ali javadmanesh

The availability of genomic data, such as quantitative trait loci (QTL), has played a pivotal role in understanding the genetic components of various traits. This study aims to investigate critical and hub genes related to economic traits such as growth rate, body fat deposition, and feed consumption by investigating known QTLs by using protein-protein interaction networks (PPI) in chicken species. QTL coordinates for these traits were acquired through the Animal QTL database. Then, genes related to each QTL were obtained from the chicken reference genome (Gallus gallus bGalGal1.mat.broiler. GRCg7b) provided in the NCBI database. Critical genes related to known QTLs based on PPI were identified using Network Analyzer, CytoHubba, and MCODE applications in Cytoscape_v3.8.0 software. The results of this study showed 452, 83, and 75 genes involved in growth rate, body fat deposition, and feed consumption traits, respectively. Several new hub genes related to each trait were found and confirmed by PPI in Cytoscape. Some novel genes for studied traits were EEF1D, UBE2D1, TRIP13, PSMB3, and FZR1 for growth rate, ARPC2, NCAN, and SUGP1 for body fat deposition and LAP3, and SGPP2 for feed consumption. Some hub genes reported in previous studies were also identified in this research for growth rate (NCAPG, MED1, KPNA3, and EP300), body fat deposition (TULP), and feed consumption (MED9, LCORL, COPS3, LAP3, and TAPT1). The common important genes identified between the three traits that were reported in previous studies related to the traits were MNR2, CRYBA2, and MIR375 genes. It can be concluded that novel genes have molecular functions related to economically important traits. Therefore, newly discovered hub genes can be suggested to be used for selecting birds in future broiler breeding programs and basic research on functional genomics.

The current study aimed to determine the optimum level of ground flaxseed needed to improve performance and enrich broiler meat with omega-3 fatty acids (n-3 FA). A total of 360 twenty-five-day-old male broilers (Ross 308) were reared on floor pens and fed diets supplemented with ground flaxseed during the finisher phase (d 25-45). The chickens were assigned to four treatments of six replicates as follows: 1) corn-soybean meal (CSM) based diet as control; 2) CSM supplemented by 3% ground flaxseed (flax3); 3) CSM supplemented by 6% ground flaxseed (flax6); 4) CSM supplemented by 9% ground flaxseed (flax9). Results showed that flax6 increased (P < 0.05) daily gain (ADG) and feed intake (ADFI), while it did not affect feed conversion ratio (FCR). In addition, flax9 decreased (P < 0.05) ADG and ADFI, and impaired (P < 0.05) FCR compared to the control group at the end of the experiment (d 45). Feeding flax6 increased (P < 0.05) polyunsaturated fatty acids (PUFA) and n-3 FA in breast and thigh muscles and lowered (P < 0.05) abdominal fat pad weight compared to the control group. Results revealed that feeding birds with ground flax6 improves growth performance, reducing fat depots and enriching meat with n-3 PUFA without negatively affecting gut morphology.

Manganese is an essential trace element that acts as an activating component of many crucial enzymes such as alginase and pyruvate carboxylase. It is involved in carbohydrate, lipid, and protein metabolism, as well as in vital biochemical reactions (Hassan et al., 2020). Additionally, manganese serves as a cofactor in the synthesis of chondroitin sulfate and plays a significant role in bone formation in broiler chickens (Mwangi et al., 2019). Moreover, manganese is vital for the antioxidant and immune systems of animals (Patra and Lalhriatpuii, 2020; Wang et al., 2018). In the production of broiler chickens, manganese sources commonly used include inorganic Mn (Mn sulfate, Mn carbonate and Mn oxide) and organic Mn (Mn chelated with amino acid and protein). Inorganic sources of manganese are cheaper, although they have low digestibility (Tufarelli and Laudadio, 2017; Yenice et al., 2015). Organic sources have excellent chemical stability and high absorption efficiency. They have not been widely used in poultry diet due to different quality levels of manufactured products, unpredictable effects and high cost (Tufarelli and Laudadio, 2017; Brooks et al., 2012). Therefore, it is important to assess new sources of manganese that have higher digestibility and lower cost. Manganese hydroxychloride is a group of minerals which solubility in water is minimal, but it becomes more soluble in acidic conditions in intestine (Wang et al., 2011). The purpose of this experiment was to investigate the different levels and sources of manganese in the diet of broiler chickens by investigating their effects on growth performance, immunity, the digestibility of different sources in different solvents, and the digestibility using the technique of Everted Gut Sacs. Manganese sulfate, organic manganese, and manganese Hydroxychloride were obtained from Ariana company. In order to measurement of the amount of dry matter and ash, one gram in four repetitions was sampled from each of the sources. They were dried at 105°C for 12 hours and dry matter was calculated through subtraction. Then samples were transferred to the oven at 550°C for 16 hours and their ash content was determined. Finally, they were digested in hydrochloric acid and passed through Whatman filter paper No. 42. After making up to volume with mili-Q water, they were read by an atomic absorption device at a wavelength of 520 to 560 nm (AOAC, 1995; Williams, 1972). In order to evaluate the solubility, three samples (0.1 g) were prepared and dissolved in 100 ml of 2% citric acid, 0.4% hydrochloric acid and deionized water (Watson et al., 1970). For assessment ability to absorb minerals by the technique of Everted Gut Sacs, 180 one-day-old broilers of the Ross 308 commercial strain were fed from one to twenty-one days old with corn and soybean based (2018). On the 22nd day to the 28th day, they were fed with a diet free of manganese and on 29th day, they were starved for one day and night. Chickens were grouped into three treatments with Hydroxychloride, organic and manganese sulfate sources with 6 replications and 10 pieces per replication. Three parts were selected from each replication for the test steps (Feng et al., 2006). Samples prepared from jejunum and ileum in two buffers, Mis-Krebs and Tris-Krebs. In order to determine the relative bioavailability of different manganese sources, an experiment was conducted with 12 treatments included four different levels of manganese (35, 70, 105 and 140 mg/kg) with three different sources including Hydroxychloride, organic and sulfate. The highest amount of dry matter of manganese was related to manganese sulfate (99.23%). The lowest was manganese hydroxychloride (92.58%). The highest ash percentage was related to manganese hydroxychloride with 86.14% and the lowest was related to organic manganese with 21.56%. The amount of manganese calculated after testing organic sources, hydroxychloride and sulfate was 5.64, 34.64 and 34.47% respectively. The organic form of manganese had the highest solubility in 2% citric acid and the lowest in deionized water with 96.12 and 34.14%, respectively. Manganese hydroxychloride also had the highest solubility in 2% citric acid solution. Manganese sulfate had the highest solubility in hydrochloric acid and the lowest solubility in deionized water. In general, manganese sulfate had the highest solubility in deionized water compared to the other two sources. Also, the highest solubility of organic manganese in 2% citric acid was 96.12% in the whole experiment. It has been reported in studies that binding minerals with proteins will be a weak chelate and when they are placed in solvents, their chelate breaks easily and dissolve (Cao et al., 2000). The results related to performance traits and primary and secondary response of antibody titer against sheep red blood cells (SRBC) showed that experimental treatments had no significant effect on them.  The results showed that the highest solubility of the organic form of manganese was in citric acid (96.12%) and the lowest was in deionized water (34.13%). Manganese hydroxychloride had the highest solubility in 2% citric acid, while manganese sulfate had the highest solubility in 0.4% hydrochloric acid. Overall, manganese exhibited the highest solubility in hydrochloric acid and the lowest in deionized water. The results of the technique of inverted intestinal segments showed that the most absorption of manganese occurs in the ileum, and these results were in line with the results of other researchers who had performed this experiment in vitro and in vivo Among the experimental treatments, the highest absorption in the technique of inverted intestinal segments was related to the organic source of manganese, and the lowest was related to the form of sulfate, 3.25% and 1.99%, respectively. At the end, the use of organic manganese in broiler diet is recommended due to its high absorption level.

