Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes.

We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.

Genetic variance components of the growth curve for Isfahan indigenous chicken.

BACKGROUND: Being able to model a growth curve using three or four non-linear functional parameters could help explain the growth phenomenon in a precise way and would allow the comparison of an animal's development rate, optimize management and feeding strategies and guide animal production strategies. OBJECTIVE: The goal of this study was to estimate the genetic parameters of growth traits of Isfahan indigenous chicken in Iran and to determine the best non-linear model describing the growth curve. METHODS: The prediction of additive genetic parameters was performed using the REML method by WOMBAT. Direct heritability of the studied traits and genetic correlations between them were obtained. The Logistic, Gompertz, von Bertalanffy, Brody, Negative exponential, Weibull, Janoschek and Bridges models were compared based on the coefficient of determination (R2 ), mean square error (MSE) and akaike information criterion. RESULTS: The Gompertz model was identified as the best model for describing the growth curve for Isfahan native chicken. The heritability of maturity weights (A), initial weight (B) and maturity rate (K) parameters were 0.223 ± 0.002, 0.016 ± 0.005 and 0.087 ± 0.001, respectively. CONCLUSION: This study shows that Isfahan indigenous chicken has the genetic potential for improving growth and reproduction based on their desirable heritabilities and correlations using appropriate models.

In Vitro Characterization of chIFITMs of Aseel and Kadaknath Chicken Breeds against Newcastle Disease Virus Infection.

Newcastle disease (ND) is highly contagious and usually causes severe illness that affects Aves all over the world, including domestic poultry. Depending on the virus's virulence, it can impact the nervous, respiratory, and digestive systems and cause up to 100% mortality. The chIFITM genes are activated in response to viral infection. The current study was conducted to quantify the mRNA of chIFITM genes in vitro in response to ND viral infection. It also examined its ability to inhibit ND virus replication in chicken embryo fibroblast (CEF) cells of the Aseel and Kadaknath breeds. Results from the study showed that the expression of all chIFITM genes was significantly upregulated throughout the period in the infected CEF cells of both breeds compared to uninfected CEF cells. In CEF cells of the Kadaknath breed, elevated levels of expression of the chIFITM3 gene dramatically reduced ND viral growth, and the viral load was 60% lower than in CEF cells of the Aseel breed. The expression level of the chIFITMs in Kadaknath ranged from 2.39 to 11.68 log2 folds higher than that of control CEFs and was consistently (p < 0.01) higher than Aseel CEFs. Similar to this, theIFN-γ gene expresses strongly quickly and peaks at 13.9 log2 fold at 48 hpi. Based on these cellular experiments, the Kadaknath breed exhibits the potential for greater disease tolerance than Aseel. However, to gain a comprehensive understanding of disease resistance mechanisms in chickens, further research involving in vivo investigations is crucial.

Genomic Prediction Accuracies for Growth and Carcass Traits in a Brangus Heifer Population.

The predictive abilities and accuracies of genomic best linear unbiased prediction (GBLUP) and the Bayesian (BayesA, BayesB, BayesC and Lasso) genomic selection (GS) methods for economically important growth (birth, weaning, and yearling weights) and carcass (depth of rib fat, apercent intramuscular fat and longissimus muscle area) traits were characterized by estimating the linkage disequilibrium (LD) structure in Brangus heifers using single nucleotide polymorphisms (SNP) markers. Sharp declines in LD were observed as distance among SNP markers increased. The application of the GBLUP and the Bayesian methods to obtain the GEBV for growth and carcass traits within k-means and random clusters showed that k-means and random clustering had quite similar heritability estimates, but the Bayesian methods resulted in the lower estimates of heritability between 0.06 and 0.21 for growth and carcass traits compared with those between 0.21 and 0.35 from the GBLUP methodologies. Although the prediction ability of the GBLUP and the Bayesian methods were quite similar for growth and carcass traits, the Bayesian methods overestimated the accuracies of GEBV because of the lower estimates of heritability of growth and carcass traits. However, GBLUP resulted in accuracy of GEBV for growth and carcass traits that parallels previous reports.

