جستجوی مقالات مرتبط با کلیدواژه « گوسفند » در نشریات گروه « علوم دام »

Pedigree and weight trait records belonging to 13633 Baluchi lambs descendent from 308 ram and 3747 dam which were collected in North-east animal breeding center from years 1989 to 2021 were used. Six univariate animal models with fixed (birth year, month, type, sex of lamb and age of dam) and different random effects were fitted to data. Effects of non-genetic factors on weight traits were investigated by Proc GLM of SAS software, and to estimate the variance components the Wombat software was used. All fixed effects had significant effect on the studied traits (P<0.001). Model with additive autosomal, sex linked, and additive maternal random with covariance between direct additive genetic and maternal genetic effect had the lowest AIC and was used for genetic analysis. For birth, weaning, 6, 9 month and yearling weight respectively additive autosomal heritability were 0.16, 0.34, 0.41, 0.49 and 0.56, additive sex-linked heritability were 0.004, 0, 0, 0.007 and 0.005 and maternal heritability were 0.34, 0.38, 0.32, 0.32 and 0.36. Results showed that sex-linked genes possibly have negligible and close to zero additive genetic effects on body weights at initial ages and in comparison, more noticeable effects on body weights at higher ages. In general, it is recommended to use an animal model for genetic analysis of growth traits in sheep, which is able to separate the total genetic variance into three autosomal, sex-dependent and maternal components in order to be more effective in genetic selection.

associated with milk related traits and somatic cell scores through genome-wide association study based on gene-set enrichment analysis in Valle del Belice sheep breed. To this end, the genotypic information of 476 sheep of this breed along with phenotypic records related to production traits including milk yield and milk composition were evaluated using PLINK v. 1.9. After performing various quality control steps, finally 42285 SNP markers in 426 animals were used for follow-up analysis. The results of the genome wide association study (GWAS) showed that 1830, 1577, 2186, 793, 710 and 1063 SNP markers are associated with milk yield, amount and percentage of fat, amount and percentage of protein and somatic cell score in Valle del Belice sheep, respectively (P-value ≤ 0.05). The results of the analysis based on gene-set enrichment led to the identification of pathways (candidate genes) of lipid phosphorylation (including TTC7B candidate gene), lipoprotein transport (ZDHHC17 gene), regulation of calcium ion transport (ATP2B2 gene) and pathway of peptide hormone processing (PCSK6 gene) associated with milk yield; regulation of fatty acid metabolic process (IRS1 and SLC45A3 genes) related to milk fat; the signal transduction by protein phosphorylation (ERCC6 gene) and the pathway of sulfur amino acid metabolic process (NOX4 gene) in relationship with milk protein; and finally the pathways of positive regulation of response to biotic stimulus (PRKCA gene), response pathway to external stimuli (CACNA2D1 gene), regulation of response to stress (EGFR and HSP90B1 genes) and response to bacterium (candidate gene ANXA3) related to somatic cell score.

In this study in order to estimate inbreeding coefficient and identify the ROH Islands associated with the genes under selection, the 50k BeadChip genotyped data of 206 sheep from 3 different Egyptian breeds were used. After quality control, 48361 SNPs in 204 sheep were remained for the future analysis. Inbreeding coefficient was calculated using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using the GCTA 1.0 software and run of homozygosity (FROH) using the PLINK 1.9 software. One percent of SNP with the highest frequency in ROH were considered as ROH Islands. The lowest rate of inbreeding according to (FGRM, FHOM, and FUNI) was related to Wahati and the highest was related to Saidi breed. The highest amount of FROH (0.043) was observed in Saidi and the lowest amount (0.018) was observed in Barki breed. Average length of ROH ranged from 45.02 to 205.87 Mb, while the average number of ROH ranged from 8.14 to 14.07. The highest number ROH was observed on chromosome 2, while the lowest was on chromosome 26. Average inbreeding coefficient from FROH in Barki, Saidi and Wahati were estimated 0.018, 0.043 and 0.027 respectively. A total of 62 ROH Islands with length: 24.60 Kb to 13 Mb were identified, which covering less than 1% of the sheep genome. The ROH Islands was not distributed across the genome uniform and varied among breeds, but some common were identified. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with reported genes that directly or indirectly influenced traits for adaptation and immune system (SEMA3D, CSF2, ITPR1), development of the skeletal muscle (UGGT1, ITGA2), and reproduction (ABHD16B). The results of this study revealed that, the selection processes in different sheep breeds for economic traits during several years, has led to the formation of many ROH islands in sheep genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits.

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.

