فصلنامه پژوهشهای علوم دامی ایران
سال پانزدهم شماره 4 (زمستان 1402)

One of the important by-products is the pomegranate pulps which is pulp left after pomegranate juice. The presence of significant amounts of biologically active compounds such as phenolic acid, flavonoids, and tannins in pomegranate fruit ensures its high nutritional value. Pomegranate peel is a part of the fruit that has very high antioxidant properties and contains high amounts of polyphenols such as tannins. There have been numerous reports of the negative effects of tannins on consumer animals. One of the compounds that can bind to tannins and reduce their harmful effects is the tannase enzyme. So, this study aimed to investigate the effects of using different levels of pomegranate pulp without or in combination with tannase enzyme in the diet of fattening lambs on performance, nutrient digestibility, and some blood parameters. After preparing pomegranate pulp, drying it, and preparing tannase enzyme, 25 male Moghani lambs with an average weight of 30±2 kg and the average age is about 7 months, were used in four treatments in a completely randomized design. experimental treatments include 1- control, 2- 2.5% pomegranate pulp powder, 3- 5% pomegranate pulp powder, 4- 2.5% pomegranate pulp powder + 0.05 % dry matter of tannase enzyme 5- 5% pomegranate pulp powder + 0.05 % dry matter of tannase enzyme. During the experimental period, the performance parameters including feed intake, weight gain, and feed conversion ratio were measured. The concentration of blood parameters and the activity of liver enzymes containing ALP, ALT, and AST in the blood of lambs were determined. The Data obtained were analyzed using SAS (9/1) statistical software. The experimental treatments demonstrated no significant impact on the weight gain and feed intake of the lambs. However, when examining the amount of feed consumption and daily feed consumption, higher values were observed during the second 30 days of the rearing period in comparison to the initial 30 days.While nutrient digestibility remained largely unaffected, a notable trend in the digestibility of dry matter was observed. Further comparisons between treatments revealed a higher digestibility of organic matter, neutral detergent fiber (NDF), acid detergent fiber (ADF), and ash in the group receiving 2.5% pomegranate pomace. These findings provide insights into the potential influence of pomegranate pomace supplementation on specific aspects of nutrient utilization in lamb diets. Fat in the treatment of 2.5% pomace with enzyme and digestibility of crude protein was higher in the treatment of 5% pomace with the enzyme. The comparison of different pomace levels showed that the use of high levels of pomegranate pomace (5%) increased blood glucose and the lowest blood urea concentration was obtained by feeding 5% pomace. The lowest concentrations of HDL and LDL in the blood also belonged to the control treatment. The use of tannase enzymes in the diet also increased the concentration of glucose parameters and decreased blood urea. The highest amount of glucose of the studied lambs were observed in the first thirty days of sampling. In the present study, the use of pomegranate pomace increased glucose in both rearing periods and decreased blood triglyceride levels in the second rearing period. Alanine phosphatase (ALP) enzyme activity was significant in the second period, the breeding period (P<0.05). The highest level of activity of this enzyme was observed in the blood of lambs fed with 2.5% of dung. The activity of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) was not significant between sampling periods (P<0.05). Feeding different levels of pomegranate pomace powder with or without tannase enzyme had no significant effect on blood malondialdehyde concentration as an antioxidant index of the blood of fattening lambs. However, the comparison between the experimental treatments showed that the highest level of this index was found in the blood samples obtained from lambs fed with a diet containing 5% of pomegranate pomace powder + 0.05% of the dry matter of the tannase enzyme diet. The inclusion of different levels of pomegranate pomace in the diet led to a significant difference in the activity of the alanine phosphatase enzyme among the experimental treatments (P<0.05) and increased blood glucose (P<0.05). None of the functional parameters, including weight gain, and feed consumption, were affected by the use of pomegranate pulp with or without tannase enzyme during the entire experimental period. However, the food conversion coefficient improved in the treatments containing pomegranate pomace with tannin enzyme. The highest amount of antioxidant index related to the diet containing 5% of pomegranate pomace powder + 0.05% of the diet's dry matter was tannase enzyme. Therefore, the level of 5% of pomegranate pomace along with the tannase enzyme increases animal health and improves animal growth performance.