Genetic Parameters of Growth Traits and Quantitative Genetic Metrics for Selection and Conservation of Mecheri Sheep of Tamil Nadu.

Determining the genetic and non-genetic sources of variation in a breed is vital for the formulation of strategies for its conservation and improvement. The present study was aimed at estimating the (co)variance components and genetic parameters of Mecheri sheep by fitting six different animal models in the restricted maximum likelihood method, with a preliminary investigation on the performance of animals for non-genetic sources of variation. A total of 2616 lambs were studied, and varying levels of significance were found for the effects of period, season, parity of dam, and birth type on different body-weight traits. Direct heritability estimates derived from the best animal model for body weight at birth, three months, six months, nine months, and twelve months were 0.21, 0.24, 0.10, 0.15, and 0.09, respectively, and the maternal heritability of the corresponding traits was 0.12, 0.05, 0.04, 0.04, and 0.04, respectively. The genetic correlations between the body-weight traits were all positive and moderate-to-strong, except for the correlation between birth weight and the other body-weight traits. The significance of non-genetic factors studied in this work demanded a correction to improve the accuracy of the direct selection of lambs for body-weight traits. The estimated genetic parameters identified the weaning weight as a selection criterion for the improvement in body weight of Mecheri lambs at different ages. Inbred individuals accounted for approximately 13% of the total population in the Mecheri sheep population studied. There were 877 founders in the population, and the actual effective population size was 128.48. The population's mean generation interval was 3.26. The mean inbreeding values ranged from 0.005 to 0.010 across generations. The population's average relatedness ranged from 0.001 to 0.014 across generations. Individual inbreeding was found to be 0.45 per cent for the entire population and 3.4 per cent for the inbred population.

Differential Expression of Innate and Adaptive Immune Genes during Acute Physical Exercise in American Quarter Horses.

Overtraining syndrome (OTS) is the reduction in performance due to excess training and lack of proper recovery, which can lead to a chronic deprivation of energy and reduction in the repair of damage that can accumulate over time. Here, the effect of acute, intense physical exercise on the expression of innate and adaptive immune genes in 12 racing-bred American Quarter Horses, after resting for 3 days and immediately after intense exercise for 1.8 miles were compared. The expression of 84 genes related to innate and adaptive immune responses was analyzed. Significant variation among individuals and between sexes was observed. The analysis showed that five genes were differentially expressed in both females and males, three only in females, and two in males. The upregulated genes were IL13 (male only), CCR4 (female only), TLR6, TLR9 (female only), NFKBIA, CXCR3, and TLR4, while the downregulated genes were IL6 (female only), CD4 (male only), and MYD88. The three main pathways containing genes that were affected by acute, intense physical exercise were Th1 and Th2 cell differentiation, and the NF-kappa B and chemokine signaling pathways, suggesting the activation of the proinflammatory responses as a result of the stress from the acute exercise. Gene expression could be used to assess indications of OTS.

Multi-trait Bayesian analysis and genetic parameter estimates in production characters of Mecheri sheep of India.

The present study was carried out to estimate the genetic parameters for direct and maternal influences on Mecheri sheep (Ovis aries) growth traits using Bayesian multi-trait animal model. The genetic parameters were calculated using data from 2825 Mecheri lambs born between 2010 and 2020 that were kept in semi-arid tropical climate. Mecheri sheep body weight (mean ± SE) at various stages, viz. BW, WW, and BW12, were 2.6 ± 0.01, 11.1 ± 0.05, and 20.7 ± 0.13 kg, respectively. The Mecheri sheep gained 71.5 percent of their body weight at the age of 6 months. With the exception of birth weight, the weights of the animals varied considerably (P < 0.01) by the year of birth. The fixed effect of sex significantly (P < 0.01) influenced all the growth traits examined. The direct estimates of heritability (± SD) for BW, WW, BW6, and BW12 was 0.21 ± 0.041, 0.21 ± 0.041, 0.12 ± 0.052, and 0.13 ± 0.053, respectively, and the maternal heritability for BW, WW, BW6, and BW12 was 0.18 ± 0.021, 0.08 ± 0.023, 0.11 ± 0.022, and 0.13 ± 0.033, respectively. Significant variance was indicated by moderately larger direct heritability estimates for BWT and WWT, indicating that there will be more opportunities for selection response during the genetic improvement programme. For the majority of the variables examined, direct heritability values were higher than maternal heritability values. The additive genetic correlation between WW and BW6, BW9, and BW12 was 0.70 ± 0.145, 0.57 ± 0.171, and 0.50 ± 0.194, respectively. The maternal genetic correlations ranged from 0.06 ± 0.152 (BW-BW12) to 0.86 ± 0.046 (BW6-BW9), and the residual correlation varied from 0.18 ± 0.034 (BW-WW) to 0.85 ± 0.013 (BW9-BW12). The BW had a stronger genetic relationship with WW and a weaker relationship with other growth traits. The WW and BW6 showed a favourable genetic relationship, even if the tendency was decreasing in the latter stages of maturation. The BW6 and BW9 demonstrated the strongest positive genetic relationship (0.90 ± 0.052) of all the variables analysed. After examining the heritabilities and genetic correlation between WW and BW6, it was established that selection based on at WW was beneficial, since it manifests early in life and would result in moderate genetic progress through selection.