Artificial and natural selection not only increases the frequency of new-useful mutations but also remains some signals throughout the genome. Since these regions often control economically important traits, identifying and tracking these regions is the most important subject in animal genetics. Also, natural and artificial selection related to adaptation and economic traits, such as litter size, results in changes at the genomic level which leads to the appearance of selection signatures. Several tests including the linkage disequilibrium-based approach, site frequency spectrum, and population differentiation-based approach have been developed to explore the footprints of selection in the genome. Domestication and selection have significantly changed the behavioral and phenotypic traits in modern domestic animals. The selection of animals by humans left detectable signatures on the genome of modern sheep. The identification of these signals can help us to improve the genetic characteristics of economically important traits in sheep. Over the last decade, interest in the detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. 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. This study aimed to identify selection signature regions and candidate genes related to adaptation and the number of lambs born.
To identify the signatures of selection in Iranian native sheep and Egyptian breeds, genomic information of 96 native sheep (including 96 Zandi) and 107 Egyptian sheep (including 59 Barki and 48 Rahmani) were used. The genomic information of foreign breeds was extracted from the Dryad database (https://dryad.com/articles/dataset). To determine the genotype of the samples, Illumina Bead Chip 50K was used. Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-6. After the quality control of the data, the hapFLK statistical method, with hapFLK v1.4 software, was used to identify selection signatures. The genomic version of the Oar_v4.0 database in NCBI was used for detecting the genomic position of single nucleotide polymorphisms (SNPs) in the sheep genome. Candidate genes were identified by SNPs located at 0.1% upper range of hapFLK using BioMart software in ensemble 109. Then, using the PANTHER database, the general biological function of the genes was checked. 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, and the QTLs in the selected region were extracted using the Animal Genome database, and the genes were compared with other research. GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.
Based on the results of hapFLK, by comparing the Zandi population with Egyptian breeds (Barki and Rahmani), seven genomic regions on chromosomes 1, 2 (three regions), 10, 25, and 26 were identified. Candidate genes of DNAJB4, FNDC3B, GULP1, ACVR1, and FGF9 were in these regions. Further investigation using bioinformatics tools showed these genomic regions overlapped with the immune system, adaptation, litter size, and lipid and muscle metabolism.
The results of this study may provide an important source to facilitate the identification of genomic regions and then, the genes affecting economically important traits in the sheep industry. However, it will be necessary to carry out more association and functional studies to demonstrate the implications of these genes. 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.

Nowadays, new studies are being conducted based on the results of GWAS studies and the mapping of gene regulation networks based on the use of AWM matrix algorithms. In the present study, to map gene networks using AWM-PCIT matrix algorithms and and the association of SNPs with sheep milk production phenotypes and compositions was used. For this purpose, data on milk production traits in Valle del Belice sheep were used. After data quality control, 469 ewes and 37228 SNPs were used for final analysis. Phenotypic data were retained for analysis and contained 5586 Test day records for six milk production traits. and their gene regulation network was plotted using the cytoscape program. The results showed that using AWM-PCIT matrix algorithms, among the candidate genes that are directly and indirectly related to milk production traits were identified GENES OSBPL3, ERBB4, VGLL4, BAZ1A, DDX25, CDH23, ITSN2, DPY30, FAT3 and CAPN10. The present study and other studies have shown that the complex process of milk production and composition is important under the influence of the gene regulation network of more than 10 genes and is associated with many other genes.In total, this study supported previous results from GWAS of milk production and composition traits, also revealed additional regions in the sheep genome associated with these economically important traits. Using these findings could potentially be useful for genetic selection in the breeding programs.

Genetic architecture of sheep reproduction is increasingly gaining scientific interest due to the major impact on sheep production systems. The present study aimed to conduct for identifying the loci associated with total number of progeny born and first lambing age in highly prolific Chios sheep using the 50K arrays.

In this research, phenotypic and genotypic data related to total number of lambs born and first lambing age in lifetime and first lambing age were obtained from 538 highly prolific sheep. The gene set analysis consists basically in three different steps: the assignment of SNPs to genes, the assignment of genes to functional categories and finally the association analysis between each functional category and the phenotype of interest. Genome wide association study was performed with reproductive traits using GEMMA software. Using the biomaRt2 R package the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 15 kb up- and downstream of the gene. Finally, a gene enrichment analysis was performed with the KOBAS platform from online bioinformatics databases for the assignment of the genes to functional categories, the GO, KEGG, DAVID and PANTHER databases were used.

In this research, 11 SNP markers on chromosomes 1, 2, 5, 7, 8, 10, 13, 15, 17, 22 and 23 were identified. Also, we identified different sets of candidate genes related to reproductive traits: QULP1, AURKA, TEX12, DLG1T, ACVR1, LCP2 and PPFIA2 in Chios sheep. Some of these genes identified in this research were consistent with previous studies. In the enrichment analysis of gene sets, 19 biological pathways related to reproduction traits were identified. Some of these pathways have important role in fertilization, ovulation rate, estrogen biosynthesis, conception rate, skeletal muscle development, early development of the fetus and puberty.

The results of this research can further reveal the role of genetic mechanisms affecting reproductive traits. Considering the conformation of previous genomic region and the new genomic regions identified in this study, the findings of this research can be used more confidently in breeding programs for important economic traits in sheep.