Due to the increasing global demand for Gamma-aminobutyric acid (GABA) in the food and pharmaceutical industries, the expression of the recombinant Glutamate decarboxylase (GAD) and its industrial production is currently requested. Culture conditions were optimized to increase the expression level of the recombinant enzyme in different pH, temperature, incubation time, aeration levels, inoculation concentrations, concentrations of IPTG, and several carbon sources using the RSM based on a central composite design. According to the results of the quadratic regression equation, recombinant Escherichia coli BL21 (DE3) had the highest GAD expression at pH=7.2, aeration at about 120 rpm, inoculation concentrations of about 3% v/v, 2.25 mM IPTG, 37 °C, and 6 h of incubation time in the presence of 0.2% glucose. Using pure glucose as a carbon source on an industrial scale is not cost-effective for producing recombinant proteins. Therefore, using low-cost carbon sources such as corn syrup and molasses with concentrations of 1.5 and 5.65% (w/v) is an efficient method for the industrial production of recombinant GAD. The concentration of purified recombinant GAD in carbon sources of 0.2% glucose, 1.5 corn syrup and 5.65% molasses was 2.155, 2.07 and 1.96 mg/mL, respectively. In this way, the global need for GABA can be met by the industrial production of GAD.

In ovo injection of camel lactoferrin (cLF36) as an antimicrobial peptide was applied in Ross 308 fertile eggs and tested in 320 post-hatched chickens challenged with Clostridium perfringens (Cp). In 8 treatments and five replicates of 8 birds each, performance, jejunum morphometry and ileal microbial counts of chickens were assayed. Feed intake and feed conversion ratio of the chickens affected by treatments. Together with the positive control group under the Cp (10 8 cfu/g) challenge and the negative control group under the antibiotic (AB) challenge, the highest villi length was observed. The highest crypt depth was related to the treatment with the Cp challenge and the lowest value was related to the in ovo injection of cLF36 group and combined Cp and AB challenges. The number of Clostridium spp. in the ileal contents increased in the chickens challenged with Cp (P < 0.05). The greatest change was observed in the treatment with injection of cLF36 during the embryonic period and challenge with Cp and the lowest value was related to negative control treatment. In addition, the difference between treatments with cLF36 in ovo injection during the embryonic period and challenge with or without Cp challenge was significantly increased. In the groups under the Cp challenge, the population of E. coli was numerically increased. Based on the obtained results, cLF36, derived from camel milk, could change some of the indices in performance. It caused morphological changes in the villi of ilium and caused a decrease the microbial counts of Clostridium spp., similar to the AB group in the chickens challenged with Cp. Our research attempts to create a new window for in ovo administration of cLF36, according to its beneficial effects in the present study, can be introduced as a candidate for growth-promoting antibiotics.

Ascites syndrome, as a metabolic disorder, is one of the most non-infectious causes of death in the old age of breeding in the poultry industry, which causes annual losses of over one hundred million dollars and is an important economic concern. The growth rate of broiler and their high need for oxygen causes an increase in pumping, followed by heart failure, and heart failure is often associated with other diseases. Due to the relationship between the heart and the kidney, chronic heart failure leads to a decrease in filtered blood volume and a decrease in kidney function, which over time causes permanent damage to the kidneys. lncRNAs play important roles in a variety of different mechanisms related to cellular homeostasis and in a wide range of pathophysiological processes and pathogenesis of many diseases, including cardiovascular disorders, respiratory and kidney diseases, preliminary studies in human samples show shows that lncRNAs are strongly involved in the development and disease of the kidney. For this reason, the lncRNAs obtained from the RNA-seq data of the kidney tissue were investigated in the occurrence of ascites.

700 one-day-old chicks from one of the paternal lines of a commercial strain were kept under standard conditions until 21 days old. On the 21st day of the breeding period, cold stress (24 degrees Celsius) began and continued until the age of 48 days. After applying cold stress, the birds with ascites symptoms were grouped in the Ascites group and the rest in the Healthy group. On the 39th day of the breeding period, 70 slaughtered birds and kidney tissue samples from each bird were immediately transferred to the liquid nitrogen tank after separation. 16 ascites birds and 16 healthy birds were used for RNA extraction. Total RNA extraction was done individually using trizol (YTzol) solution, and then an equal amount of RNA from four tissue samples was combined and then cDNA was prepared from 4 ascites tissue samples and 4 healthy tissue samples. All small RNAs, such as rRNAs, tRNAs, etc., were removed by dt oligo beads, and finally, all mRNAs were used to prepare the library. Novagen company was used for sequencing using Illumine hiseq 2500 technology and paired-end reads. Several software such as hisat2, cufflinks, stringtie, cuffmerge and cuffdiff were used for mapping, aligning and analysis of gene expression differences. In order to extract coding and non-coding genes, FEELnc software was used with default settings. Potential target genes of lncRNAs were investigated by searching for protein coding genes located within 100 kb upstream and downstream of each lncRNA. In the following, a positive and negative correlation of 90% was obtained between two groups of coding and non-coding genes based on the degree of expression change. In order to investigate the metabolic, structural and functional pathways of significant genes, the Enrichr database, which is connected with other databases such as KEGG, was used.

In the current research, a total of eight samples produced 187640642 million paired reads with a size of 150 nucleotides and after quality control, 185258819 uncontaminated reads were obtained. The number of 1421 lncRNA transcripts related to 921 gene loci and 154 related target genes were identified in the comparison between ascites and healthy birds. Then, this number of genes were identified (154 genes) in order to check their functional characteristics using the Enrichr database, five functional pathways Glycine, serine and threonine metabolism, Rap1 signaling pathway, Sphingolipid metabolism, Phosphatidylinositolsignaling system, Mucin type O-glycan biosynthesis and related genes were significant. Out of 13 significant lncRNAs in these biological pathways, 12 are located on the antisense direction and one is located on the sense direction. In addition, 9 lncRNAs are exonic, 3 intronic and 1 in downstream position. These pathways are activated as damage modifiers in hypoxic conditions caused by ascites and provide the required energy and maintain kidney homeostasis in response to oxygen tension caused by ascites. On the other hand, they act as cell survival, increase proliferation and anti-apoptosis, which on the one hand reduce kidney damage and on the other hand make it function better, and in this way, reduce complications caused by ascites kidney damage.

