantly lower in EG2 than in CG2. The polyunsaturated fatty acids Linolenate (C18:3 n-3) and cis-5,8,11,14,17-Eicosapentaenoate (C20:5 n-3) increased in CG2 and EG2. The content of Linoleate (C18:2 n-6) and γ-Linolenic acid (C18:3 n-6) significantly increased in CG2. The content of cis-11,14-Eicosatrienoic acid (C20:2) decreased significantly in CG2, but increased significantly in EG2.Thus, a high-fat diet can increase the formation of unhealthy fatty acids. Conversely, weight loss due to a restricted diet leads to an increase in unsaturated fatty acids in the femoral muscle, indicating that it reduces obesity symptoms and it may improve meat quality in rabbit.

Untargeted Metabolomic Characteristics of Skeletal Muscle Dysfunction in Rabbits Induced by a High Fat Diet.

Type 2 diabetes and metabolic syndrome caused by a high fat diet (HFD) have become public health problems worldwide. These diseases are characterized by the oxidation of skeletal muscle mitochondria and disruption of insulin resistance, but the mechanisms are not well understood. Therefore, this study aims to reveal how high-fat diet causes skeletal muscle metabolic disorders. In total, 16 weaned rabbits were randomly divided into two groups, one group was fed a standard normal diet (SND) and the other group was fed a high fat diet (HFD) for 5 weeks. At the end of the five-week experiment, skeletal muscle tissue samples were taken from each rabbit. Untargeted metabolomic analysis was performed using ultra-performance liquid chromatography combined with mass spectrometry (UHPLC-MS/MS). The results showed that high fat diet significantly altered the expression levels of phospholipids, LCACs, histidine, carnosine, and tetrahydrocorticosterone in skeletal muscle. Principal component analysis (PCA) and least squares discriminant analysis (PLS-DA) showed that, compared with the SND group, skeletal muscle metabolism in HFD group was significantly up-regulated. Among 43 skeletal muscle metabolites in the HFD group, phospholipids, LCACs, histidine, carnosine, and tetrahydrocorticosteroids were identified as biomarkers of skeletal muscle metabolic diseases, and may become potential physiological targets of related diseases in the future. Untargeted metabonomics analysis showed that high-fat diet altered the metabolism of phospholipids, carnitine, amino acids and steroids in skeletal muscle of rabbits. Notably, phospholipids, LCACs, histidine, carnopeptide, and tetrahydrocorticosteroids block the oxidative capacity of mitochondria and disrupt the oxidative capacity of glucose and the fatty acid-glucose cycle in rabbit skeletal muscle.

Untargeted Metabolomics Reveals Intestinal Pathogenesis and Self-Repair in Rabbits Fed an Antibiotic-Free Diet.

The prohibition of the use of growth-promoting drug additives in feeds was implemented in China in 2020. However, rabbits can experience symptoms of intestinal disease, such as diarrhea and flatulence, when switching from standard normal diets with antibiotics to antibiotic-free diets. The molecular mechanisms related to the occurrence of these diseases as well as associated physiological and metabolic changes in the intestine are unclear. Thus, the objectives of this study were to study the pathogenesis of intestinal inflammation using untargeted metabolomics. This was done to identify differential metabolites between a group of antibiotic-free feed Hyplus rabbits (Dia) whose diet was abruptly changed from a standard normal diet with antibiotics to an antibiotic-free diet, and an antibiotic diet group Hyplus rabbits (Con) that was fed a standard normal diet with antibiotics. Morphological damage to the three intestinal tissues was determined through visual microscopic examination of intestinal Dia and Con tissue samples stained with hematoxylin and eosin (HE). A total of 1969 different metabolites were identified in the three intestinal tissues from Dia and Con rabbits. The level of 1280 metabolites was significantly higher and the level of 761 metabolites was significantly lower in the Dia than in the Con group. These differential metabolites were involved in five metabolic pathways associated with intestinal inflammation (tryptophan metabolism, pyrimidine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, lysine degradation, and bile secretion). Rabbits in the Dia group developed metabolic disorders that affected the intestinal microbiota and changed the permeability of the intestinal tract, thereby triggering intestinal inflammation, affecting feed utilization, reducing production performance, and activating the intestinal tract self-repair mechanism. Thus, the abrupt transition from a diet with antibiotics to an antibiotic-free diet affected the structure and metabolism of the intestinal tract in Hyplus rabbits. Consequently, to avoid these problems, the antibiotic content in a rabbit diet should be changed gradually or alternative antibiotics should be found.