Crude protein is one of the most expensive components of feed and nutrients needed by animals. One of the ways to optimally use crude protein is to oscillating the level of crude protein in the diet and feeding it intermittently at intervals of one to several days. This study was conducted in order to investigate the effect of oscillating dietary protein concentration on growth performance and some rumen and blood parameters in fattening male lambs.

Three diets were adjusted with crude protein of 12, 14 and 16% and with the same metabolic energy. 36 male lambs with an average weight of 23.94±2.04 kg were used in four treatments in a completely randomized design. The first treatment received a diet with a crude protein level of 14%. The second to fourth treatments received diets with 12 and 16% crude protein at intervals of 24, 48 and 72 hours, respectively. Feed consumption, growth performance, feed conversion ratio, digestibility and some rumen and blood parameters were measured.

No significant difference was observed in terms of feed consumption and growth performance among the treatments, although the feed conversion ratio improved in the treatment with a 48-hour crude protein consumption interval and showed a tendency to be significant compared to the control treatment (p=0.063). The highest digestibility of organic matter was related to the treatment with 48-hour consumption interval, which shows a tendency to be significant compared to other treatments (p=0.091). No significant difference was observed between experimental treatments in terms of digestibility of dry matter, crude protein and neutral detergent fiber. The highest rumen ammonia nitrogen and blood urea nitrogen were in the treatment with 48-hour crude protein consumption interval (p<0.05).

The results of this research showed that the feed conversion ratio improves to some extent when using the method of creating oscillations the crude protein level of the ration and its intermittent feeding, but it had no effect on the growth performance of male lambs and feed digestibility, as well as rumen ammonia nitrogen and blood urea nitrogen increased. Therefore, it is recommended to use this strategy in feeding fattening male lambs.

Estrus synchronization is a valuable management tool that has been employed in enhancing reproductive efficiency in ewes. Synchronization of estrus and ovulation for fixed-time artificial insemination in sheep is mostly based on the insertion of intravaginal devices containing either progesterone CIDR (Controlled Internal Drug Release) inserts or progestagens (sponges impregnated with fluorogestone acetate (FGA) or medroxyprogesterone acetate (MAP)). Intravaginal sponges are usually inserted over periods of 12 to 14 day and used together with eCG, particularly out of season, administered at the time of sponge withdrawal or 48 hours prior to sponge removal. It has now been indicated that shortening the duration of progesterone treatment with intravaginal instruments, while being effective in inducing estrus and ovulation, reduces the incidence of vaginal infections and consequently improves fertility. On the other hands, it has been reported that pregnancy rates of progestagen-synchronized ewes were lower during anestrus than during the breeding season. Therefore, this study was conducted to investigate the reproductive performance of indigenous ewes in Khanmirza city with short-term and long-term estrous synchronization programs accompanied by eCG during breeding and anestrous season. Moreover, efficacy of estradiol injection instead of gonadotropin during short-term progesterone treatment was evaluated in both seasons. The experiment was performed at two periods, during the breeding and the anestrus seasons on 2 different groups of 400 ewes. During each season, ewes (2 to 5 years of age and average body weight of 45±2.5 kg) were allocated to 4 groups of 100, in the way that each experimental group contained an equal number of ewes of a particular age. Experimental groups were: Control (without any synchronization program), Short term-estradiol group (ewes received 12 days progesterone treatment and intramuscular injection of 1mg estradiol benzoate at the time of sponge removal), Short term-eCG group (ewes received 12 days progesterone treatment and intramuscular injection of 400 IU eCG at the time of sponge removal) and Long term-eCG group (ewes received 14 days progesterone treatment and intramuscular injection of 400 IU eCG at the time of sponge removal). The progesterone treatment consisted on a vaginal sponge which contained 60 mg Medroxyprogesterone Acetate. Then, the ewes were placed in pens and one healthy ram was introduced for every 5 ewes, in order to detect heat and mating. Estrus signs were detected and recorded every hour for 5 days. The percentages of ewes that showed overt signs of estrus during a period of five days (estrus rate), estrus onset (the time elapsed between sponge removal and the first accepted mating) and pregnancy rate (The number of ewes without showing signs of estrous after 42 days of mating/total number of ewes×100) were recorded. Fecundity and prolificacy rate was calculated based on the number of lambs born. Lambs were monitored for 30 days after birth and deaths among them during this period were recorded against the ewes which were their mothers, and the survival rate was determined. The multiple birth rate was calculated by combining the twin and triplet birth rates. The results showed that reducing the duration of treatment with progesterone sponge in both trial period (autumn and spring) led to a significant reduction in estrus rate (P ≤ 0.05), but had no significant effect on other reproductive parameters (P > 0.05). Regardless of the season, injection of estradiol instead of eCG on sponge removal day, while increasing the estrus rate of ewes, led to a sharp increase in the rate of return to estrus (P ≤ 0.05) and caused decreases in the percentage of pregnant ewes, percentage of parturition ewes and lambing rate (P ≥ 0.05). In the breeding season, the mortality rate of lambs born from progesterone-synchronized ewes decreased and fecundity increased numerically compared to the corresponding group in breeding season group. Lack of possible effect of the anestrus season during synchronization programs on estrous rate and fertility of ewes can be attributed to optimal nutritional conditions of ewes in this season. Short term progesterone treatment (12 day) as well as injection of estradiol benzoate instead of eCG is not recommended to synchronize the estrous of ewes during both reproductive and anestrus seasons. In other words, short-term progesterone treatment (12 days) was not effective to synchronize estrus in breeding and anestrous sheep which can be attributed to follicular dynamics.