Therefore, by targeting the important pathways of biology obtained and the genes affecting them for the prevention and treatment of ascites disease, it will provide a new insight for breeding.

15acetyl-deoxynivalenol (15ADON) is the most common chemotype of dioxynivalenol (DON) mycotoxin, which cannot be controlled by common methods such as absorbents. Hence, enzyme-based methods are suggested for detoxification of these types of mycotoxins, which requires bioinformatics studies before laboratory investigations. Therefore, the aim of the present study was to investigate the binding energy of DEP-A and DEP-B enzymes with 15ADON through molecular docking. The three-dimensional structures of DEP-A and DEP-B proteins were predicted using the SWISS MODEL server. Then, the stability of these structures was evaluated in molecular dynamic conditions. For this purpose, the simulation was carried out with GROMACS software and then the RMSD curve of these two enzymes was drawn to check the stability of the predicted structure. H-DOCK online server was used to performed the interaction of DEP-A enzyme with 15ADON and DEP-B with Oxid15ADON intermediate. Checking the accuracy of the predicted structures by ERRAT Verify3D, Z-score and Ramachandran plots showed that the prediction of tertiary structures successfully performed. The RMSD curves showed that DEP-A and DEP-B were stabilized in 240 and 40 nanoseconds with 0.58 and 0.35 nm, respectively. The results of molecular docking also showed that both DEP-A and DEP-B enzymes could bind to their substrates with relatively strong binding energy -157.90 and -141.78, respectively. Overall, it can be concluded that both studied enzymes were able to bind to the 15ADON chemotype of DON in the appropriate position, which shows that these enzymes can be effective in deactivating this chemotype, although laboratory studies are needed to confirm the results

Phytases are classified as 3-phytases (E.C.3.1.3.8), 5-phytases (E.C. 3.1.3.72) and 6-phytases (E.C. 3.1.3.26) based on the position of the first phosphate residue removed from the myo-inositol ring of phytate. Yeasts are particularly suited to expression of foreign proteins for numerous features mean while some of them shows probiotic properties. Pichia pastoris, has been developed for the production of various recombinant proteins and growth into high cell densities in an inexpensive medium. Accordingly, Pichia pastoris is an appropriate secretory system for obtaining larger quantities of correct products, in compared to other host cells. The coexpression of digestive enzymes in a single recombinant cell system would thus be advantageous. The objective of this study is to determine whether combining fungal phytases (3-phytase) with bacterial phytase (6-phytase) was more effective than each phytase alone in degrading of plant phytate. we tested the new vector, aimed to clone and coexpress the phytase genes isolated from E. coli and aspergillus niger and transformed into Pichia pastoris. Evaluations were made for the biochemical properties of the active expressed phytase.

The nucleotide sequence of phyA and appA2, 2a peptide and alpha factor were obtained from NCBI database. A coexpression system for the extracellular production of phytase of Aspergillus Niger (3-phytase) and phytase of E. coli (6-phytase) will be established in Pichia pastoris yeast. Plasmid that used in this study was pPIC9k. The genes for each enzyme are fused in-frame with the “a-factor” secretion signal and linked by the 2A-peptide-encoding sequence. After receiving the synthetic plasmid with fragments, plasmid that contained phyA and appA2 was cloned in DH5@ and after that digested by SacI and electrotransfered into Pichia pastoris. Positive cells are resuspended at BMMY containing methanol as an inducer. To follow the induction, methanol was injected into the culture every 24 hours in order to reach a definitive concentration of 0.5 percent. The recombinant protein was analyzed using sds-page.

The results showed that the recombinant phytase gene was transferred to Pichia pastoris and the results of PCR confirmed that. The molecular weight of the produced recombinant phytases was estimated to be around 45 and 80 kDa for appA and phyA, respectively. The recombinant protein has phytase activity equal to 160.97 U/mlConclusions;The designed phytase genes containing phyA and appA were successfully cloned in DH5a and the recombinant plasmid was transferred to Pichia pastoris for high expression. Recombinant yeast will be used for further experiments.

Sheep are used as a genetic model to study the relationship between genetic diversity and ovulation rate. Previous studies have shown that ovulation rate and litter size can be controlled by a set of genes called fecundity genes . Three fertility genes have been identified in sheep called BMPR1B or FecB, GDF9 or FecG and BMP15 or FecX. Tetra-ARMS-PCR is a suitable alternative method in the context of expensive methods such as sequencing and PCR-RFLP to identify SNPs whose sequences are known. The entry of the Booroola allele into the Afshari breed increased the frequency of litter size. The aim of this study was to investigate the polymorphism of two fertility genes including FecB and FecG in Mughani, Afshari and Baluchi sheep in Khorasan Razavi province.Blood samples were taken from 95 Afshari, Baluchi and Mughani sheep. Two pairs of control (outer) and specific (inner) primers were used to amplify FecB and FecG gene fragments by the Tetra-ARMS PCR method. Temperature cycling of PCR amplification for FecB started at 94°C for 4 minutes, followed by 35 cycles consisting of 94°C for 25 seconds, annealing temperature at 54°C for 35 seconds, extension at 72°C for 20 seconds and a final extension at 72°C for 5 minutes. For amplification of the G1 point mutation on the FecG gene, the annealing temperature was 54°C for 35 s, extension was 70°C for 40 s, and final extension was 70°C for 5 minutes. The PCR products were electrophoresed on a 2% agarose gel.Three genotypes have been observed for the FecB gene in Afshari sheep; wild homozygous (++), heterozygous (B+) and homozygous mutant (BB). All Mughani and Baluchi sheep were homozygous for this gene. A 108 bp band was detected for mutant homozygotes. A band of 213 bp was observed in wild homozygotes. The frequency of wild homozygotes was high in the three breeds,. The frequency of the wild allele in this breed was 0.39 and that of the mutant allele 0.61, the overall frequencies for the three breeds being 0.8 and 0.2, respectively. The result of Tetra-ARMS-PCR for the G1 point mutation of the GDF9 gene showed polymorphism in all three breeds, however, the frequency of wild homozygotes was high. In the Balochi breed, only two animals (4%) were heterozygous and 96% of the animals showed the wild homozygous genotype. In the Mughani breed, 16% were heterozygous and only one animal was homozygous mutant. In addition, only one heterozygote was observed in the Afshari breed. Several studies have shown the association of the FecB, FecG and FecX genes with litter size in sheep. Due to the high frequency of wild homozygotes and the fact that Mughani and Baluchi ewes mostly gave birth to single lambs, the role of FecB mutation in litter size of Afshari ewes was observed. The ram used in this herd was heterozygous for FecB. In general, it can be concluded that the mutant FecB allele has a correlation with litter size in Iranian sheep. However, the statistical confirmation of this issue requires a dedicated study with a detailed record of reproductive traits.The results of this study demonstrated the presence of a Booroola mutation in the Afshari ewes that were offspring of heterozygous rams. In addition, all of these ewes had litter size in at least one of the two pregnancies. Hence, the Booroola mutation may potentially increase the litter size of ewes. However, a more comprehensive study measuring biological indicators such as sex hormone levels, ovulation rate and follicle size is needed to demonstrate the effect of these types of mutations on increasing fertility.