Genomic Approaches Reveal Pleiotropic Effects in Crossbred Beef Cattle.

Carcass and meat quality are two important attributes for the beef industry because they drive profitability and consumer demand. These traits are of even greater importance in crossbred cattle used in subtropical and tropical regions for their superior adaptability because they tend to underperform compared to their purebred counterparts. Many of these traits are challenging and expensive to measure and unavailable until late in life or after the animal is harvested, hence unrealistic to improve through traditional phenotypic selection, but perfect candidates for genomic selection. Before genomic selection can be implemented in crossbred populations, it is important to explore if pleiotropic effects exist between carcass and meat quality traits. Therefore, the objective of this study was to identify genomic regions with pleiotropic effects on carcass and meat quality traits in a multibreed Angus-Brahman population that included purebred and crossbred animals. Data included phenotypes for 10 carcass and meat quality traits from 2,384 steers, of which 1,038 were genotyped with the GGP Bovine F-250. Single-trait genome-wide association studies were first used to investigate the relevance of direct additive genetic effects on each carcass, sensory and visual meat quality traits. A second analysis for each trait included all other phenotypes as covariates to correct for direct causal effects from identified genomic regions with pure direct effects on the trait under analysis. Five genomic windows on chromosomes BTA5, BTA7, BTA18, and BTA29 explained more than 1% of additive genetic variance of two or more traits. Moreover, three suggestive pleiotropic regions were identified on BTA10 and BTA19. The 317 genes uncovered in pleiotropic regions included anchoring and cytoskeletal proteins, key players in cell growth, muscle development, lipid metabolism and fat deposition, and important factors in muscle proteolysis. A functional analysis of these genes revealed GO terms directly related to carcass quality, meat quality, and tenderness in beef cattle, including calcium-related processes, cell signaling, and modulation of cell-cell adhesion. These results contribute with novel information about the complex genetic architecture and pleiotropic effects of carcass and meat quality traits in crossbred beef cattle.

Multi-Omics Analysis of Key microRNA-mRNA Metabolic Regulatory Networks in Skeletal Muscle of Obese Rabbits.

microRNAs (miRNAs), small non-coding RNA with a length of about 22 nucleotides, are involved in the energy metabolism of skeletal muscle cells. However, their molecular mechanism of metabolism in rabbit skeletal muscle is still unclear. In this study, 16 rabbits, 8 in the control group (CON-G) and 8 in the experimental group (HFD-G), were chosen to construct an obese model induced by a high-fat diet fed from 35 to 70 days of age. Subsequently, 54 differentially expressed miRNAs, 248 differentially expressed mRNAs, and 108 differentially expressed proteins related to the metabolism of skeletal muscle were detected and analyzed with three sequencing techniques (small RNA sequencing, transcriptome sequencing, and tandem mass tab (TMT) protein technology). It was found that 12 miRNAs and 12 core genes (e.g., CRYL1, VDAC3 and APIP) were significantly different in skeletal muscle from rabbits in the two groups. The network analysis showed that seven miRNA-mRNA pairs were involved in metabolism. Importantly, two miRNAs (miR-92a-3p and miR-30a/c/d-5p) regulated three transcription factors (MYBL2, STAT1 and IKZF1) that may be essential for lipid metabolism. These results enhance our understanding of molecular mechanisms associated with rabbit skeletal muscle metabolism and provide a basis for future studies in the metabolic diseases of human obesity.