An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish.

The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein-protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ2 = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish.

Molecular Evolution and Inheritance Pattern of Sox Gene Family among Bovidae.

Sox genes are an evolutionarily conserved family of transcription factors that play important roles in cellular differentiation and numerous complex developmental processes. In vertebrates, Sox proteins are required for cell fate decisions, morphogenesis, and the control of self-renewal in embryonic and adult stem cells. The Sox gene family has been well-studied in multiple species including humans but there has been scanty or no research into Bovidae. In this study, we conducted a detailed evolutionary analysis of this gene family in Bovidae, including their physicochemical properties, biological functions, and patterns of inheritance. We performed a genome-wide cataloguing procedure to explore the Sox gene family using multiple bioinformatics tools. Our analysis revealed a significant inheritance pattern including conserved motifs that are critical to the ability of Sox proteins to interact with the regulatory regions of target genes and orchestrate multiple developmental and physiological processes. Importantly, we report an important conserved motif, EFDQYL/ELDQYL, found in the SoxE and SoxF groups but not in other Sox groups. Further analysis revealed that this motif sequence accounts for the binding and transactivation potential of Sox proteins. The degree of protein-protein interaction showed significant interactions among Sox genes and related genes implicated in embryonic development and the regulation of cell differentiation. We conclude that the Sox gene family uniquely evolved in Bovidae, with a few exhibiting important motifs that drive several developmental and physiological processes.

Assessment of Mutation Drift Equilibrium and the Occurrence of a Recent Genetic Bottleneck in South Indian Zebu Cattle.

During the last few decades, the effective population size of indigenous zebu cattle breeds has declined drastically, resulting in the classification of some of them into the vulnerable, endangered, or critically endangered category. Drastic reductions in the effective size of a population may result in genetic bottlenecks and can affect within-breed genetic variability and its viability. The present study was undertaken with the objective of evaluating South Indian zebu cattle populations for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck events. A total of 293 cattle from eight indigenous breeds were genotyped at 27 FAO/ISAG-recommended microsatellite marker loci. Three different statistical tests, viz., the sign test, standardized differences test, and Wilcoxon sign rank test were performed using allele frequency data to detect loci with heterozygosity excess under the infinite alleles, stepwise, and two-phase mutation models. Under the infinite alleles model, the observed number of loci with heterozygosity excess (He > Heq) ranged between 10 and 19 among the investigated cattle breeds. However, the observed heterozygosity excess was not statistically significant (p > 0.05) in any of the studied breeds. Similarly, the standardized differences test and Wilcoxon sign rank test revealed no concrete evidence for the occurrence of a recent genetic bottleneck in South Indian zebu cattle breeds. The qualitative test for mode-shift distortion revealed a normal L-shaped distribution of allele frequencies, suggesting a lack of evidence for the loss of low-frequency alleles in all the investigated South Indian zebu cattle breeds.

Constraint-Based, Score-Based and Hybrid Algorithms to Construct Bayesian Gene Networks in the Bovine Transcriptome.