Introduction[1]: Over the years, animals have been exposed to various factors such as natural selection, genetic drift, and multiple mutations, so such factors have caused changes between and within species. The genetic mutations that occur in the populations of domestic animals, will be added to the merits of animals who contain these genetic mutations and they will have more breeds. These mutations are also repeated in their breeds. If a new SNP in a population increases the competence of its carriers compared to other members of society, this choice will make the more deserving individual more involved in shaping the next generation. The most important statistical tests based on demographic differentiation are the FST statistics, which identify distinct positions under positive selection, which are of particular importance for economic characteristics. One of the best ways to understand physiological processes is to analyze gene regulation networks. Identification of genes involved in economic traits as molecular markers in breeding is of special importance. Gene regulation networks enable the researcher to study all of the genes together. The aim of this study was to identify selection signature regions and candidate genes related to economic traits. The necessary data for this research were acquired from two sources, namely NEXTGEN and HAPMAP. The dataset encompassed breeds such as Afshari (41 individuals), Ghezel (35 individuals), Moghani (35 individuals), and eight wild sheep. The initial objective was to assess data quality and perform filtration on raw data. For the remaining single nucleotide polymorphisms (SNPs), those not conforming to Hardy-Weinberg equilibrium were considered indicative of genotyping errors. A stringent probability level of 10⁻⁶, determined through Bonferroni correction, was applied. Various stages of quality control were meticulously executed using PLINK v1.9. Additionally, the study involved identifying animals positioned outside their respective groups, contributing to a comprehensive understanding of the population structure within the two groups. Principal component analysis (PCA) were done in R software. The FST index was proposed to study the distinction between subpopulations and identification of selection signature. the population structure of wild and domestic sheep breeds was analyzed. PCA analysis was performed using genotype information of the samples to investigate how the animals were grouped Investigation of identified genes using SNPs in the upper 1% range of FST were identified by Plink v1.9 software. In addition, the DAVID database (http://david.abcc.ncifcrf.gov) was used to determine biological routes. At this stage, it is assumed that genes that belong to a functional class can be considered as a group of genes that have some specific and common characteristics. GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes. The results showed that adjacent SNPs are highly dispersed in several genomic regions. From 34556 SNPs after filtration above 1%, SNPs with higher FST stabilization index (340 SNP) with FST range from 0.304 to 0.472 were selected. Selected SNPs consisted of 95 genomic regions on 23 chromosomes between domestic and wild sheep. Most regions were located on chromosomes 13 and 7 had 14 and 9 gene regions, respectively. Examination of the relationship between QTLs and important genes in selected areas showed that 95 genes related to economic traits were identified. QTLs with important economic characteristics including quality and quantity of meat, milk, fat, bone, immune system and parasite resistance were reported. Most QTLs were located on chromosomes 2, 3, 5, 6, and 7, indicating that the most positive mutations occurred on these chromosomes. Most of the identified biological pathways related to ion channels through cell membranes are neuromuscular processes, Brain and cerebellum growth, metencephalon growth, membrane ion membrane transport, and pathways involved in regulating ion transport in cell membranes. Genes identified in different genomic regions can be considered as selective candidates. A number of genes studied as selection signatures reported were consistent with previous studies. Important genes were included: GABRB1, GRM3, HERC1, HERC3 and KCND2. The study of genomic regions showed that these regions are directly and indirectly related to the quality and quantity of meat, milk, fat, bone, immune system and parasite resistance. Identifying important economic traits and locating parts of the genome that have changed as a result of selection could be used in sheep breeding programs. However, in this research we had limitations such as the incompleteness of information related to functional annotation of genes in sheep species and also the small sample size of this study. Therefore, in subsequent studies with more samples and more breeds of domestic and wild sheep in Iran, a better understanding of candidate genes for important economic traits in domestic and wild species would be achieved.

Among different sheep breeds in the world, the Texel breed is known as a meaty and muscular breed. Skeletal muscle growth is a step-by-step and exponential process from differentiation, development and maturation, which is regulated by gene networks and cell signaling pathways, and several genes and factors are involved in the process of muscle fiber formation and their growth and hypertrophy (Badday Betti et al. 2022). The study of gene expression is done with several methods, and this gene expression information is used in breeding programs as a tool to improve phenotypic choices. Databases are a large source of expression data that can be used by bioinformatics methods to integrate heterogeneous data from different studies and platforms. In this study, by integrating the microarray and RNA-Seq data available in the database belonging to the muscle tissue of Texel breed sheep, the transcriptomic profile of the muscle was compared at two ages of embryonic and adult. Microarray data related to longissimus dorsi muscle tissue with three replicates d-70 embryos from GEO database with accession number GSE23563 and RNA-Seq data related to muscle tissue from six samples with two replicates from adult individuals from ArrayExpress database were selected. Limma, Biobase and GEOquery software packages were used to calculate the expression values of the microarray data related to the embryonic age  in the R environment, and Tuxedo, HTSeq and DESeq2 packages were used in the Linux and R environment to calculate the expression values of the RNA-Seq data (Kamali et al. 2022; Sahraei et al. 2019). Then two types of expression values were integrated and to eliminate non-biological effects, the batch effects were also removed. Next, differential genes were identified with the limma software package. In order to identify the relationship between the identified differential genes, the gene network was drawn between them by software of Cytoscape version 3.7.1 and String 1.5.1 program. next, due to the vastness of the gene network, each network was clustered with MCODE 1.6.1 and CytoCluster 2.1.0 programs (ClusterOne algorithm) and significant clusters (P-value < 0.05) were identified (Saedi et al. 2022). In order to better understand the ontology and function of the identified differential genes, the Gene Ontology of the genes was investigated using software of Cytoscape version 3.7.1 and ClueGO 2.5.9 and CluePedia 1.5.9 programs. After receiving the Gene Ontology results, significant Gene Ontology terms (P-Value < 0.05) related to functional groups were identified. Finally, the selected genes (Adj P-Value < 0.05) were identified and introduced in these two age groups. After quality control, correcting and normalizing the microarray data, the GPL10778 platform annotation file with 1042520 Probe ID was used to calculate their expression values. After relevant analyzes of 9289 Probe ID identified related to the data of this study, 7918 Gene Symbol was identified finally. After quality control, trimming and normalizing the RNA-Seq data in total, the number of Ensembl_Genes based on which the reading values were calculated by HTSeq was 27056. After removing IDs that had zero readings in all 6 samples, 10855 IDs remained. Then, these 10855 Ensembl ID were merged with the annotation file to obtain Gene Symbol, and finally 9417 common genes were identified between the six samples of adult age. The results of differential expression analysis showed that there were significant differences in the expression of 62 genes (37 increased and 25 decreased) in the muscle tissue between adult and embryonic age. By creating a gene network between differential genes, 15 selected genes were identified, including MYH1, ACTN3, CASQ1, TMOD4, FBP2, SLC2A4, MX1, COX4I1, SOD2, MFN2, UQCRB, UCP3, PRKAB2, PHKG2, PPP1R3C. The function of these genes has been proven in cell proliferation, protein synthesis, myofibril formation, and lipid metabolism. Differential gene enrichment analysis revealed some biological processes such as Vasculogenesis, positive regulation of ossification, positive regulation of muscle tissue development, regulation of muscle contraction, contractile fiber part, calcium signaling, calcineurin-NFAT signaling cascade and regulation of receptor signaling pathway via JAK-STAT, the molecular function of regulating cation channel activity and the cellular components of the contractile fiber. This study in addition to confirming the accuracy of the integration method of two types of heterogeneous data, provided a general view of the transcriptomic differences of Texel sheep muscle tissue at two important age points to be a useful source for biological investigations of genes related to muscle growth and development in sheep.