The BRCA1 gene, which is called “gate keeper” It plays an important role in the process of repairing DNA damage, regulating the cell cycle, regulating the transcription process, maintaining chromosome stability, and other important pathways for the maintenance of genome stability. The current research was conducted with the aim of bioinformatic analysis and comparison the genetic diversity and phylogenetic structure of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 6 geographical regions: Western Asia, Europe, China, North Africa, South Africa and wild (Iran) using the NCBI genome databas.

The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. Also, the number of mutations, nucleotide diversity, haploid diversity, the number of positions in which similar or non-similar substitutions occurred, the percentage of gene differentiation, gene conversion were also analyzed using Dnaspv5 software.

The analyzes related to the comparison of breeds in 6 geographical regions showed 112 polymorphisms, which led to the creation of 19 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences (k) among breeds were estimated as 0.205 and 0.052, respectively. The genetic differentiation between the Chinese sheep population and the wild sheep population was the lowest. The average genetic distance between all geographical regions was calculated to be 0.29. The average nucleotide ratio (A+T):(G+C) was equal to 38:62%, which indicates the predominance of cytosine and guanine bases. The amount of conserved sequence (c) in this research was 0.313 on average, which indicates the high polymorphism of this gene and the creation of new proteins as well as new functions to adapt to different homeostasis conditions. The effective number of codons (ENC) in this research was calculated to be 56.41. The value of D in the Tajima neutrality test was 0.478, which indicates that the selection pressure is balanced.

The high genetic diversity in the wild population, the reasons for which are the presence of forest and open environments, prevention of genetic drift and reduction of inbreeding, which affects muscle strength, eating habits, aggressive behaviors, defense responses, sensory perception of confrontation with environmental conditions and stress that related to BRCA1 gene expression in these populations.

The aim of the present study was to compare sponge and cider with two different brands in estrous synchronicity, vaginal health and off-breeding performance in Moghani ewes. For this purpose, 120 ewes of Moghani breed were selected and randomly divided into four experimental groups. Ewes in the first and second groups, using sponge Sponjavet and CIDER Eazi breed (as valid and common brands) for 12 days, respectively, and the third and fourth groups, respectively, using sponge Fluorojest and CIDER Progest (as New brands made jointly by Iran and China) were treated for 12 days. Ewes in all groups received 400 IU units of eCG at the time of sponge and cider harvest. The rate of vaginal mucosal discharge and adhesion in sponge was higher than cider (P< 0.01). However, there was no significant difference between reproduction and progesterone concentrations between CIDER and sponge as well as brands of these two tools.Therefore, due to lower price and similar efficiency, Sponge Fluorojest and CIDER Progest can be considered as an appropriate alternative to common commercial sponge and CIDER..

Considering that the significant numbers of eggs are broken during transport, storage and sale and are not consumable by humans, so it can be used as a high quality feed in livestock diet. Egg is an important alternative feed ingredient that contains high quality crude protein and crude fat. It is estimated that 8% of produced commercial eggs had not a good quality which has good nutritional value for animal consumption. It has been thought that, as a high quality nutrient, unmarketable cracked eggs could be used in animal nutrition and a few studies have been carried out on that respect. Therefore, the purpose of this experiment was to investigate of the effect of feeding different levels of wasted egg as the main source of dietary protein on sheep rumen fermentation, nutrient digestibility and blood parameters.

Whole waste egg were prepared from a commercial laying hen farm during 10 consecutive days. The collected eggs were air-dried away from direct sunlight then grounded. After determining the chemical composition of wasted eggs, levels of 0, 2.5, 5 and 7.5% were used in experimental diets. For determine the effects of wasted egg on sheep, four mature ram (with 44±0.5 live weight) were used in a change-over design with four periods of 21 days. Nutrients digestibility determined by fecal total collection method. In the 5 days at the end of each period at 0, 3 and 6 h after morning feeding, rumen fluid was sampled from sheep by esophagus tube and were filtered through three layers of cheesecloth. Blood samples were collected at the end of each period and 3 h after morning feeding in 10-mL. To determine the amount of allantoin and microbial protein synthesis, the daily urine produced during 24 hours was collected.