Genome-wide identification and characterization of perirenal adipose tissue microRNAs in rabbits fed a high-fat diet.

MicroRNAs (miRNAs) are a class of endogenous single-stranded RNA molecules that play an important role in gene regulation in animals by pairing with target gene mRNA. Extensive evidence shows that miRNAs are key players in metabolic regulation and the development of obesity. However, the systemic understanding of miRNAs in the adipogenesis of obese rabbits need further investigation. Here, seven small RNA libraries from rabbits fed either a standard normal diet (SND; n=3) or high-fat diet (HFD; n=4) were constructed and sequenced. Differentially expressed (DE) miRNAs were identified using the edgeR data analysis package from R. Software miRanda and RNAhybrid were used to predict the target genes of miRNAs. To further explore the functions of DE miRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. A total of 81449996 clean reads were obtained from the seven libraries, of which, 52 known DE miRNAs (24 up-regulated, 28 down-regulated) and 31 novel DE miRNAs (14 up-regulated, 17 down-regulated) were identified. GO enrichment analysis revealed that the DE miRNAs target genes were involved in intermediate filament cytoskeleton organization, intermediate filament-based process, and α-tubulin binding. DE miRNAs were involved in p53 signaling, linoleic acid metabolism, and other adipogenesis-related KEGG pathways. Our study further elucidates the possible functions of DE miRNAs in rabbit adipogenesis, contributing to the understanding of rabbit obesity.

Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity.

The gut microbiota is a complex ecological community that plays multiple critical roles within a host. Known intrinsic and extrinsic factors affect gut microbiota structure, but the influence of host genetics is understudied. To investigate the role of host genetics upon the gut microbiota structure, we performed a longitudinal study in which we evaluated the hindgut microbiota and its association with animal growth and immunity across life. We evaluated three different growth stages in an Angus-Brahman multibreed population with a graduated spectrum of genetic variation, raised under variable environmental conditions and diets. We found the gut microbiota structure was changed significantly during growth when preweaning, and fattening calves experienced large variations in diet and environmental changes. However, regardless of the growth stage, we found gut microbiota is significantly influenced by breed composition throughout life. Host genetics explained the relative abundances of 52.2%, 40.0%, and 37.3% of core bacterial taxa at the genus level in preweaning, postweaning, and fattening calves, respectively. Sutterella, Oscillospira, and Roseburia were consistently associated with breed composition at these three growth stages. Especially, butyrate-producing bacteria, Roseburia and Oscillospira, were associated with nine single-nucleotide polymorphisms (SNPs) located in genes involved in the regulation of host immunity and metabolism in the hindgut. Furthermore, minor allele frequency analysis found breed-associated SNPs in the short-chain fatty acids (SCFAs) receptor genes that promote anti-inflammation and enhance intestinal epithelial barrier functions. Our findings provide evidence of dynamic and lifelong host genetic effects upon gut microbiota, regardless of growth stages. We propose that diet, environmental changes, and genetic components may explain observed variation in critical hindgut microbiota throughout life.

Growth, behavioural, serum biochemical and morphological changes in female rabbits fed high-fat diet.