Identification of several genomic markers sequenced in farm animal enable us to study the structure of their genome. Samples from different parts of the world are usually used for sequencing genomic markers. Information on the sequence of specific markers of domestic animals of each geographical area will improve our knowledge about their genomic structure. The sequence of specific genome markers for Iranian native sheep were not yet identified. Present study aims to identify single-nucleotide polymorphism (SNPs) influencing important economic and physiological traits of Iranian domestic and wild sheep as candidate markers using selection signature.

In order to identify significant genetic variants under selection in domestic and wild sheep, the whole genome sequence of 20 domestic (Ovis aries) and 14 wild sheep (Ovis orientalis) obtained from the Next Gene project was used. After doing quality control, variant under selection were detected using statistical methods consisting iHS and XP-EHH. Genetic variance for identified variants were estimated. The genetic variance of known variants in Merino, Suffolk, texel and Afshari were also estimated. The threshold for selecting variants based on iHS and XP-EHH methods were considerd to be 99.9% in domestic sheep and 99.9% and 0.001% in wild sheep, respectively. Finally, variants with genetic variances higher than 0.25, were identified and suggested as candidate markers.

In present study, 170 genomic variants with iHS and XP-EHH values higher than 3.83 and 3.44 in domestic sheep and 150 genomic variants with iHS values higher than 3.05 and XP-EHH values lower than -4.43 in wild sheep were identified and suggested as candidate markers. Genetic variance of these variants were 0.27 to 0.50 and the genetic variance of known variants in Merino, Suffolk, Texel and Afshari were from 0.02 to 0.50. This comparison shows the importance of identified variants in Iranian domestic and wild sheep. Most of identified variants in domestic and wild sheep associated with economically important traits including carcass, milk and wool related traits. The ontology of genes related to identified variants showed that these variants are located near genes related to metabolic process of production and reproduction traits

Present results showed that there are many significant genetic variants associated with economic traits in domestic and wild Iranian sheep which are not included in the commercial sheep arrays available in the market. Identification of new SNPs related to economic traits in domestic and wild sheep may help to improve the studies related to genomic structure of Iranian sheep. These results together with similar studies could be efficiently used for producing SNP arrays designed for Iranian native sheep.

Habitat eradication and loss of animal species have created a new international hazard for wildlife conservation. National parks are considered as suitable places that can serve dual functions of biodiversity conservation and ecotourism. As recommended by the Food and Agriculture Organization (FAO), microsatellites have been used for animal biodiversity assessment. For this reason, Iranian urials population genetic diversity was studied by analyzing of 10 microsatellite markers in 75 skeletal muscle samples that were collected from Tandooreh National Park, Northeastern of Iran. Species of samples validated by sequencing of the control region from mtDNA. Allelic frequencies for each locus in the population and different measurements of within-breed genetic variations were computed by the POPGENE32 software. The number of alleles per locus counted from 5 to 8, with an average of 6.1. The polymorphism information content was calculated between 0.66-0.74 with the average of 0.7. Observed heterozygosity ranged from 0.223 (MaF214) to 0.776 (OarFCB128) with an average about 0.584 while the average expected heterozygosity for all studied loci was 0.785 ranging from 0.765 (BM8125) to 0.807 (MaF36). High levels of expected heterozygosity can be attributed to some factors such as low level of inbreeding, low selection pressure, and high allele number. However, findings of the present study of the high variability of the Iranian urials showed the presence of a possible ‘hot spot’ genetic diversity for wild urial population in the Northeast of Iran. In conclusion, values of genetic diversity revealed that the Iranian urial population harbor unique and appreciable reservoirs of diversity.

DNA-based approaches can now be utilized as low-risk methods to change gene expression. It appears that this approach has the ability to partially replace RNA-based approaches for altering gene expression, which in the majority of cases leads to immunological responses in patients. When utilized as a technique to silence target gene expression, DNA interference (DNAi) is a single-stranded DNA created to complement the upstream region of a gene. This DNAi molecule is stabilized using a variety of chemical changes, including phosphorothioates, methylphosphonate setC, etc. Several studies of the efficient application of DNA-based methods both in eukaryotic cell lines and the therapy of various disorders, such as Duchenne muscular dystrophy, cancer, etc., have been mentioned. Understanding the DNAi process, its transfer carriers, stabilization techniques, and their limitations is crucial for advancing these applications and predicting the future of DNAi both in basic science and the treatment of disorders brought on by abnormal gene expression. The main purpose of this review is introducing benefits of using DNAi in gene silencing. this review has discussed about different applications of DNAi in drug discovery and treatment, criteria of designing DNAi, possible modifications, introducing different types of carriers and limitations of DNAi administration.

Globally, clinical mastitis (CM) is a significant disease in the dairy industry and has a tremendous economic impact because of the significantly reduced amount of milk production. Antibiotics are medicines used to treat infections, particularly those of bacterial origin. Misusing these common drugs leads to emerging resistance bacteria and public health concerns in human and animal medicine worldwide. Therefore, the use of natural alternatives with low effects is recommended. This article aims to evaluate the antibacterial activity of peptide nisin on mastitis bacteria and its synergistic effect with CLF36 peptide in vitro. Recombinant peptide nisin and CLF36 were obtained from previous research. The minimum inhibitory concentration (MIC) test was performed using the microdilution method on bacteria extracted from animal mastitis, such as Clostridium perfringens, Proteus mirabilis, Enterococcus faecalis, Salmonella typhimurium, Pseudomonas aeruginosa, and Listeria monocytogenes. This study showed that nisin and CLF36 alone had an inhibitory effect on all the studied bacteria in the 64-32 and 256-32 μg/ml concentration range, respectively. Also, the combination of nisin and CLF36 showed a general synergistic interaction for all used strains (FIC I < 0.5). This study demonstrated that combining these two peptides could reduce the risk of developing drug resistance by creating synergistic effects with a minimum concentration of each of the two peptides.