Bayesian gene networks are powerful for modelling causal relationships and incorporating prior knowledge for making inferences about relationships. We used three algorithms to construct Bayesian gene networks around genes expressed in the bovine uterus and compared the efficacies of the algorithms. Dataset GSE33030 from the Gene Expression Omnibus (GEO) repository was analyzed using different algorithms for hub gene expression due to the effect of progesterone on bovine endometrial tissue following conception. Six different algorithms (grow-shrink, max-min parent children, tabu search, hill-climbing, max-min hill-climbing and restricted maximum) were compared in three higher categories, including constraint-based, score-based and hybrid algorithms. Gene network parameters were estimated using the bnlearn bundle, which is a Bayesian network structure learning toolbox implemented in R. The results obtained indicated the tabu search algorithm identified the highest degree between genes (390), Markov blankets (25.64), neighborhood sizes (8.76) and branching factors (4.38). The results showed that the highest number of shared hub genes (e.g., proline dehydrogenase 1 (PRODH), Sam-pointed domain containing Ets transcription factor (SPDEF), monocyte-to-macrophage differentiation associated 2 (MMD2), semaphorin 3E (SEMA3E), solute carrier family 27 member 6 (SLC27A6) and actin gamma 2 (ACTG2)) was seen between the hybrid and the constraint-based algorithms, and these genes could be recommended as central to the GSE33030 data series. Functional annotation of the hub genes in uterine tissue during progesterone treatment in the pregnancy period showed that the predicted hub genes were involved in extracellular pathways, lipid and protein metabolism, protein structure and post-translational processes. The identified hub genes obtained by the score-based algorithms had a role in 2-arachidonoylglycerol and enzyme modulation. In conclusion, different algorithms and subsequent topological parameters were used to identify hub genes to better illuminate pathways acting in response to progesterone treatment in the bovine uterus, which should help with our understanding of gene regulatory networks in complex trait expression.

Phenotypic and genetic parameters of productive traits in Rahmani and Romanov sheep and crossbreds.

Data of 651 lambs (68 Romanov, 49 Rahmani, 151 [♀1/2 Rahmani X ♂1/2 Romanov) and 383 (♀3/4 Rahmani and 1/4♂ Romanov]) were collected from Mehalet Mousa Farm, belonging to Animal Production Research Institute from the period of 2009 to 2016 to estimate phenotypic and genetic parameters. The traits studied were birth weight (BW), body weight at four week (BW4), body weight at eight weeks (BW8) and body weight at twelve weeks (BW12) or weaning weight. Least squares analysis of variance shows significance of the effects of breed groups, gender of lambs, birth type; month of birth and year of birth on all traits studied. Rahmani lambs had heavier BW, BW4, BW8 and BW12 while Romanov lambs had the lowest ones. The first generation (♀1/2 Rhamani X ♂1/2 Romanov) had heavier body weights than Romanov and the second generation (♀3/4 Rahmani X ♂1/4 Roamnov). Gender of lambs had highly significant effect on body weights. Males were significantly (p < 0.01) heavier than females for all traits studied. Least square means of BW, BW4, BW8 and BW12 for single lambs were 2.69, 10.43, 13.53 and 16.10 kg, respectively. Least square means of BW, BW4, BW8 and BW12 for twin lambs were 2.50, 9.37, 12.5 and 15.16 kg, respectively, while least square means of BW, BW4, BW8 and BW12 for triple lambs were 2.09, 7.86, 10.83 and 13.67 kg, respectively. Estimates of direct heritability measured by single trait animal model were 0.14, 0.23, 0.25 and 0.26 for BW, BW4, BW8 and BW12, respectively, and the corresponding measured by multi trait animal model were 0.17, 0.24, 0.32 and 0.36 for the same traits, respectively. All genetic and phenotypic correlations among different traits studied are positive and significant.

Effects of a blend of mannan and glucan on growth performance, apparent nutrient digestibility, energy status, and whole-blood immune gene expression of beef steers during a 42-d receiving period.