In the present study, dry matter intake and digestibility in sheep fed experimental diet were not significantly altered. Ruminal pH was not affected by waste egg. But, ammonia nitrogen and total protozoa population (13.54 and 9.94 respectively) in rumen fluid at three hours after morning feeding increased (P<0.05) by adding of waste egg in sheep’s diet. Total purine derivatives and microbial protein synthesis did not change. Blood cholesterol levels in sheep fed wasted egg were significantly higher (58.75 in control diet vs 69 in 7.5 % whole waste egg diet) than other groups (P<0.05).

In conclusion, waste egg has suitable nutrients for using livestock feed. Whereas, feeding 7.5% of wasted egg increased of total protozoa population and ammonia nitrogen, and improved fermentation condition. Because alter in ruminal fermentation characteristics, this waste can be used as part of a concentrate in the diet of sheep.

Coat color is one of the important economic traits in sheep and it can be used for breed identification and characterization as well. The aim of the present study was to perform genome wide association study (GWAS) and pathway analysis based on gene set enrichment analysis for identifying the loci associated with coat color in Lori-Bakhtiari sheep breed. The GWAS was carried out using PLINK v. 1.90. The gene enrichment analysis was performed by goseq R package in R v.3.6.1 with the aim of identifying functional clusters and biological pathways of the genes in selected candidate regions and finally, for bioinformatics analysis we used online databases and softwares of GO, Metacyc, KEEG, Reactome and panther. In this study significant SNP markers were identified on chromosomes 1, 2, 6, 9, 10, and 16 that overlapped with EDNRB, PDGFRA, TCF25, and TYRP1 genes. According to pathway analysis, four GO pathways were associated with the coat color trait (P˂0.05). Among these pathways, regulation of protein tyrosine kinase activity, regulation of protein kinase A signaling and activation of protein kinase activity biological pathways, were previously reported to have an important role on the melanocyte development and coat pigmentation. Considering that the genomic regions identified in the current study have been confirmed to be associated with coat color in sheep and other species in previous reports, as well as the identification of some novel putative regions, the identified candidate genes in our study could be further studied and eventually used in genetic selection for coat color in sheep.

Reproduction is one of the most important economic traits in sheep with within and between-breeds variation. Reproductive traits normally show low to medium heritability and therefore response to conventional selection methods is not satisfactory for these traits. Considering the genetic information of the genetic variants underlying reproduction variability could efficiently increase the selection efficacy. Genome-wide association studies (GWAS) have been used to identify associations between genotypes and phenotypes as well as candidate genes for economically important traits. Statistical power in GWAS is mostly affected by sample size. The low sample size is hence a main obstacle in GWAS. Combining multiple data sets of different studies for joint (mega) GWAS provides an opportunity to increase the sample size required for GWAS. This study was performed to identify genomic regions affecting litter size in sheep using the mega-analysis of GWAS.
Multi-population joint GWAS was performed using genotypic and phenotypic data of six sheep breeds retrieved from the database. Quality control was performed using the Plink software. The markers or individuals were removed from the further study based on the following criteria: (1) unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-6. Before analysis, imputation of missing genotypes for combined data set was implemented by LD-kNNi method. Mega-analysis was performed using a mixed linear model in TASSEL software considering kinship and population structure (top five components of principal component analysis (PCA)) as confounding effects. The quantile–quantile (Q–Q) plot was visualized by plotting the distribution of obtained vs. expected log10 (P-value). The association results along the genome and the significant SNPs were visualized in the Manhattan plot. To account for multiple test problem and identify the genome-wide and chromosome-wide significance level, Bonferroni test was used based on the number of independent SNPs obtained from pairwise linkage disequilibrium analysis. After GWAS analysis, the 300 bp sequence upstream and downstream of the significant SNP was explored to identify the adjacent candidate genes using Ovis aries_v4.0 (UCSC).
In the present study, we implemented a mega GWAS using six different sheep breed data to identify the genetic mechanisms responsible for litter size in sheep. After quality control, 305 animals and 351,615 SNP markers with a mean MAF of 0.33 were kept for further analysis. The results of the mega-analysis identified one marker on chromosome 21 at the genome-wide level and 10 markers at the chromosome-wide level on chromosomes 1, 2, 3, 14, 17, and 22. The quantile–quantile plot that features the total distribution of the observed P-values (−log10 P-values) of quality passed SNPs vs. the expected values, showed the effective control for confounding effects. Many of the significant SNPs identified in this study were located in or very adjacent to known genes (OPCML, GULP1, RBP4, MMP2, and LPCAT2) that have been already reported for their contribution to fertility and pregnancy success. It has been reported that OPCML is more consistently expressed in cells lining the uterus, oviduct, and rete ovarii. OPCML has been reported as a tumor suppressor protein that is frequently inactivated in epithelial ovarian cancer. It has been reported that the RBP4 gene is expressed during the period of fast elongation of the pig blastocyst which is a crucial period for the survival of the embryos. Also, it has been suggested that RBP4 has the main contribution in uterine and conceptus physiology during the establishment of pregnancy and therefore can be considered as a candidate gene for litter size. MMP2 has an essential function during ovulation and pregnancy through extracellular matrix (ECM) components degradation and therefore enabling cell migration and angiogenesis.
Comparison of the results of this study with previous reports showed that the mega-analysis of GWAS, compared to the meta-analysis already reported for GWAS results, had comparable power in identifying genomic regions influencing litter size in sheep but identified fewer genomic regions than individual GWAS for each breed. No previously reported major genes controlling litter size in sheep were identified using our mega GWAS. The results of our research are suggested for further investigations in identifying causal genetic variants or genomic regions underlying the litter size variation in sheep and can be used to understand the genetic mechanism controlling this trait.