Lactoferrin is secreted in the apo-form from epithelial cells in most exocrine fluids, such as saliva, bile, pancreatic and gastric fluids, tears and, particularly, in milk. Lactoferrin is the most dominant protein in milk after casein. This protein plays a crucial role in many biological processes including the regulation of iron metabolism, induction and modulation of the immune system, the primary defense against microorganisms, inhibiting lipid peroxidation and presenting antimicrobial activity against various pathogens such as parasites, fungi, bacteria, and viruses. The major antimicrobial effect of lactoferrin is related to its N-terminal tail where different peptides for instance lactoferricin and lactoferrampin which are important for their antimicrobial abilities are present. cLF chimera (CLF36 peptide ) was derived from camel lactoferrin (cLF) consisting of 42 amino acids and has primary sequence of DLIWKLLVKAQEKFGRGKPSKRVKKMRRQWQACKSSHHHHHH. In addition, the results of previous study showed that cLFchimera had anti-inflammatory and regulatory activity of the immune system. Nuclear factor kappa B (NF-kB) transcription factors regulate several important physiological processes, including inflammation and immune responses, cell growth, apoptosis, and the expression of certain viral genes. NF-kB dimers are located in the cytoplasm in an inactive form through association with any of several IkB inhibitor proteins. The phosphorylation and degradation of IkB have received great attention as key steps for the regulation of Nuclear factor kappa B (NF-kB) complexes. Phosphorylation of the IkB by IKK signals it for ubiquitination at specific lysine residues. The aim of this study was to investigate the inhibitory effects of the recombinant camel Lactoferrampin-Lactoferricin on nuclear factor kappa B (NF-кB) pathway.

CLF36 peptide was prepared through a previous study in Biotechnology Laboratory of Animal Science Department, Faculty of Agriculture, Ferdowsi University of Mashhad (GenBank accession number: MH327768.1). Protein data for inhibitory combinations of the Nuclear factor kappa B (NF-kB) pathway was collected from the Protein Data Bank (PDB) And UniProt.Physico-chemical properties analysis (atomic state, isoelectric point, half-life, hydrophobicity hydrophilicity , barometric and pH) was done using Expasy Prot Param online server. The inhibitory effects of this peptide was assessed by Molecular Docking Simulation (In silico). the simulation of the interaction (Docking) of CLF36 peptide with Nuclear factor kappa B (NF-kB) signaling pathway in upstream, pro-inflammatory cytokines (e.g., TNF-α and IL-6) and in downstream, cytoplasmic IKKB and NF-κBp65 was done using ClusPro 2.0 software online.interaction diagram created by LigPlot+ showing the hydrogen bond network and the hydrophobic interactions of CLF36 peptid with the upstream and downstream Nuclear factor kappa B (NF-kB) pathways.

Bioinformatics analysis on The molecular interaction of this peptide with the active site of NF-κB proteins suggested that in may have role of the modulators and Anti-Inflammatory of immune processes by inhibitory effect on the TNF-α and IL-6 cytokines in upstream and IKK-β and NF-κB-p65 in downstream of the NF-κB signaling pathway. This results are similar to the inhibitory effects of Infliximab, Camelid Fab , NEMO and  GILZ on the Nuclear factor kappa B (NF-kB) signaling pathway. Infliximab (Remicade) is a chimeric mAband its use is not very well tolerated in the majority of patients, infliximab therapy leads to the production of antibodies to infliximab in a small subset of patients. the  Camelid Fab antibody with the highest (femtomolar) potency, displays a very large surface of interaction with IL-6. the regulatory role of NEMO in the IKK complex, since a number of genetic and biochemical studies clearly demonstrate that proinflammatory IKK activation is absolutely dependent upon the presence of functional NEMO. Glucocorticoid-induced leucine zipper (GILZ) is a glucocorticoid responsive protein that links the nuclear factor-kappa B (NFκB) and the glucocorticoid signaling pathways. Func tional and binding studies suggest that the proline-rich region at the carboxy terminus of Glucocorticoid-induced leucine zipper (GILZ) binds the p65 subunit of Nuclear factor kappa B (NF-kB) and suppresses the immunoinflammatory response.

  The results of the interaction (Docking) of CLF36 peptide with Nuclear factor kappa B (NF-kB) signaling pathway indicates that, in upstream, will be inhibitory effect of CLF36 peptide in active site of pro-inflammatory cytokines (e.g., TNF-α and IL-6) and in downstream, cFL36 peptide will bind to protein receptors of cytoplasmic IKKB and NF-κB p65. Therefore, these findings may provide a theoretical basis for therapeutic mechanisms of CLF36 peptide.

Today, ostrich breeding has been widely developed in Iran and other countries due to the ability of this animal to produce quality meat, leather, and oil. However, one of the main problems in breeding them is sex determination using aggressive techniques with low accuracy. This study aimed to determine the sex of immature ostriches using specific primers in a multiplex PCR reaction. This study considered  20 specimens of unspecified immature and six specimens (three adult males and females) of known-sex African ostriches as controls. SS and OSFES primers were used to amplify part of the female-specific sequence and 18S primer was used as a control in a PCR reaction. The presence of SS and OSFES bands in gel electrophoresis indicated the amplification of the desired parts related to the female sex and the absence of these bands indicates the male sex of the species. In total, out of 20 African ostriches studied, 50% of them belonged to females and 50% of them belonged to males. Later, with the growth of immature individuals, the results of this experiment were confirmed. In this study, it was found that the use of feather samples for DNA extraction and multiplex PCR is a suitable, accurate, and cost-effective method in identifying and determining the sex of young ostrich and leads to more real and reliable results, avoiding stress in birds.

In recent decades, advances in DNA-based marker technology and the availability of genomic data such as quantitative trait locus and the study of gene utilization through bioinformatics methods have played an important role in understanding the genetic potential of different traits. In this study, QTLs related to parasite resistance in sheep were prepared through Animal QTL database. The genes for each QTL were then obtained from the sheep reference genome in the NCBI database. Next, in order to understand the relationship between the obtained genes, gene networks for each trait were drawn using Cytoscape v3.8.0 software, and finally Cytoscape software was used to interpret gene networks and study gene ontology. The results of this study showed that there were a total of 71 QTLs for the parasite resistance trait, which included 198 genes. Most of these markers were mapped using methods such as the Genome-Wide Association Study (GWAS), Regional Heritability Mapping (RHM), or Single Nucleotide Polymorphisms (SNPs). Ontological analysis in this study showed 20 biological pathways that four pathways contributed more than others, including: pyruvate metabolic process, antigen processing and presentation of peptide antigen via MHC class I, neural migration and cell adhesion molecule binding. In this study, the ontology of genes was investigated and the metabolic pathways associated with the parasite resistance trait in sheep were obtained through QTLs. Regarding methods and result of the current study, genes and gene ontology associated with other economic traits in sheep a well as other livestock species could be determined.

