Network visualization of genes involved in skeletal muscle myogenesis in livestock animals.

BACKGROUND: Muscle growth post-birth relies on muscle fiber number and size. Myofibre number, metabolic and contractile capacities are established pre-birth during prenatal myogenesis. The aim of this study was to identify genes involved in skeletal muscle development in cattle, sheep, and pigs - livestock. RESULTS: The cattle analysis showed significant differences in 5043 genes during the 135-280 dpc period. In sheep, 444 genes differed significantly during the 70-120 dpc period. Pigs had 905 significantly different genes for the 63-91 dpc period.The biological processes and KEGG pathway enrichment results in each species individually indicated that DEGs in cattle were significantly enriched in regulation of cell proliferation, cell division, focal adhesion, ECM-receptor interaction, and signaling pathways (PI3K-Akt, PPAR, MAPK, AMPK, Ras, Rap1); in sheep - positive regulation of fibroblast proliferation, negative regulation of endothelial cell proliferation, focal adhesion, ECM-receptor interaction, insulin resistance, and signaling pathways (PI3K-Akt, HIF-1, prolactin, Rap1, PPAR); in pigs - regulation of striated muscle tissue development, collagen fibril organization, positive regulation of insulin secretion, focal adhesion, ECM-receptor interaction, and signaling pathways (PPAR, FoxO, HIF-1, AMPK). Among the DEGs common for studied animal species, 45 common genes were identified. Based on these, a protein-protein interaction network was created and three significant modules critical for skeletal muscle myogenesis were found, with the most significant module A containing four recognized hub genes - EGFR, VEGFA, CDH1, and CAV1. Using the miRWALK and TF2DNA databases, miRNAs (bta-miR-2374 and bta-miR-744) and transcription factors (CEBPB, KLF15, RELA, ZNF143, ZBTB48, and REST) associated with hub genes were detected. Analysis of GO term and KEGG pathways showed that such processes are related to myogenesis and associated with module A: positive regulation of MAP kinase activity, vascular endothelial growth factor receptor, insulin-like growth factor binding, focal adhesion, and signaling pathways (PI3K-Akt, HIF-1, Rap1, Ras, MAPK). CONCLUSIONS: The identified genes, common to the prenatal developmental period of skeletal muscle in livestock, are critical for later muscle development, including its growth by hypertrophy. They regulate valuable economic characteristics. Enhancing and breeding animals according to the recognized genes seems essential for breeders to achieve superior gains in high-quality muscle mass.

Data of whole-genome sequencing of Karakul, Zel, and Kermani sheep breeds.

OBJECTIVE: The data provided herein represent the whole-genome sequencing data associated with three sheep breeds of Iranian native breeds. Sheep are the first domesticated animals that, during the long path of the evolution process, have created gene variants with desirable phenotypic effects, so they can be suitable models for biomedical research. In addition, sheep have a vital role in providing protein to a notable part of the human population around the world. DATA DESCRIPTION: Ten blood samples were taken from three Iranian native sheep breeds, the Zel, Karakul, and Kermani kinds. Blood samples genomes were extracted using the salting-out technique. The Illumina NovaSeq 6000 platform was used to carry out sequencing of the whole genome in a laboratory in China. All sequence information is available through the NCBI database in the sequence read archive (SRA) format under the accession number PRJNA904537. The dataset presented here can provide a useful resource for genome analysis of livestock breeds adapted to hot and dry regions.

Introduction of a Newcastle disease virus challenge strain (sub-genotype VII.1.1) isolated in Iran.