We examined the effects of dietary supplementation of a blend of mannan and glucan on the growth performance, energy status, and whole-blood immune gene expression of newly weaned beef steers during a 42-d receiving period. Forty-eight newly weaned Angus crossbred steers (2-d post-weaning; 199 ± 13 kg of initial body weight [BW]) from a single source were stratified by BW and randomly assigned to one of the two treatments: basal diet with no additive (CON; n = 24) or a basal diet top-dressed with 5 g of a blend of mannan and glucan (MANGLU; n = 24). Average daily gain (ADG) and feed efficiency (FE) from days 1 to 14, 15 to 42, and 1 to 42 were calculated from daily dry matter intake (DMI) and weekly BW. Blood samples were collected on days 0, 14, and 42 for measurement of plasma glucose and nonesterified fatty acids (NEFA). Blood samples collected on days 14 and 42 were composited for each steer for untargeted carbonyl-metabolome analysis (measurement of carbonyl-containing metabolites). Expression of 84 immune-related genes was analyzed on blood samples collected on day 42. Beginning on days 37 to 42, total mixed ration, refusals, and fecal samples were collected once daily to determine apparent total tract digestibility of DM, CP, NDF, and ADF using indigestible NDF as an internal marker. Over the 42-d feeding trial, supplemental MANGLU tended to increase final BW (P = 0.07) and ADG (P = 0.06). Compared to CON, beef steers fed supplemental MANGLU had greater (P = 0.01) DMI during the first 14 d, greater DM digestibility (P = 0.03), and tended to have greater NDF digestibility (P = 0.09). No treatment effects (P > 0.10) on plasma glucose and NEFA on days 14 and 42 were detected; however, carbonyl-metabolome analysis revealed increased (FDR ≤ 0.05) plasma concentrations of galactose and glyceraldehydes, and altered (FDR ≤ 0.05) concentrations of some microbiome-derived metabolites in beef steers fed MANGLU. Compared with CON, MANGLU increased (P ≤ 0.05) the expression of five immune-related genes involved in recognition of and mounting immune defense against microbial pathogens. In conclusion, the results of this study demonstrated that supplemental MANGLU enhances beef cattle immunocompetence and productivity during feedlot receiving period.

Plasma Carboxyl-Metabolome Is Associated with Average Daily Gain Divergence in Beef Steers.

We applied an untargeted metabolomics technique to analyze the plasma carboxyl-metabolome of beef steers with divergent average daily gain (ADG). Forty-eight newly weaned Angus crossbred beef steers were fed the same total mixed ration ad libitum for 42 days. On day 42, the steers were divided into two groups of lowest (LF: n = 8) and highest ADG (HF: n = 8), and blood samples were obtained from the two groups for plasma preparation. Relative quantification of carboxylic-acid-containing metabolites in the plasma samples was determined using a metabolomics technique based on chemical isotope labeling liquid chromatography mass spectrometry. Metabolites that differed (fold change (FC) ≥ 1.2 or ≤ 0.83 and FDR ≤ 0.05) between LF and HF were identified using a volcano plot. Metabolite set enrichment analysis (MSEA) of the differential metabolites was done to determine the metabolic pathways or enzymes that were potentially altered. In total, 328 metabolites were identified. Volcano plot analysis revealed 43 differentially abundant metabolites; several short chain fatty acids and ketone bodies had greater abundance in HF steers. Conversely, several long chain fatty acids were greater in LF steers. Five enzymatic pathways, such as fatty acyl CoA elongation and fatty-acid CoA ligase were altered based on MSEA. This study demonstrated that beef steers with divergent ADG had altered plasma carboxyl-metabolome, which is possibly caused by altered abundances and/or activities of enzymes involved in fatty acid oxidation and biosynthesis in the liver.

Comparative accuracies of genetic values predicted for economically important milk traits, genome-wide association, and linkage disequilibrium patterns of Canadian Holstein cows.