Mitochondrial DNA (mitogenome) is a small and extra-chromosomal DNA, located in the cytoplasm and presents an ideal model to study evolution and genetic similarity. Classical phylogenetics is based on the morphological characteristics of the organisms, while in modern approaches, the phylogenetic distance and its related comparative methods are estimated based on observed genetic diversity in the studied genetic sequences. The aim of the present study was to investigate the divergence and percentage of genetic similarity along with the phylogenetic analysis of the seven main known species of wild and domestic sheep based on the complete sequence of the mitochondrial genome and the separate sequences of 13 protein-coding genes for each genome.
In the present study, complete mitochondrial genome sequences along with separate sequences of 13 protein-coding genes (including NADH ubiquinone oxidoreductase (ND1, ND2, ND3, ND4, ND5, and ND6), cytochrome c oxidase (COX1, COX2, and COX3), ATP synthase (ATP6 and ATP8), NADH dehydrogenase 4 L (ND4L), and cytochrome b (CYTB))  per each genome from six wild species of sheep including Asian Mouflon (Ovis orientalis), Bighorn (Ovis canadensis), Argali (Ovis ammon), Urial (Ovis vignei), Snow (Ovis nivicola), Dall (Ovis dalli), and domesticated species of sheep (Ovis aries) were retrieved from NCBI database and compared to each other. Mitochondrial genomes and genes’ alignment were accomplished by the MegAlign module of DNASTAR software and compared by the Clustal W method. The Sequence Distances sub-section of the MegAlign module of DNASTAR also was used for the analysis of complete genome and gene sequences divergence and similarity percentage. For phylogenetic analysis, complete mitochondrial genomes and protein-coding genes’ sequences were aligned using MEGA7 software. Based on the alignment, phylogenetic tree was constructed using the maximum likelihood method. The percentage of replicate trees of 1000 replicates of bootstrap test was used to represent the evolutionary history for the studied sheep species.
The results obtained from sequence distance analysis showed high genetic similarity (99.8 %) between Ovis orientalis and Ovis aries. Also, the lowest similarity (95 %) was observed between Ovis aries and Ovis dalli. In phylogenetic analysis, two main clusters, each with different sub-clusters were identified. Domesticated species of sheep (Ovis aries) along with Ovis orientalis, Ovis vignei, and Ovis ammon wild species of sheep formed distinct cluster, and Ovis nivicola, Ovis dalli, and Ovis Canadensis fell in a same cluster. In terms of all 13 protein-coding genes (including NADH ubiquinone oxidoreductase (ND1, ND2, ND3, ND4, ND5, and ND6), cytochrome c oxidase (COX1, COX2, and COX3), ATP synthase (ATP6 and ATP8), NADH dehydrogenase 4 L (ND4L) and cytochrome b (CYTB)), the results obtained from sequence distance similarity analysis and phylogenetic trees were similar to the sequences of the complete mitochondrial genomes. More than 99% of the genetic similarity for ND1, ND2, ND5, ND6, COX1, COX2, COX3, and ATP6 genes and 100% of the genetic similarity for ND3, ND4, ND4L, ATP8, and CYTB genes between domestic sheep (Ovis aries) and Mouflon (Ovis orientalis) sheep species were found. Also, similar to the results obtained from the comparison of the complete mitochondrial genome, the domestic sheep species (Ovis aries) showed the least genetic similarity with the Dall (Ovis dalli) and Bighorn (Ovis canadensis) wild sheep species in all 13 protein-coding genes. Similar to the results of phylogenetic analysis of complete mitochondrial genomes, domestic sheep species (Ovis aries) together with Ovies orientalis wild sheep were placed in the same sub-cluster and Ovis vignei and Ovis ammon species were placed in other distinct sub-clusters. In addition, the Ovis nivicola, Ovis dalli, and Ovis canadensis wild species fell in another main cluster, and in this cluster, Ovis dalli and Ovis canadensis were placed in a similar sub-cluster and Ovis nivicola in another distinct sub-cluster.
In previous studies, small parts of the mitochondrial genome (such as a part of the control region or cytochrome b gene) have been considered to show the genetic differences and phylogenetic relationships between different species and breeds of sheep. In the present study, the complete sequences of the mitochondrial genome along with the complete sequences of 13 protein-encoding genes per each genome in seven main species of wild and domestic sheep have been considered for examining genetic similarity and divergence and phylogenetic analysis for the first time. Based on the results obtained from the present study, mitochondrial genome sequences could be used for accurate phylogenetic analysis and clustering of different species of sheep.