Newcastle disease virus (NDV) sub-genotype VII.1.1 is the most common circulating NDV in Iran. In this study, a velogenic NDV isolate was plaque purified and then characterized according to Office International des Epizooties (OIE) standard protocols. The biological properties of the purified isolate named CH/RT40/IR/2011 were characterized using sequencing and phylogenetic analysis, measurement of pathogenicity indexes and challenge studies. The isolate was plaque purified on chicken embryo fibroblast cells for three rounds and then characterized using molecular and biological approaches. Phylogenetic and evolutionary distance analysis of fusion and hemagglutinin-neuraminidase genes classified the virus in sub-genotype VII.1.1. No mutation was observed in the glycosylation and neutralizing epitope sites of the fusion and hemagglutinin-neuraminidase proteins compared to other reported Iranian NDV VII.1.1 isolates. The presence of the 112RRQKRF117 motif in the fusion protein cleavage site together with mean death time, intracerebral pathogenicity index and intravenous pathogenicity index of 57 hr, 1.80 and 2.50 respectively, revealed that the RT40 isolate was a velogenic NDV. In the challenge study, all chickens were inoculated via eye drop, and intranasal route with RT40 isolate died within a week. While all chickens in the vaccinated and challenged group survived and showed no clinical signs. In conclusion, according to genetic analysis, pathotyping and challenge study, the RT40 isolate was similar to virulent NDVs in Iran and was a suitable candidate for a national standard challenge strain, vaccine trials and vaccine production in commercial levers.

Correlation between insulin-like growth factor 1 gene expression and fennel (Foeniculum vulgare) seed powder consumption in muscle of sheep.

It has been shown that addition of fennel in the diets of domestic animals has positive and beneficial effects on growth and meat production traits. Thus, the purpose of current study was to investigate the effect of adding fennel in the ration on growth characteristics and on insulin-like growth factor 1 (IGF1) gene expression in muscle tissue of Kermani lamb. Feeding of animals were performed with three levels of fennel including zero, 10 and 20 g/kg dry matter (DM) for 90 days. After slaughter, small pieces of tissues were removed and rapidly transferred to a nitrogen tank. Then, total RNA extracting and the Real-Time PCR reaction was performed. Results showed that as the level of fennel in the diet increases the amount of IGF1 gene expression also increases significantly in humeral muscle and femur (leg) muscle tissues (p < 0.05). In animals fed with fennel, femur muscle weight, back muscle weight, lean meat weight, final weight, warm carcass weight and live daily gain were greater than in animals fed with diet without fennel (p < 0.05). According to the findings of this investigation, it can be concluded that fennel, by creating positive effects on IGF1 gene expression can be used to improve muscle structure.

Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study.

Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of -9.9 and -8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.

Identification of Key Genes and Biological Pathways Associated with Skeletal Muscle Maturation and Hypertrophy in Bos taurus, Ovis aries, and Sus scrofa.

The aim of the current study was to identify the major genes and pathways involved in the process of hypertrophy and skeletal muscle maturation that is common for Bos taurus, Ovis aries, and Sus scrofa species. Gene expression profiles related to Bos taurus, Ovis aries, and Sus scrofa muscle, with accession numbers GSE44030, GSE23563, and GSE38518, respectively, were downloaded from the GEO database. Differentially expressed genes (DEGs) were screened out using the Limma package of R software. Genes with Fold Change > 2 and an adjusted p-value < 0.05 were identified as significantly different between two treatments in each species. Subsequently, gene ontology and pathway enrichment analyses were performed. Moreover, hub genes were detected by creating a protein−protein interaction network (PPI). The results of the analysis in Bos taurus showed that in the period of 280 dpc−3-months old, a total of 1839 genes showed a significant difference. In Ovis aries, however, during the period of 135dpc−2-months old, a total of 486 genes were significantly different. Additionally, in the 91 dpc−adult period, a total of 2949 genes were significantly different in Sus scrofa. The results of the KEGG pathway enrichment analysis and GO function annotation in each species separately revealed that in Bos taurus, DEGs were mainly enriched through skeletal muscle fiber development and skeletal muscle contraction, and the positive regulation of fibroblast proliferation, positive regulation of skeletal muscle fiber development, PPAR signaling pathway, and HIF-1 signaling pathway. In Ovis aries, DEGs were mainly enriched through regulating cell growth, skeletal muscle fiber development, the positive regulation of fibroblast proliferation, skeletal muscle cell differentiation, and the PI3K-Akt signaling, HIF-1 signaling, and Rap1 signaling pathways. In Sus scrofa, DEGs were mainly enriched through regulating striated muscle tissue development, the negative regulation of fibroblast proliferation and myoblast differentiation, and the HIF-1 signaling, AMPK signaling, and PI3K-Akt signaling pathways. Using a Venn diagram, 36 common DEGs were identified between Bos taurus, Ovis aries, and Sus scrofa. A biological pathways analysis of 36 common DEGs in Bos taurus, Ovis aries, and Sus scrofa allowed for the identification of common pathways/biological processes, such as myoblast differentiation, the regulation of muscle cell differentiation, and positive regulation of skeletal muscle fiber development, that orchestrated the development and maturation of skeletal muscle. As a result, hub genes were identified, including PPARGC1A, MYOD1, EPAS1, IGF2, CXCR4, and APOA1, in all examined species. This study provided a better understanding of the relationships between genes and their biological pathways in the skeletal muscle maturation process.