Genomic selection methodologies and genome-wide association studies use powerful statistical procedures that correlate large amounts of high-density SNP genotypes and phenotypic data. Actual 305-d milk (MY), fat (FY), and protein (PY) yield data on 695 cows and 76,355 genotyping-by-sequencing-generated SNP marker genotypes from Canadian Holstein dairy cows were used to characterize linkage disequilibrium (LD) structure of Canadian Holstein cows. Also, the comparison of pedigree-based BLUP, genomic BLUP (GBLUP), and Bayesian (BayesB) statistical methods in the genomic selection methodologies and the comparison of Bayesian ridge regression and BayesB statistical methods in the genome-wide association studies were carried out for MY, FY, and PY. Results from LD analysis revealed that as marker distance decreases, LD increases through chromosomes. However, unexpected high peaks in LD were observed between marker pairs with larger marker distances on all chromosomes. The GBLUP and BayesB models resulted in similar heritability estimates through 10-fold cross-validation for MY and PY; however, the GBLUP model resulted in higher heritability estimates than BayesB model for FY. The predictive ability of GBLUP model was significantly lower than that of BayesB for MY, FY, and PY. Association analyses indicated that 28 high-effect markers and markers on Bos taurus autosome 14 located within 6 genes (DOP1B, TONSL, CPSF1, ADCK5, PARP10, and GRINA) associated significantly with FY.

Evolutionary Pattern of Interferon Alpha Genes in Bovidae and Genetic Diversity of IFNAA in the Bovine Genome.

Interferons are secretory proteins induced in response to specific extracellular stimuli which stimulate intra- and intercellular networks for regulating innate and acquired immunity, resistance to viral infections, and normal and tumor cell survival and death. Type 1 interferons plays a major role in the CD8 T-cell response to viral infection. The genomic analysis carried out here for type I interferons within Bovidae family shows that cattle, bison, water buffalo, goat, and sheep (all Bovidae), have different number of genes of the different subtypes, with a large increase in the numbers, compared to human and mouse genomes. A phylogenetic analysis of the interferon alpha (IFNA) proteins in this group shows that the genes do not follow the evolutionary pattern of the species, but rather a cycle of duplications and deletions in the different species. In this study we also studied the genetic diversity of the bovine interferon alpha A (IFNAA), as an example of the IFNA genes in cattle, sequencing a fragment of the coding sequence in 18 breeds of cattle from Pakistan, Nigeria and USA. Similarity analysis allowed the allocation of sequences into 22 haplotypes. Bhagnari, Brangus, Sokoto Gudali, and White Fulani, had the highest number of haplotypes, while Angus, Hereford and Nari Master had the least. However, when analyzed by the average haplotype count, Angus, Bhagnari, Hereford, Holstein, Muturu showed the highest values, while Cholistani, Lohani, and Nari Master showed the lowest values. Haplotype 4 was found in the highest number of individuals (74), and in 15 breeds. Sequences for yak, bison, and water buffalo, were included within the bovine haplotypes. Medium Joining network showed that the sequences could be divided into 4 groups: one with highly similar haplotypes containing mostly Asian and African breeds, one with almost all of the Bos taurus American breeds, one mid-diverse group with mostly Asian and African sequences, and one group with highly divergent haplotypes with five N'Dama sequences and one from each of White Fulani, Dhanni, Tharparkar, and Bhagnari. The large genetic diversity found in IFNAA could be a very good indication of the genetic variation among the different genes of IFNA and could be an adaptation for these species in response to viral challenges they face.

Study on the prevalence and genetic diversity of Eimeria species from broilers and free-range chickens in KwaZulu-Natal province, South Africa.

This study was conducted from January to October 2018 with the objective to determine the prevalence and genetic diversity of Eimeria species in broiler and free-range chickens in KwaZulu-Natal province, South Africa. A total of 342 faecal samples were collected from 12 randomly selected healthy broiler chicken farms and 40 free-range chickens from 10 different locations. Faecal samples were screened for the presence of Eimeria oocysts using a standard flotation method. The species of Eimeria isolates were confirmed by amplification of the internal transcribed spacer 1 (ITS-1) partial region and sequences analysis. Among broiler and free-ranging chickens, 19 out of 41 pens (46.3%) and 25 out of 42 faecal samples (59.5%) were positive for Eimeria infection. Molecular detection revealed the following species: Eimeria maxima, Eimeria tenella, Eimeria acervulina, Eimeria brunetti and Eimeria mitis in all the samples screened. Similarly, polymerase chain reaction assays specific for three cryptic Eimeria operational taxonomic units were negative for all the samples. Phylogenetic analysis of the ITS-1 sequences supported species identity with the greatest variation detected for E. mitis. This study provides information on the range and identity of Eimeria species, and their genetic relatedness, circulating in commercially reared broilers and free-ranging chickens from different locations in KwaZulu-Natal province.