Environmental pollution, including pollution caused by urban and industrial sewage, factories and vehicles, causes pollution of natural resources in the environment, including water and fodder. The entry of these elements into the body of animals and their accumulation increases their concentration in products and enters the human food chain. Contamination of milk, meat and other edible tissues of animals with heavy metals is also a worrying issue and threatens food hygiene and human health because these elements are not naturally present in edible tissues and even very small amounts of them can be cause severe side effects. Scientists have mentioned the main cause of contamination of meat and animal tissues is feeding them from contaminated fodder sources or rearing them near contaminated areas. In the studies conducted in different countries, the amounts of heavy elements were more than allowed. In order to investigate the amounts of heavy metals including lead, cadmium, chromium, arsenic and nickel in milk and body tissues of dairy cows in North Khorasan province, two experiments were conducted in three regions and the amounts of heavy metals in milk and body tissues of dairy cows using the device Inductively coupled plasma-atomic diffusion (ICP) was measured, and studied.In the first experiment, three dairy cattle farms were selected from three regions, two farms were located in two regions at equal distances from large industries, and the third region was selected as a control region far from large industries. In each of the farms, 10 dairy cows (5 first lactation and 5 second lactation and above) was sampled and the amounts of elements were measured. In the second experiment, muscle, heart, liver, kidney and lung tissues were sampled from 5 dairy cows from each region that were removed and sent to the slaughterhouse for reasons such as mastitis and reproductive problems. Heavy metals, including lead, cadmium, chromium, arsenic and nickel, were measured in the tissues by an inductively coupled atomic diffusion plasma (ICP) device. The initial experiment's findings indicate that the levels of arsenic, cadmium, and lead in the milk of Holstein cows remained unaffected by varying regions. However, there were significant regional impacts on the levels of chromium and nickel in the milk of Holstein cows. Furthermore, the concentrations of arsenic, cadmium, nickel, and lead in the milk of Holstein cows were not influenced by the age of the cows or the interaction between region and age. In contrast, the concentration of chromium exhibited sensitivity to age and the interaction between region and age. These nuanced insights highlight the diverse influences on trace metal concentrations in Holstein cow milk, providing valuable information for understanding regional and age-related variations. The amount of arsenic, cadmium and lead metals in the thigh muscle tissue of Holstein cows in different regions was not significantly affected by regions. However, the amount of chromium and nickel in the thigh muscle tissue was significantly affected in different areas. The amount of arsenic, chromium, nickel and lead in the heart tissue was not significant in any of the regions (Shirvan, Esfrayen and Bojnoord). The amount of cadmium in the heart tissue of Holstein cows was significantly affected by different regions. Thus, the highest amount of cadmium in heart tissue was observed in Bojnord region and the lowest in Esfrayen region. The amount of chromium, nickel and lead in the tissue of all Holstein cows in different regions was not affected. However, the amount of arsenic and cadmium in the kidney tissue was significantly affected in different areas (Shirvan, Esfrayen and Bojnoord). Based on the obtained results, there was no significant difference in the amount of arsenic, cadmium and lead in lung tissue in different regions. However, the amount of chromium and nickel in the lung tissue of Holstein cows was significantly affected in different regions. Chromium enters various environmental sources (air, water and soil) from a wide range of natural and human sources, the most of which is emitted from industrial activities. When heavy metals are present in the air, feed and water of animals, they eventually accumulate in their tissues. While the levels of heavy metals did not exhibit significant differences across many investigated areas, it is noteworthy that the concentrations surpassed the standard values established for these metals in products like milk. The elevated concentrations raise concerns about the potential health implications associated with consuming products containing such heightened metal levels. An interesting observation emerges from the examination of elemental concentrations in tissues, irrespective of regions and distances. The lead element, in particular, demonstrated the highest concentrations, with the liver exhibiting the most notable accumulation compared to other tissues. This underscores the need for strategic interventions, and the consideration of solutions such as the application of absorbents to mitigate metal concentrations in dairy cattle products emerges as a viable recommendation. Implementing such measures could play a crucial role in ensuring the safety and compliance of dairy products with established standards.