Identification of Candidate Genes Regulating Carcass Depth and Hind Leg Circumference in Simmental Beef Cattle Using Illumina Bovine Beadchip and Next-Generation Sequencing Analyses.

Genome-wide association studies are a robust means of identifying candidate genes that regulate economically important traits in farm animals. The aim of this study is to identify single-nucleotide polymorphisms (SNPs) and candidate genes potentially related to carcass depth and hind leg circumference in Simmental beef cattle. We performed Illumina Bovine HD Beadchip (~670 k SNPs) and next-generation sequencing (~12 million imputed SNPs) analyses of data from 1252 beef cattle, to which we applied a linear mixed model. Using a statistical threshold (p = 0.05/number of SNPs identified) and adopting a false discovery rate (FDR), we identified many putative SNPs on different bovine chromosomes. We identified 12 candidate genes potentially annotated with the markers identified, including CDKAL1 and E2F3, related to myogenesis and skeletal muscle development. The identification of such genes in Simmental beef cattle will help breeders to understand and improve related traits, such as meat yield.

An Origanum majorana Leaf Diet Influences Myogenin Gene Expression, Performance, and Carcass Characteristics in Lambs.

Myogenin is a protein in the myogenic regulatory factor family that plays an important role in determining carcass and meat traits and is vital for the growth and development of livestock muscles. The objective of this study was to determine the impact of Origanum majorana leaf (MOL) on the myogenin gene expression of lambs. Twenty-four male Kermani lambs were used in a completely randomized design using two experimental groups (0% Origanum majorana L. = MOL0 and 4% Origanum majorana L. = MOL4). Final weight, average daily gain, hot and cold carcass weight, feed conversion ratio, empty body weight, hot and cold dressing percentage, the weight of the shoulder, loin, leg, and lean meat, and the lean/bone ratio were measured. A standard kit was used for extracting total RNA from the loin, leg, and shoulder muscles of the lambs' tissues. The cDNA was synthesized, a real-time PCR was performed, and the obtained data were analyzed. The results of this study showed that the effect of MOL4 on dry matter intake is not significant. The MOL4 diet increased final weight by 8.22%, average daily gain by 28.57%, hot carcass weight by 11.38%, cold carcass weight by 13.43%, feed conversion ratio by 31.03%, empty body weight by 9.38%, hot dressing percentage by 2.92%, cold dressing percentage by 3.75%, shoulder weight by 56.70%, loin weight by 8.98%, leg weight by 10.90%, lean meat weight by 14.62%, and the lean/bone ratio by 2.85% (p < 0.05) compared to the MOL0. Along with adding MOL4 in the lambs' diets, in comparison with MOL0, there was higher expression of myogenin in the loin (3.5 times), leg (3.9 times), and shoulder (3.6 times) muscles of the lambs. Due to the fact that adding Origanum majorana to the diet of the lambs enhanced the expression of the myogenin gene in the loin, leg, and shoulder muscles and increased parameters related to growth, it can be used to improve the parameters related to growth and to increase myogenin gene expression in the muscle of lambs.

Fennel (Foeniculum vulgare) seed powder increases Delta-Like Non-Canonical Notch Ligand 1 gene expression in testis, liver, and humeral muscle tissues of growing lambs.