Differential Expression of IGF1, IGFBP5, MSTN, and MYH1 Across Different Age Classes in American Quarter Horses.

The objective of this study was to determine the influence of age on expression of insulin-like growth factor 1 (IGF1), insulin-like growth factor binding protein (IGFBP5), myostatin (MSTN), and myosin (MYH1) genes which are related to growth and muscle development in the American Quarter Horse. Thus, horses (n = 10) from weanling, yearling, 2-, 3-, and 10-year-old age classes were sampled and gene expression was assessed by RT-qPCR. ΔCT was calculated using the hypoxanthine-guanine phosphoribosyltransferase gene as an internal normalizer. The generalized linear model was used to determine differentially expressed genes, by pairwise comparison between ages. Among technical replicates, the coefficient of variation ranged from 1.0 to 5.2% and was lower than the variation observed between biological replicates (2.1-12.9%). IGF1 demonstrated significantly lower expression in the 3-year-old age class than in weanlings and yearlings, but the 10-year-old age class displayed a significantly higher level than 2- and 3-year-old age classes. Expression of IGFBP5 was highest in weanlings compared with all other age classes. Expression of MSTN was significantly higher in weanlings than in other age classes, whereas 10-year-old horses had an intermediate level of expression, but significantly different from yearlings, 2- and 3-year-old fillies. Finally, expression of MYH1 was lower in 2- and 10-year-old horses than in weanlings and yearlings, whereas 3-year-old fillies demonstrated an intermediate level of expression. Differential expression patterns observed in this preliminary study provide insight into the physiological changes occurring throughout the life span of horses. These patterns could also help explain the variation in performance and endurance between individuals at different developmental stages.

Comparative effects of two multispecies direct-fed microbial products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers.

We examined the effects of two direct-fed microbials (DFM) containing multiple microbial species and their fermentation products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers. Nine ruminally cannulated Holstein steers (mean ± SD body weight: 243 ± 12.4 kg) were assigned to three treatments arranged in a triplicated 3 × 3 Latin square design with three 21-d periods. Dietary treatments were 1) control (CON; basal diet), 2) Commence (PROB; basal diet plus 19 g/d of Commence), and 3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both multispecies DFM products. From day 16 to 20 of each period, feed and fecal samples were collected daily to determine the apparent total tract digestibilities of nutrients using indigestible neutral detergent fiber method. On day 21 of each period, blood samples were collected for analysis of plasma glucose and nonesterified fatty acid. Ruminal contents were collected at approximately 1, 3, 6, 9, 12, and 18 h after feeding on day 21 for analysis of volatile fatty acids (VFA), lactate, ammonia-N concentrations, bacterial community, and metabolome profile. Total tract digestibilities of nutrients did not differ (P > 0.05) among treatments. Compared with CON, steers fed either supplemental PROB or SYNB had greater (P = 0.04) plasma glucose concentrations. Compared with CON, total ruminal VFA, propionate, isovalerate, and valerate concentrations increased (P ≤ 0.05) or tended to increase (P ≤ 0.10) with either supplemental PROB or SYNB, but were not different (P > 0.05) between PROB and SYNB. Compared with CON, PROB reduced (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Rikenellaceae RC9, Succinivibrionaceae UCG-001, Succiniclasticum, and Ruminococcaceae UCG-002. Supplemental SYNB decreased (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Prevotella 7, Succinivibrio, Succiniclasticum, and Ruminococcaceae UCG-014. Compared with CON, metabolome analysis revealed that some amino acids were increased (P ≤ 0.05) in steers fed PROB. This study demonstrated that, compared with CON, supplementation of either PROB or SYNB altered the ruminal bacterial community and metabolome differently; however, their effects on the ruminal VFA profile and energy status of the steers were not different from each other.