One of the most important problems in the sheep breeding industry is its low reproduction capacity. According to the advances made in the field of reproduction, new methods have led to the improvement of the reproduction process. One of the important and effective indicators in reproduction is the level of energy used in the diet during the reproductive season. The use of fat supplements in the diet increases the energy density, and by reducing the inhibitory effects of the negative energy balance, it improves reproductive and productive performance. The right amount of oil consumption guarantees health and food safety. It is recommended that 10% or less of the energy needed by the body per day comes from saturated fat sources and 20-35% of daily energy comes from unsaturated fat. Due to the importance of oil seeds, their cultivation is also very important and they have a wide cultivated area all over the world. The purpose of this research was to investigate the effects of levels and sources of oil and fat on reproductive performance and blood factors of Kurdish sheep. The experiment was conducted at the Research Unit Farm of the Light Livestock Breeding Shightogan Delaware Company, located in the southern Khorasan province, Iran. Fifty-six ewes with Non-pregnant with an average age of one year and average body weight of 41.35±2.5 kg were divided into 7 treatments and 8 replications for 60 days (habituation period 14 days). Experimental treatments include: 1- base diet without oil, 2- Basic ration containing 2% sunflower oil, 3- Basic ration containing 2% canola oil, 4- Basic ration containing 2% tallow, 5- Basic ration containing 4% sunflower oil, 6- Basic ration containing 4% canola oil and 7- Basic ration It contained 4% tallow. Estral synchronization was performed in spring with CIDR. Ewes after CIDR (14 day) extraction and PMSG injection as soon as the signs of estrus were observed, the ewes were isolated from the others and artificially inseminated with fresh sperm using the transcortical method. Energy and chemical composition of rations were similar and were examined simultaneously with CIDR removal and estrus observation. Then, in each experiment parameters such as the time of estrus initiation (hour), rate of return to estrus, parturition rate, rate of multiple births, number of lambs and rate of lambing were evaluated Body weight (BW) and body growth measures were recorded First and period End. Data obtained were analyzed by statistical software SAS (version 1.9). Estral synchronization was performed in spring with CIDR. Ewes after CIDR (14 day) extraction and PMSG injection as soon as the signs of estrus were observed, the ewes were isolated from the others and artificially inseminated with fresh sperm using the transcortical method. The nutrition program with software (SRNS) version was adjusted based on the pregnancy diet. The results showed that the highest pregnancy rate (100%) and lambing rate (125%) were related to ewes receiving rations with 2% tallow oil and 4% sunflower oil. The highest increase in body weight was observed in ewes consuming ration with 2% sunflower oil, which was significantly different from the control group. But with other groups, this difference was insignificant. The highest body weight gain and the best (lowest) feed conversion ratio were observed in ewes consuming 2% sunflower oil diet, which was significantly different from the control group. But with other groups, this difference was insignificant. Triglyceride concentration, plasma total protein concentration and plasma albumin were not affected by oil and fat sources in the diets and no significant difference was observed between the diets. There was a significant difference in the average apparent digestibility coefficients of dry matter, crude fat and organic matter of nutrients between treatments. In general, use of vegetable and animal oils in the diet can positive effect on the productive and reproductive performance of sheep results of this research showed that in order to reduce the rate of consumption costs, 2% in the ration is suggested.