Delta-Like Non-Canonical Notch Ligand 1 (DLK1) is one of the key genes involved in the development of muscle, liver, pancreas, and lung cells; adipocytes production; and the improvement of digestion, growth performance, and meat quality. It has been documented that fennel is effective on increasing the DLK1 gene (DLK1) expression in the testis, liver, and muscle tissues, which may consequently have important implications for sheep production. Hence, the aim of the current investigation was to evaluate the fennel seed powder's effect on DLK1 expression in testis, liver, and humeral muscle tissues in growing lambs. For the purpose of this study, 30 male Kermani sheep were fed with three different group of diets (number of animals in each group was 10), including control (without any fennel seed powder), treatment 1 (with 10 g/kg of dry matter (DM) fennel seed powder), and treatment 2 (with 20 g/kg of DM fennel seed powder) during a 3-month period. Thereafter, total RNA was extracted, cDNA was synthesized, and Real-Time PCR was performed. The addition of fennel seed powder (in the treatment 1 and treatment 2 groups) in the growing lambs diets consequently resulted in greater expression of DLK1 in both the liver and humeral muscle tissues compared to the testis tissue (P < 0.05). Furthermore, the increased DLK1 expression was higher in the tissue of humeral muscle (P < 0.05) in comparison to the other two tissues. As well, the concentration of blood testosterone was greater (P < 0.05) for the animals fed with fennel powder compared to growing lambs fed with the control diet. However, the concentrations of blood liver enzymes, including serum glutamic oxaloacetic transaminase (SGOT) and serum glutamic pyruvic transaminase (SGPT), decreased by the addition of 10 g/kg DM fennel to diets of lambs compared to the control diet (no fennel). Therefore, it can be concluded that using fennel seed powder in the diet of growing lamb by affecting the expression of DLK1, can improve the concentrations of blood testosterone, SGOT, SGPT, and muscle structure (increased mass of muscle and size of muscle fiber).

Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds.

BACKGROUND: Sheep were among the first animals to be domesticated. They are raised all over the world and produce a major scale of animal-based protein for human consumption and play an important role in agricultural economy. Iran is one of the important locations for sheep genetic resources in the world. Here, we compared the Illumina Ovine SNP50 BeadChip data of three Iranian local breeds (Moghani, Afshari and Gezel), as a population that does not undergone artificial breeding programs as yet, and five other sheep breeds namely East Friesian white, East Friesian brown, Lacaune, DorsetHorn and Texel to detect genetic mechanisms underlying economical traits and daptation to harsh environments in sheep. RESULTS: To identify genomic regions that have been targeted by positive selection, we used fixation index (Fst) and nucleotide diversity (Pi) statistics. Further analysis indicated candidate genes involved in different important traits such as; wool production included crimp of wool (PTPN3, NBEA and KRTAP20-2 genes), fiber diameter (PIK3R4 gene), hair follicle development (LHX2 gene), the growth and development of fiber (COL17A1 gene)), adaptation to hot arid environments (CORIN gene), adaptive in deficit water status (CPQ gene), heat stress (PLCB4, FAM107B, NBEA, PIK3C2B and USP43 genes) in sheep. CONCLUSIONS: We detected several candidate genes related to wool production traits and adaptation to hot arid environments in sheep that can be applicable for inbreeding goals. Our findings not only include the results of previous researches, but also identify a number of novel candidate genes related to studied traits. However, more works will be essential to acknowledge phenotype- genotype relationships of the identified genes in our study.

Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals.

Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders' aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers' demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.

Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed.

BACKGROUND: The identification of genomic regions under selection can potentially permit a better understanding of the biology of the specific phenotypes which are useful for the development of tools designed to increase selection efficiency. OBJECTIVE: The aim of this study was to detect any traces of recent selection signatures as well as to identify corresponding genes and QTLs underlying these selection signatures in Sarabi cattle. METHODS: Samples from 20 animals were genotyped for 777,962 SNPs across the genome using the Illumina BovineHD BeadChip. Selection signatures analysis was performed using the integrated haplotype score (iHS) methodology. RESULTS: A total of eight significant regions (P < 0.0001) of possible recent selection signatures were detected on BTA14 and BTA17. In addition, nine genes were identified in regions harboring selection signatures, such as KCNQ3, HHLA1, OC90, EFR3A, ADCY8, ASAP1, TMEM132B, and TMEM132C. Study of the reported QTLs in these regions of the bovine genome has showed that they are associated with important traits such as milk, reproduction and production traits. CONCLUSION: The results revealed multiple genomic regions as well as multiple new genes under positive selection on BTA14 and BTA17. Moreover, candidate selected regions that overlap with QTL reported in the cattle QTL database provided additional evidence for the significance of the detected regions under selection. This study provides a foundation for detailed analysis of the identified putative selection signatures in the cattle genome particularly of the indigenous and locally-developed cattle breeds and provides an avenue for a well-structured breed improvement.