This study aimed to determine whether high-fat diet (HFD) could cause growth, behavioural, biochemical and morphological changes in young female rabbits. Thirty-six female rabbits were randomly divided into two groups fed with either a high-fat diet (HFD) or a standard normal diet (SND) for 5 weeks. Growth and behavioural changes were recorded during the 5-week feeding period. Tissue samples, including blood and adipose tissue, were obtained after slaughter. HFD rabbits weighed more by the end of the feeding period, had a higher percent body weight and adipose tissue weight change and had longer body and bust lengths than SND rabbits. HFD rabbits significantly reduced their feed intake and feeding frequency during the fourth and fifth weeks. HFD rabbits also showed lower frequency of drinking and resting and increased stereotypical behaviour. Besides, HFD rabbits showed significant physiological abnormalities. HFD rabbits had higher serum cholesterol (TC) and triglycerides (TG) levels than SND rabbits at the end of the feeding period, and higher free fatty acid (FFA) levels than rabbits in the SND group after the third week of feeding. Serum thyroxine (T4) increased significantly in week 2 and week 5 and triiodothyronine (T3) increased significantly in week four. However, there was no significant change in serum glucose (GLU) and insulin (INS) levels. Additionally, HFD reduced the area and diameter of perirenal and subcutaneous fat cells and increased their density. Our findings suggest that HFD rabbits had higher weight gains, accumulation of fat, and more behavioural changes than SND rabbits. Although high levels of fat in the diet had a low impact on hyperglycaemia, it could lead to hyperlipidemia and hyperthyroidism. Our results also suggest that sustained HFD may cause the proliferation of adipocytes in young female rabbits.

Genetic parameters and trends for growth traits in Blanco Orejinegro cattle.

Since 1940, efforts have been made to preserve the Blanco Orejinegro (BON) cattle breed by maintaining gene banks. Nine years ago, a BON genetic improvement program was implemented to increase genetic gain based on control of productivity and the use of performance tests, polygenic and genomic evaluations, and selection indices. The objective of this study was to estimate genetic parameters and trends for growth traits by using polygenic (PM) and genomic-polygenic (GPM) models. Productive information from the years 1980 to 2019 was used. The following data were used: 7,304 birth weight (BW) records, 1,281 records of body weight adjusted to 120 days (W120), 4,791 records of weight adjusted to 240 days (W240), 3,339 records of weight adjusted to 480 days (W480), and 1,364 records of weight adjusted to 720 days (W720). The relationship matrix included 13,612 pure animals belonging to the Colombian Corporation for Agricultural Research - AGROSAVIA and the Producer Network program. A total of 1,224 individuals were genotyped with chips of different densities and all were imputed up to 50,932 SNPs. Polygenic and genomic-polygenic models were used to estimate genetic parameters and correlations between the genetic values estimated by each model. A generalized additive model with smoothing was used to estimate trends of genetic values from 1980 to 2019. Heritabilities between 0.29 and 0.40, genetic correlations between 0.13 and 0.94, and phenotypic correlations between 0.23 and 0.72 were observed. Close-to-zero genetic growth was observed for BW and W120. Genetic trends for the other traits were positive, with higher growth in the last 7 years. The heritabilities observed in this population indicate that the traits measured would respond to selection. Greater genetic progress can be achieved in W240, W480, and W720 by continuing with genetic evaluations and developing performance tests and strategies to make genetic material readily available to producers.

RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef.

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.

Mitochondrial oxygen consumption in early postmortem permeabilized skeletal muscle fibers is influenced by cattle breed.

Functional properties and integrity of skeletal muscle mitochondria (mt) during the early postmortem period may influence energy metabolism and pH decline, thereby impacting meat quality development. Angus typically produce more tender beef than Brahman, a Bos indicus breed known for heat tolerance. Thus, our objectives were to compare mt respiratory function in muscle collected early postmortem (1 h) from Angus and Brahman steers (n = 26); and to evaluate the effect of normal and elevated temperature on mt function ex vivo. We measured mt oxygen consumption rate (OCR) in fresh-permeabilized muscle fibers from Longissimus lumborum (LL) at 2 temperatures (38.5 and 40.0 °C) and determined citrate synthase (CS) activity and expression of several mt proteins. The main effects of breed, temperature, and their interaction were tested for mt respiration, and breed effect was tested for CS activity and protein expression. Breed, but not temperature (P > 0.40), influenced mt OCR (per tissue weight), with Brahman exhibiting greater complex I+II-mediated oxidative phosphorylation capacity (P = 0.05). Complex I- and complex II-mediated OCR also tended to be greater in Brahman (P = 0.07 and P = 0.09, respectively). Activity of CS was higher in LL from Brahman compared to Angus (P = 0.05). Expression of specific mt proteins did not differ between breeds, except for higher expression of adenosine triphosphate (ATP) synthase subunit 5 alpha in Brahman muscle (P = 0.04). Coupling control ratio differed between breeds (P = 0.05), revealing greater coupling between oxygen consumption and phosphorylation in Brahman. Our data demonstrate that both Angus and Brahman mt retained functional capacity and integrity 1-h postmortem; greater oxidative phosphorylation capacity and coupling in Brahman mt could be related to heat tolerance and impact early postmortem metabolism.