Genetic differences in expression of traits between sexes can be applied for developing efficient genetic evaluation of animals. The aim of the present study was to investigate the existence of sexual dimorphism (SD) in birth weight (BW), weaning weight (WW) and six months weight (6MW) and also correspondingly the genetic analysis of SD in male and female Kermani lambs applying pedigree information and records, collected from 1993 to 2013 in Breeding Station of Kermani sheep,. The SD values, defined as mean body weight of male lambs to mean body weight of female lambs were 1.04, 1.09 and 1.13 for BW, WW and 6MW, respectively. Six bivariate animal models, contained different combinations of direct additive genetic, maternal additive genetic and maternal permanent environmental effects, were used for genetic analysis of SD. Each body weight traits were considered as distinct traits in male and females. The considered bivariate animal models was evaluated via Bayesian Information Criterion (BIC). Direct heritability estimates for BW, WW and 6MW in male lambs were 0.11, 0.35 and 0.32, respectively. The corresponding estimates in female lambs were 0.10, 0.36 and 0.23, respectively. Cross-sex genetic correlations for BW, WW and 6MW were 0.92, 0.93, and 1.00, respectively. High and positive genetic correlations indicated that the studied traits in male and female lambs are control by common genes. Due to high and positive cross-sex genetic correlations for the studied body weight traits it may be concluded that selection in male lambs would result in a positive correlated response in females.

There is an increasing interest in the use of spineless cactus (Opuntia fícus-indica) as fodder for cows, goats, and sheep around the world especially in the arid and semi-arid regions. Cactus withstands water shortage, high temperature, and poor soil fertility, and thus adapted to the arid and semi-arid zones of the world. Cactus is useful not only because it can withstand drought, but also because its conversion efficiency is greater than C3 grasses and C4 broadleaves. Biomass generation per unit of water is on average about three times higher than for C4 plants and five times higher than for C3 plants.The spineless cactus has low crude protein but it has high levels of non-fiber carbohydrates (Barbera et al 1995). High levels of fermentable energy could support rumen fermentation, thus increasing microbial protein synthesis, the production of volatile fatty acids, and the subsequent nutrients supply for the host animal. Data on spineless cactus nutritive value and digestibility is scarce. Furthermore, no data is available regarding the feeding behavior of individual ewes fed diets containing spineless cactus. The objective of this study was to investigate the effects of partial replacement of corn silage by spineless cactus on feed intake, nutrient digestibility, blood metabolite, and feeding behavior of ewes.

A total of 21 Arabian ewes (37.1±1 kg live weight) were used in a completely randomized design with three treatments for 30 days. Experimental diets included control, diets containing 10 and 20% spineless cactus. Ewes were housed individually in pens (1.3 m×1.5 m) in an open shed building and were allowed ad libitum access to feed and water throughout the trial. All diets contained 60% forage (wheat straw, corn silage, and spineless cactus) and 40% concentrate (60: 40; forage: concentrate). The chemical composition of the spineless cactus is presented in Table 1. The ingredients and chemical composition of the rations fed to ewes are shown in Table 2. The ewes were fed the total mixed rations ad libitum twice daily at 0800 h and 1600 h and had free access to fresh water at all times. Feed offered and refusal of each lamb were recorded daily. Digestibility was measured by the total collection of feces during a 5-d period. Samples of ruminal fluid were collected from each ewe 3 h post-feeding using a stomach tube attached to an Erlenmeyer flask and vacuum pump. The first 50 ml of collected rumen fluid was discarded to avoid saliva contamination. The remaining was filtered through four layers of cheesecloth. Rumen fluid pH was measured using a portable pH meter. Blood samples were taken from each lamb at the same time as ruminal fluid sampling by venipuncture of the jugular vein in 10-mL tubes treated with sodium heparin. Samples were centrifuged in a refrigerated centrifuge at 850 × g for 30 min within 30 min of sampling, and the plasma was frozen at −20 °C until used. Behavioral parameters were monitored by direct observations of all ewes over the total time (min) devoted to each monitored behavior. Ewes were observed every 5 min by scan sampling, and the observer recorded the event of the behaviors. Chewing behavior was divided into eating and ruminating. An observation was defined as eating when the animal had its head in the feed bunk or was chewing or swallowing food with its head over it. Ruminating included regurgitation, mastication, and swallowing of the bolus. Activity was recorded as drinking when the lamb had his mouth in the water bowl or was swallowing the water. Self-grooming was defined as non-stereotyped licking of the body or scratching with a hind limb. Social behavior was registered when a lamb was licking or nosing a neighboring animal with the muzzle or horning. Oral behaviors included the act of licking or biting the fixtures. Resting was recorded as occurring when no chewing behavior and no apparent activity were being performed.Data were analyzed using a MIXED procedure of SAS 9.2 (SAS Institute, Inc., Cary, NC) based on the statistical model Yij = μ + Ti+eij, where Yij was the observation, μ the general mean, Ti the effect of treatments and eij the residual effect. Comparisons between treatments were completed with Tukey’s test. Treatment effects were declared significant at P≤0.05.