Detection of breed-specific copy number variations in domestic chicken genome.

Copy number variations (CNVs) are important large-scale variants. They are widespread in the genome and may contribute to phenotypic variation. Detection and characterization of CNVs can provide new insights into the genetic basis of important traits. Here, we perform whole-genome short read sequence analysis to identify CNVs in two indigenous and commercial chicken breeds to evaluate the impact of the identified CNVs on breed-specific traits. After filtration, a total of 12 955 CNVs spanning (on average) about 9.42% of the chicken genome were found that made up 5467 CNV regions (CNVRs). Chicken quantitative trait loci (QTL) datasets and Ensembl gene annotations were used as resources for the estimation of potential phenotypic effects of our CNVRs on breed-specific traits. In total, 34% of our detected CNVRs were also detected in earlier CNV studies. These CNVRs partly overlap several previously reported QTL and gene ontology terms associated with some important traits, including shank length QTL in Creeper-specific CNVRs and body weight and egg production characteristics, as well as muscle and body organ growth, in the Arian commercial breed. Our findings provide new insights into the genomic structure of the chicken genome for an improved understanding of the potential roles of CNVRs in differentiating between breeds or lines.

Genetics and non-genetics parameters of body weight for post-weaning traits in Raini Cashmere goats.

Genetic parameters were estimated for 6-month weight (W6), 9-month weight (W9), 12-month weight (W12), average daily gain from birth to 6 months old (ADG6), and Kleiber ratio at 6 months (KL6) traits using 6,442 records obtained from a Raini Cashmere goat flock. The parameters were estimated using the restricted maximum likelihood procedure and applying four animal models excluding or including maternal additive genetic and permanent environmental effects. Heritability estimates for W6, W9, W12, ADG6, and KL6, under the most appropriate model were 0.028, 0.26, 0.29, 0.02, and 0.25, respectively. The estimates of genetic and phenotypic correlations among W6, W9, W12, and ADG6 were high and ranged from 0.73 to 0.99. The estimates of genetic and phenotypic correlations among KL6 and others traits were negative and low. Thus, these estimates of genetic parameters may provide a basis for deriving selection indices for postweaning growth traits also low genetic correlation between growth traits with KL6, it is possible to increase efficiency in Raini kids by multitrait selection.

Estimating non-genetic and genetic parameters of pre-weaning growth traits in Raini Cashmere goat.

Data and pedigree information used in the present study were 3,022 records of kids obtained from the breeding station of Raini goat. The studied traits were birth weight (BW), weaning weight (WW), average daily gain from birth to weaning (ADG) and Kleiber ratio at weaning (KR). The model included the fixed effects of sex of kid, type of birth, age of dam, year of birth, month of birth, and age of kid (days) as covariate that had significant effects, and random effects direct additive genetic, maternal additive genetic, maternal permanent environmental effects and residual. (Co) variance components were estimated using univariate and multivariate analysis by WOMBAT software applying four animal models including and ignoring maternal effects. Likelihood ratio test used to determine the most appropriate models. Heritability (h(a)(2)) estimates for BW, WW, ADG, and KR according to suitable model were 0.12 ± 0.05, 0.08 ± 0.06, 0.10 ± 0.06, and 0.06 ± 0.05, respectively. Estimates of the proportion of maternal permanent environmental effect to phenotypic variance (c(2)) were 0.17 ± 0.03, 0.07 ± 0.03, and 0.07 ± 0.03 for BW, WW, and ADG, respectively. Genetic correlations among traits were positive and ranged from 0.53 (BW-ADG) to 1.00 (WW-ADG, WW-KR, and ADG-KR). The maternal permanent environmental correlations between BW-WW, BW-ADG, and WW-ADG were 0.54, 0.48, and 0.99, respectively. Results indicated that maternal effects, especially maternal permanent environmental effects are an important source of variation in pre-weaning growth trait and ignoring those in the model redound incorrect genetic evaluation of kids.