Poultry and meat products are the largest sources of non-typhoid salmonella infections in most countries. Studies have shown that raw foods of animal origin, especially poultry and its products, are the main source of contamination of kitchens and restaurants. In terms of growth conditions, these microorganisms are resilient bacteria and easily adapt to their environmental conditions. Salmonella has been known to cause intestinal disease for many years and has been reported as the most important cause of food poisoning. According to Iranian and international standards, there should be no S. enteritidis or S. typhimurium in 25 grams of food. DNA-based methods for the identification and differentiation of Salmonella serovars have been designed and applied using specific primers at the genus and serovar levels. Therefore, they can be used as useful and rapid screening tests, as well as to supplement or replace conventional biochemical and serological tests. Real-time PCR, with the most accurate and reliable results using a fluorescence probe, which of course has a high cost. In this method, sequence specific fluorescence probes are used, and as a result, in the target molecule, screening and determination the presence or even the concentration of specific sequences is possible. Therefore, even in the presence of other types of nucleic acid molecules, the results are obtained quickly and have a high level of specificity. Under these conditions, if specific probes with different florescence dyes are used, even multiple targets can be detected in a single PCR reaction. The aim of this study was to identify S. enteritidis or S. typhimurium by PCR and Salmonella spp. by real time PCR method in poultry products. 

In total, 45 samples of poultry products, including chicken breast, liver and gizzard (15 samples each) were purchased from different regions of Mashhad and from various companies and transferred to the laboratory in accordance with hygienic standards. For each sample, 25 g of tissue was isolated and homogenized under sterile conditions and DNA extraction was then performed using a DNA extraction kit. The extracted DNA was evaluated by agarose gel electrophoresis. The purity and quantity of DNA extracted from each sample was examined by spectrophotometry method. In the next step, in order to identify the genus Salmonella, the samples were examined by real time PCR. In this method we used an internal control to ensure that negative results are not false negative due to inhibitors. The results of real time PCR showed that out of 45 samples, nine samples were infected with Salmonella. Then, these nine samples were evaluated for Salmonella typhimurium and Salmonella enteritidis infection by conventional PCR method. 

The results showed that out of nine samples that were positive in real time PCR test, seven samples were contaminated with Salmonella typhimurium, of which five samples were related to chicken breast and two to liver. Regarding Salmonella enteritidis infection, out of nine samples, only one sample was contaminated, which was related to chicken breast. Conventional methods have been traditionally used to enumerate target bacteria in food. However, these methods have some limitations and require considerable time and labor. Previous studies have already shown that real time PCR is more effective than conventional bacteriological methods for the detection of Salmonella spp. In a study by Whyte et al. (2002) The presence of Salmonella was assessed by traditional culture methods and by a Salmonella-specific polymerase chain reaction (PCR) test. Salmonella was recovered from 16% of samples using traditional culture methods. In contrast, the PCR assay proved to be more sensitive and detected Salmonella DNA in 19% of the examined samples (Whyte et al. 2002). Results of PCR with specific primers showed that reactions in real time PCR with general primers of Salmonella spp. were done correctly. Despite of accuracy and speed of real time PCR to detect DNA of microorganisms, further studies are developed to have more advantages. Loop-mediated isothermal amplification (LAMP) showed a higher sensitivity of Salmonella detection in compare to qPCR (Vichaibun & Kanchanaphum, 2020). Although LAMP could detect trace amount of Salmonella DNA but primer design for this reaction is very difficult. However, it is important to highlight that non-viable cells can be detected by real time PCR or other DNA-based methods, which does not occur in traditional methods of culture and isolation that require viable cells for quantification (Zeng et al., 2016).

Myostatin (MSTN) is primarily expressed in skeletal muscle tissue and acts as a negative regulator of skeletal muscle growth by inhibiting differentiation and proliferation of myoblasts. Inhibition of MSTN expression could result in muscular hypertrophy. An effective therapeutic approach based on specific silencing of a target gene is provided by RNA interference. The distribution of biologically active small interfering RNAs (siRNAs) inside the target cells/ tissue, is a significant problem due to the limited stability and delivery of siRNAs. Strategies depending on vector delivery have also a limited clinical utility due to safety concerns. Thus direct application of active siRNAs in vivo is the preferred strategy. We described the efficiency of intramuscular and intraperitoneal injections of MSTN-siRNA conjugated with cholesterol into the skeletal muscle of mice. The designed siRNA molecule was complementary to the exon II of the mouse MSTN gene. Mice were injected with a weekly dose of 10 μg/kg conjucated siRNA-cholesterol intraperitoneally or intramuscularly. Our findings suggested that within a few weeks of application, siRNA-treated mice showed a significant increase in muscle mass and suppressed MSTN gene expression. Even though both types of injections increased muscle weight, intramuscular siRNA injections suppressed the MSTN gene more effectively, whereas intraperitoneal RNA injections had a more significant impact on total body weight. The cholesterol-conjugated siRNA platform discussed here may hold promise for treating several skeletal muscle-related diseases, such as atrophic muscle disease, muscular dystrophy, and type II diabetes.

The effects of curcumin and its nano-micelle form on body weight, insulin resistance, adiponectin, and blood biochemical parameters of streptozotocin-induced diabetic rats were studied. Diabetes was induced in fifty male Wistar rats which were divided into five groups treated with 1) no dietary supplements, 2 and 3) 40 and 80 mg curcumin/kg of feed, and 4 and 5) 40 and 80 mg nano-micelle curcumin/kg of feed. A group of ten untreated male Wistar rats was also considered a healthy control group. The serum concentrations of AST, ALT, glucose, insulin, triglycerides, cholesterol, HDL-C, LDL-C, and adiponectin, as well as insulin resistance, were assessed. Body weight and weight of liver, heart, and pancreas were also evaluated. Induction of diabetes increased the serum concentrations of AST, ALT, glucose, triglycerides, cholesterol, LDL-C, and insulin resistance and decreased the serum levels of insulin, adiponectin, and HDL-C, as well as body weight and weight of the heart and pancreas (p < 0.05). Nano-micelle form of curcumin alleviated the negative effects of glucose, lipid profile, and liver enzymes in diabetic rats (p < 0.05). In conclusion, the nano-micelle form of curcumin showed better efficiency compared to curcumin for improving the adverse effects of diabetes. It can be suggested that the nano-micelle form of curcumin at specific doses might be useful for diabetes treatment.