The intake of dry matter, organic matter, and neutral detergent fiber were higher in the control group as compared with the 20% cactus group (P <0.05). The decrease in total DMI with the increase in the proportion of cactus may be explained by the high moisture content of cactus occupying a considerable volume in the rumen, leading subsequently to limited DMI (Gebremariam et al 2006). Also, forages with high ash contents have poor DMI due to their mineral effect on rumen microbes (Ben salem et al 1996).In the diet containing 20% cactus, the apparent digestibility of organic matter was increased compared to the control (P <0.05). Ammonia nitrogen concentration, rumen pH, and protozoa population in the rumen showed a significant increase in the treatment containing 20% cactus compared to the control (P <0.05). The increase in ruminal pH with an increase in the proportion of cactus in the diet may be explained by its high content of minerals (Barbera et al 1995). An increase in rumen ammonia concentration with increased cactus inclusion rate could be attributed to the higher degradability of protein content in spineless cactus (Batista et al 2003). Blood cholesterol concentration was lower in the treatments containing 10% cactus (P <0.05). Time spent eating per gram of dry matter consumed was higher in cactus-fed sheep than in control. In the cactus-containing diets, the rate of feed intake and amount of feed consumed decreased compared to the control group (P <0.05). Sheep fed diet containing 20% cactus spent a shorter time ruminating compared to the control group.

The results of this study showed that using 20% spineless cactus in the diet replacing corn silage could decrease dry matter intake and rumination time and increase rumen pH. Spineless cactus inclusion in the diet increased organic matter digestibility. Spineless cactus is thus recommended as part of the ewes’ diet, up to 10 percent, in Iran's arid and semiarid regions.

Run of homozygosity (ROH) was used to detecting the genomic inbreeding in sheep. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. As detecting the ROH Islands, the genomic regions containe economic traits could be detectable.

In this study in order to identify the ROH Islands associated with the genes under selection, the 50k BeadChip genotyped data of 2536 sheep from 68 different breeds from all over the world were used. After quality control, ROHs were identified using Plink v1.09 software. One percent of SNP with the highest frequency in ROH were considered as ROH Islands.

A total of 465 ROH Islands (length: 27.43 Kb to 17 Mb) were identified, which covering less than 1% of the sheep genome. The ROH Islands was not distributed across the genome uniform and varied among breeds, but some common were identified. The highest and largest ROH islands were observed in European breeds. In contrast, the lowest and shortest were detected in African and American breeds, respectively. In this study, 256 genes were identified in 111 ROH Islands from total of 465 ROH Islands. of A quarter of the total reference genes identified in the sheep genome, were detected within the ROH islands. Totally 103 QTLs associated with milk, carcass, body weight, and wool traits were identified in these regions.

The results of this study revealed that, the formation of sheep breeds and selection for economic traits during several years, has led to the formation of many ROH islands in sheep genome, therefore scanning these regions at the genome can be an alternative strategy to identify genes and associated loci with economic traits.

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.

Accurate estimation of genetic variance components is essential for the correct prediction of breeding values. The discovery of SNP markers and advances in molecular genetics and the discovery of new methods for sequencing the entire genome of living organisms and the development of bioinformatics methods and computer science, etc. have provided a great deal of molecular data and created a branch of genetics called genomics. This study aimed to estimate the genomic variance components of Border sheep using SNP data.

For this study, the SNP panel, which was genotyped with a 50k marker chip from Illumina, was used. Data were collected at Falkiner Farm in Australia. The studied traits were birth and weaning weights, diameter, and length of wool yarn. To study the relationship between allelic frequency and the amount of justified genetic variance justified, SNPs were classified into five different groups of rare allelic frequency (MAF), with approximately equal numbers in each group. The analyses were performed with the approach of limited genomic maximum likelihood and the method of analysis of complex genome traits with GCTA software.

Genomic heritability estimated by SNPs with a rare allelic frequency of more than one percent for birth weights, weaning, diameter, and length of wool were 0.58, 0.47, 0.59, and 0.2, respectively. The contribution of different groups of SNPs with rare allelic frequencies in justifying genetic variance for different traits was different and in general a significant part of genetic variance was justified by SNPs with

Although the number of SNPs was different in different groups, the amount of genetic variance justified by different MAF groups was different. According to the results, a very large, ideal sample size and better coverage of low-frequency variants are needed to obtain a stronger and more reliable inference.