Fertility is one of the main factors influencing the economic result in poultry flocks and it is influenced by several variables including breed, nutrition quality, flock age and sperm quality. As a result, the decrease in the fertility of beef mother herds after the peak of production is one of the most important factors in reducing the economic profit of breeding units. It has been shown that fertility decline at the end of the productive period can be partially prevented through artificial insemination. The requirement for optimal use of artificial insemination in any species is the possibility of storing sperm in liquid and frozen form. Fertility rate of poultry sperm in frozen conditions is facing a serious challenge compared to other species, this challenge may be related to some special physiological characteristics of rooster sperm that lead to increased sensitivity in frozen conditions. Ginger is a plant that has strong antioxidant substances, which increases the level of antioxidant enzymes and collects free radicals and protects the cell membrane against the risk of oxidation and peroxidation of fats. The main antioxidant compounds in ginger are gingerols, sesquiterpenes, shogaols and some phenolic ketone derivatives, which have the ability to neutralize superoxide and hydroxyl radicals. This evidence shows that adding ginger powder to the diet of broilers can improve the quality of sperm after thawing and increase the fertility rate by improving the antioxidant properties of semen and protecting sperm from damage caused by freezing-thawing. In this research, twenty-seven Ras 308 breeding broilers were tested in the southern desert research farm in collaboration with Khuzestan University of Agricultural Sciences and Natural Resources.  At the age of 47 weeks, the sows were habituated for two weeks in individual cages and fed with basic ration and abdominal rubbing method for sperm collection. From the age of 49 to 60 weeks for 12 weeks, the sows were fed with a basic diet (control group) or diets with different levels of ginger powder (treatment groups) and kept at a temperature of 19-23 degrees Celsius and a photoperiod of 14 hours of light and 10 hours of darkness.  Experimental treatments included: control diet (no feeding of ginger powder), daily feeding of 7.5 grams of ginger powder and daily feeding of 15 g of ginger powder per kg of diet. During the test period, sperm samples were collected weekly by abdominal rub method and after initial evaluation, from the age of 51 weeks, they were frozen, and the quality parameters of semen, including total and progressive aspect, plasma membrane function, sperm viability and morphology after thawing were evaluated. took Frozen semen samples from weeks 59 and 60 were inoculated into broiler hens to evaluate sperm fertility after thawing. The effect of treatment and test weeks on most of the parameters measured including total and progressive motility, viability and function of sperm plasma membrane was significant. The interaction of treatment and test weeks significantly affected overall and progressive behavior, but its effect on survival tended to be significant. The effects of treatment, week and the interaction of treatment in week had no significant effect on the percentage of abnormal sperms. The study by Shafiq et al. (2015) improved the storage of rooster sperm using rosemary essential oil after the freezing and thawing process; The results of the research showed that the use of rosemary essential oil in the diluent improves the quality of rooster sperm, which is consistent with the present research.  Ginger comprises essential antioxidant compounds such as gingerols, sesquiterpenes, shogaols, and certain phenolic ketone derivatives. These compounds possess the remarkable ability to neutralize superoxide and hydroxyl radicals, contributing to their sustained antioxidant activity. Furthermore, the antioxidant enzyme glutathione peroxidase plays a crucial role in safeguarding sperm in the tissues of the testis and epididymis. A decline in the levels of this enzyme within the body has been associated with infertility. Recognizing the significance of these antioxidant components and enzymes underscores their continuous impact on maintaining reproductive health. By being placed in the sperm plasma membrane, this enzyme protects the sperm nucleus and epididymal fluid from the attack of free radicals and causes the final swelling and development of sperms. Fertility percentage and sperm yield in chicks of hens fed with 7.5 and 15 g/kg of ginger powder in the diet increased significantly compared to the control group. Among the sperm parameters, sperm motility and viability are considered to be the most important factors influencing sperm transfer to SSTs; In this research, the total and progressive motility and survival were increased in the groups of 7.5 and 15 grams per kg of diet, which can be the reasons for increasing the fertility and hatching of chicks in these groups. In a research by Masoudi et al. (2021), they investigated the effect of milk thistle, carob and ginger on the reproductive performance of Ras breed broilers and reported that supplementing the diet with plant additives significantly improved the quality of sperm and fertility of the sows compared to the control group. In generally, the results of the present study showed that the addition of 7.5 and 15 g per kg of ginger powder in the diet significantly increased the total and progressive motility, the integrity and function of the plasma membrane, and finally, the fertility and egg retrieval of sperm after thawing.

During the winter months in most parts of Iran, the external temperature often drops below 0 °C. Typically, these temperatures fall below the optimal conditions for chick growth, resulting in cold stress and potential diseases. This can subsequently impact meat quality negatively and reduce breeding efficiency. The environmental temperature beyond the upper and lower limit of the thermoneutral zone is supposed to produce heat or cold stress in animals (Meltzer, 1983). The adverse climatic condition produces physiological stress which has profound economic influence on the productive efficiency including health and disease resistant capacity (Phuong et al., 2016). Exposure of poultry birds to extreme temperature stressor modulates the immune responsiveness and hematic-biochemical parameters of birds (Hangalapura et al., 2004). Among all the environmental stressors, cold stress induces physiological responses which are of high priority and energy demanding for homeotherms. Cold temperature can increase ascites susceptibility by increasing both metabolic oxygen requirements and pulmonary hypertension (Stolz et al., 1992). The biggest obstacle in raising broilers at high altitudes and cold conditions is the ascites syndrome. This condition can be characterized by an accumulation of fluid in the abdominal cavity and elevated mortality that tends to peak between 4-6 weeks of age (James, 2005). The International Biochar Initiative (2017) defines biochar as, “Solid material obtained from thermochemical conversion of biomass in an oxygenlimited environment.” Biochar is an ash substance that is produced from the burning of biological material via pyrolysis. This process heats the biological material in an anaerobic environment causing it to decompose into an ash form. Growth promotion and therapeutic antibiotics have been used to compensate for the high levels of stress, including cold stress,that can be present in intensive animal production. Stress can lower resistance to many of the microorganisms present in the environment; however, stress in general has been reported to have variable effects on the immune system and can both enhance and suppress responses (Siegel, 1995); cold stress has been shown to both stimulate and suppress chickens’ immune response (Regnier and Kelley, 1981; Hangalapura et al., 2006). Probiotics contain live microorganisms and spores which when administered in adequate amount, confer health benefits to the host. Bacillus subtilis (B. Subtilis) and Bacillus licheniformis (B. Licheniformis) are the two most widely used strains of probiotic bacteria in animal diets. Oral administration of B. Subtilis and B. Licheniformis can have a myriad of beneficial effects, such as improved growth and meat characteristics, optimized composition of intestinal microbiota, prevention of some diarrheal diseases, and reduced stresses. For such benefits, B. Subtilis and B. Licheniformis have attracted considerable attention as a potentially beneficial dietary supplement for animal health.  For the many negative effects of antibiotic drugs used in chick production, we want to compare the positive effects of some additives on performance of cold-stressed broiler chickens.