The objective of this study was to investigate the effect of whey protein concentrate (WPC) and selenium (Se) supplementation on sperm quality, antioxidant enzymes activity and lipid peroxidation in seminal plasma, liver and testis of roosters. Forty-five Ross-308 broiler breeder roosters aged 60 weeks were used for an eight-week period in a 3 × 3 factorial arrangement of dietary treatments. Three levels of WPC (0.0, 1.5 and 3.0% of diet) and selenium supplementation (0.0, 0.2 and 0.4 mg/kg of diet) with five replications were tested. Total and progressive sperm motility, sperm concentration, plasma membrane integrity, and sperm viability were significantly lower in birds treated with Se supplementation-free diet (P < 0.05). Also, abnormal sperms were significantly higher in Se supplementation-free diets when compared to the diets supplemented with 0.4 mg/kg Se (P < 0.05). The use of 1.5% of WPC resulted in significantly increased total and progressive sperm motility compared to the WPC-free diet (P < 0.05). Selenium at the level of 0.4 mg/kg along with 3.0% WPC were associated with significantly increased Glutathione peroxidase and superoxide dismutase activity in seminal plasma as compared to other levels (P < 0.05). The highest level of total antioxidant capacity (TAC) in seminal plasma was observed at the level of 0.2 mg Se (P < 0.05). Further, 3.0% WPC resulted in significantly increased TAC concentration in seminal plasma compared to the WPC-free diet (P < 0.05). Moreover, the Malondialdehyde (MDA) level of seminal plasma in selenium supplementation-free diets was significantly higher than those of other levels (P < 0.05). Glutathione peroxidase activity, TAC, and MDA levels in the testis and liver were not affected by the WPC and Se levels. It can be concluded that dietary inclusion of WPC and Se improved the semen quality, increased antioxidant enzymes activity and decreased lipid peroxidation in seminal plasma of  broiler breeder roosters.

Tail in sheep is a valuable energy source. However, in modern intensive and semi-intensive sheep industry the lean-tailed sheep breeds have more desirable and marketable. Therefore, due to the negative effect of tail size on production efficiency, researchers are looking for methods to eliminate this trait. Identification of genes involved in the process of fat deposition in tail is necessary for reducing tail size in sheep. Several genomic methods such as genome-wide association and selection signature studies or gene expression analysis for describing a possible genetic background for deposition of fat in various fat-tail breeds have been used. The aim of this study was to identify effective genes in fat-tailed sheep breeds (Afshari and Sunite) compared to breeds without tail (Dorper and German Mutton) using selection signature and gene ontology methods.

In this study, genotype information of 366 sheep (37 Afshari, 69 Sunite, 99 Dorper and 161 German Mutton) genotyped with Illumina Ovine SNP50K BeadChip genome arrays, were used. The XP-EHH method using R software package version 1.9 was used to identify selection signature. Genomic version Oar_v4.0 database NCBI was used for detecting the genomic position of SNPs in sheep genome. Candidate genes were identified by SNPs located at 1% upper range of XP-EHH using Plink v1.9 software and gene list of Illumina in R. Additionally, the latest published version of Animal genome database was used for defining QTLs associated with fat deposition traits in identified locations.

Based on the results of XP-EHH, 18 common genes were identified from comparing Afshari population with German Mutton and Dorper breeds, in which five genes (LOC114116389, LOC114118754, KCMF1, TCF7L1 and RASSF2) were associated with QTLs related to fat deposition including carcass fat percentage, internal fat amount and fat tail deposition. 15 common genes were also identified from comparing Sunite population with German Mutton and Dorper populations, in which two genes (SEMA5B and CDH9) were associated with QTLs related to fat deposition. The results of gene ontology showed that some of these genes play effective roles in signaling Wnt, growth, development and morphology of cells.

based on the results of selection signature using XP-EHH method in Afshari and Sunite breeds, RASSF2 gene was identified as a selection signature in Afshari breeds. This gene was also related to tail fat storage QTL, which was identified for the first time in this study. LOC11411689 and LOC114118754 genes related to carcass fat percentage QTL, KCMF1 and TCF7L1 genes related to the QTL of internal fat amount in Afshari breed were also identified. In addition, the SEMA5B gene associated with the QTL of carcass fat percentage and the CDH9 gene associated with of subcutaneous fat weight were identified in the Sunite breed. The results of this study could be used in sheep breeding programs to reduce fat deposition in tail, especially for Afshari breed.

Early, specific, and sensitive detection methods of COVID-19 are essential for force stopping its worldwide infection. Although CT images of the lung and/or viral RNA extraction followed by real-time reverse-transcriptase-polymerase chain reaction (rRT-PCR) are widely used; they have some limitations. Here, we developed a highly sensitive magnetic bead-based viral RNA extraction assay followed by rRT-PCR.  Case group included oropharyngeal/nasopharyngeal and blood samples from 30 patients diagnosed positive by PCR test for COVID-19 and control group included 30 same samples from COVID-19 negative PCR test individuals. RNA was extracted, using viral RNA extraction kit as well as using our hand-made capture bead-based technique. A one-step cDNA synthesis and Real Time PCR was conducted. A two-step comparison of the different viral RNA extraction methods for oropharyngeal/nasopharyngeal and blood samples was performed. Student t-test was applied with a P<0.05 considered statistically significant.  In the case group, all 30 mucosal samples extracted either with viral RNA extraction kit or with beads-based assay were COVID-19 positive although in the latter category, Cqs were much lower. Although 43% of plasma samples extracted by bead-based method were found to be positive but no plasma samples extracted with column-based kit were detected positive by Real Time PCR.  Bead-based RNA extraction method can reduce RNA loss by its single-tube performance and enhance the test sensitivity. It is also more sensitive to lower viral loads as shown in the detection of blood samples and the lower Cqs of mucosal samples.

Long non-coding RNAs (lncRNAs) compose a plentiful category of transcripts that have gained increasing importance because of their roles in different biological processes. Although the function of most lncRNAs remains unclear. They are implicated in epigenetic regulation of gene expression, including muscle development and differentiation. We aimed to identify the effect of novel lncRNAs (Alternatively spliced) and their target genes on two stages of sheep skeletal muscle growth and development. FastQC files have been used to examine the quality control and the Trimmomatic program for trimming low-quality reads from twelve longissimus dorsal muscle tissue samples (including six young and six old from Texel sheep). Hisat2, Cufflink, Cuffmerge, and Cuffdiff investigated the expression levels. Novel lncRNAs (Alternative spliced) were distinguished using NONCODE databases and Cuffcompare software. In addition, the lncRNA–mRNA interactions and regulatory network visualization were identified via RIsearch and Cytoscape software, respectively. Those 139 novel lncRNA (Alternative spliced) transcripts had been recognized, probably 65 lncRNAs interacted with their target genes and regulated sheep skeletal muscle growth and development. Three novel lncRNA transcripts (TCONS_00041386, TCONS_00050059, and TCONS_00056428) showed a strong association and five transcripts (TCONS_00055761, TCONS_00055762, TCONS_00055763, TCONS_00055764, and TCONS_00055770) had made complex network correlations with mRNAs. Our research provided more knowledge of the associated mechanisms with novel lncRNAs, which could play a role in regulating sheep skeletal muscle tissue development and growth.