Identification of eQTLs and sQTLs associated with meat quality in beef.

BACKGROUND: Transcription has a substantial genetic control and genetic dissection of gene expression could help us understand the genetic architecture of complex phenotypes such as meat quality in cattle. The objectives of the present research were: 1) to perform eQTL and sQTL mapping analyses for meat quality traits in longissimus dorsi muscle; 2) to uncover genes whose expression is influenced by local or distant genetic variation; 3) to identify expression and splicing hot spots; and 4) to uncover genomic regions affecting the expression of multiple genes. RESULTS: Eighty steers were selected for phenotyping, genotyping and RNA-seq evaluation. A panel of traits related to meat quality was recorded in longissimus dorsi muscle. Information on 112,042 SNPs and expression data on 8588 autosomal genes and 87,770 exons from 8467 genes were included in an expression and splicing quantitative trait loci (QTL) mapping (eQTL and sQTL, respectively). A gene, exon and isoform differential expression analysis previously carried out in this population identified 1352 genes, referred to as DEG, as explaining part of the variability associated with meat quality traits. The eQTL and sQTL mapping was performed using a linear regression model in the R package Matrix eQTL. Genotype and year of birth were included as fixed effects, and population structure was accounted for by including as a covariate the first PC from a PCA analysis on genotypic data. The identified QTLs were classified as cis or trans using 1 Mb as the maximum distance between the associated SNP and the gene being analyzed. A total of 8377 eQTLs were identified, including 75.6% trans, 10.4% cis, 12.5% DEG trans and 1.5% DEG cis; while 11,929 sQTLs were uncovered: 66.1% trans, 16.9% DEG trans, 14% cis and 3% DEG cis. Twenty-seven expression master regulators and 13 splicing master regulators were identified and were classified as membrane-associated or cytoskeletal proteins, transcription factors or DNA methylases. These genes could control the expression of other genes through cell signaling or by a direct transcriptional activation/repression mechanism. CONCLUSION: In the present analysis, we show that eQTL and sQTL mapping makes possible positional identification of gene and isoform expression regulators.

Resistance to pH decline and slower calpain-1 autolysis are associated with higher energy availability early postmortem in Bos taurus indicus cattle.

Beef from Bos taurus indicus is associated with toughness compared to Bos taurus taurus, suggesting there is antagonism between adaptability to heat and beef quality. Resistance to cellular stress in muscle may be protective postmortem, thereby delaying its conversion to meat. Therefore, our objective was to determine pH decline, calpain-1 and caspase 3 activation, and proteolysis in different biological cattle types. Angus, Brangus, and Brahman steers (n = 18) were harvested, and Longissimus lumborum were assessed postmortem for pH decline, ATP content, protease activation, and calpastatin content; and myofibrillar protein degradation was evaluated in beef aged to 14d. Brahman Longissimus lumborum exhibited resistance to pH decline, greater ATP content at 1 h, and delayed calpain-1 autolysis. Although content of caspase-3 zymogen was lower in Brahman, there was no evidence of caspase-3 mediated proteolysis. Greater resistance to energetic and pH changes early postmortem in Brahman Longissimus lumborum are associated with calpain-1 autolysis but not mitochondria mediated apoptosis.