In this experiment, in order to examine the effect of solid waste biochar, probiotic and zeolite on improvement of performance, blood indices and small intestine morphology of broiler chickens reared under cold stress, in a completely randomized design, 315 Ross-308 broiler chickens (as hatched) were allocated to 7 treatments, 5 replicates and 9 birds in each in cold and warm houses. Treatments are including: 1) positive control (basal diet in recommended temperature), 2) negative control (basal diet + cold stress), 3-7) negative control + %0.5, %0.75 and 1% solid waste biochar, 0.02% probiotic Ecobacto-P and 1% zeolite, respectively. In cold stress groups, house temperature decreased to 17° C from 7d until end of the experiment (42d).

As compared to group reared in warm house, cold stress significantly decreased broiler chickens daily FI and BWG, serum total protein, albumin and globulin concentrations, thymus relative weight, lymphocyte percentage, breast and thigh meat pH, breast meat redness (b) and thigh meat yellowness (a) while increased total and ascitic mortality, red and white blood cell count, blood hemoglobin, heterophile percentage and heterophil to lymphocyte ratio, antibody titter against SRBC, breast and thigh meat whiteness and breast meat MDA concentration (P < 0.05).

In order to orthogonal contrast analysis between negative control group and additive groups, solid waste biochar, probiotic or zeolite couldn’t improve broiler chicken’s growth performance, breast and thigh meat quality parameters, blood metabolites concentration and cell count and did not ameliorate negative effects of cold stress.

Compared to other poultry, geese are more resistant to adverse environmental factors, so they are less likely to get sick. Geese are fast-growing poultry, and they are easy to raise. Due to the importance of goose meat due to its high calorie content compared to the meat of other poultry species and its high palatability, as well as its resistance to many diseases, it is necessary to raise this bird on an economic scale. In industrial goose breeding, there arises a need to develop strains tailored for specific purposes such as meat, egg, and dual-purpose. This allows breeders to align breeding objectives with associated costs and optimize productivity for the industry's requirements. Consequently, the economic coefficients of breeding, coupled with the relative selection of products, necessitate consideration in four primary aspects: achieving high weight gain, reducing the food conversion ratio, increasing the egg count, and enhancing egg fertility. It is crucial to acknowledge the negative correlation coefficient with the egg production trait within the realms of management and breeding sciences. This is because an improvement in one trait may inversely impact the values of another trait. Among the effective strategies in breeding, the selection is based on genetic markers that lead to the reduction of the generation gap and increase in production. Due to the ever-increasing growth of the population, a lot of effort is needed to overcome unfavorable environmental conditions, including biological and non-biological factors, and to increase the quantity and quality of the product. In recent years, many advances have been made in the field of molecular biology and biotechnology, which has provided a powerful tool for the genetic study of animals. Considering that the growth hormone gene (GH indicator) is one of the candidate genes for various traits, especially weight gain, but it has not been used in goose breeding programs so far. Therefore, in order to determine the contribution of this gene in goose breeding, its relationship with the weight gain trait of chickens should be determined, which is actually the purpose of designing and implementing this study. In order to implement this research, 300 gosling hatched from eggs of Malekan research station geese and reared for 5 months. The hatched goose chicks were kept and fed according to breeding standards Gosling weighted monthly and blood samples was collected from them in vacuum tubes containing EDTA at end of raising period. Genomic DNA was extracted by Pronase procedure. A spectrophotometer was used to determine the quality of the extracted DNA, and for this purpose, a wavelength of 260 nm was used to determine the amount and concentration of DNA, and a wavelength ratio of 260/280 was used to determine the purity and quality of the extracted DNA. Amplification of the desired region from exon 2 of the growth hormone gene was done by thermocycler using the designed primers GH-G F and GH-G R to amplify 162 base pairs. 2% agarose gel with ethidium bromide staining was used to identify PCR products. The SSCP technique was used to determine the genotypes of the growth hormone gene. Denatured SSCP products was electrophoresed on 10% polyacrylamide gel and stained by silver nitrate. Effects of GH gene on growth performance were analyzed by SPSS software version 23 in CRD design. Genotypes pattern of 1, 2 and 3 were recognized. Frequencies of 1, 2 and 3 patterns resulted 48.15, 44.44 and 7.15 percent, respectively. Results indicated that GH genotypes affected live weight of gosling in 1 and 2 month of age, the 3th pattern had heavier live weight in these periods. Despite of heavier live weight in pattern 3, for months of 3, 4 and 5 no significant differences observed among them. Low frequency of pattern 3, that affected live weight in gosling, can be increased in study population in favor of this pattern. The results of this research showed that the growth hormone gene and especially exon 2 of this gene can be considered as a genetic marker in the selection of geese for the weight gain trait. Given the considerable importance of the economic coefficient of egg production in geese, which outweighs the emphasis on increasing the weight of breeding geese, and considering that the economic activities of the station align more closely with augmenting the number of chicks produced per breeding goose, the observed negative correlation between egg production and weight gain in geese suggests a lower prevalence of the effective genotype influencing the weight gain of geese in this station. The selection focus at Malekan station has predominantly aimed at enhancing the egg laying rate, in stark contrast to the growth rate of geese. Consequently, this deliberate selection has led to an increase in the frequency of the effective genotype impacting egg laying and concurrently a reduction in the frequency of genotypes influencing the weight gain of goose chicks.

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.

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.

Genomic best linear unbiased prediction (GBLUP) and Bayesian methods are used for genomic selection (GS) and genome wide association study (GWAS) in animal and plant breeding. The main objective of GWAS is detection of quantitative trait loci (QTL) that is affecting trait. The GBLUP assumes equal variance for all markers but the Bayesian methods assumes specific variance for each marker. When trait are affecting by major QTLs, Bayesian methods have the benefit of marker selection. In weighted GBLUP (WGBLUP), disparate variance of marker specific weights for weighting of all markers are used. If only a deduction of animals is genotyped, single-step WGBLUP (WssGBLUP) can be used. The weighting factors were calculated using marker effect derived Bayesian methods or iteratively based on single step marker effect. In multibreed genomic evaluation, there are several specific genetic structures into a genomic relationship matrix (G). The block wise genomic relationship matrix (BG) consist of several specific relationship blocks for each and pair breeds. BG can more accurately calculated relationships among animals than G matrix in multibreed genomic evaluations. The aim of this study is comparison G and BG and weighted BG (WBG) in weighted single step GWAS.To conduct our study, we initially simulated two distinct populations, labeled as A and B, utilizing the QMsim software. The simulation involved the creation of two chromosomes, each spanning a length of two morgans. Within each chromosome, we simulated 2500 single nucleotide polymorphisms (SNPs). Subsequently, four traits were simulated, each possessing heritabilities of 0.05 and 0.3, along with varying numbers of quantitative trait loci (QTLs) set at 50 and 500. Following the simulation, we calculated the genetic value (G), the breeding value given by markers (BG), and the weighted breeding value given by markers (WBG) using SNP genotypes for all animals in the study. This comprehensive approach allowed us to evaluate and analyze the genetic and breeding values associated with the simulated traits across the populations. Genomic relationship matrices were used for single step GWAS (SSGWAS) analysis for each trait. 10 iterations was considered for single step SNP effect analyses. Moreover, the SNP effects were obtained by BayesB approach. BayesB effects was used for calculated weighting factors in WBG. Accuracies of methods and number of identified SNPs with explained genetic variance higher than 1% were reported.          using G and BG and WBG in SSGWAS led to identify 14, 16 and 21 SNP with higher than one percentage variance explained, respectively. Moreover, convergent accuracies of WssGBLUP using G and BG and WBG were 0.36, 0.39 and 0.43, respectively. WssGBLUP using WBG could be converged faster than using G and BG. Furthermore, accuracy of WssGBLUP using WBG was significantly more than using G and BG. Multibreed GWAS is led to increase power of model because phenotypic information is severely increase. In multibreed GWAS, relationships among breeds usually are rare or zero but there are several locations among breeds that shared among them and should use those for genomic relationship calculation. In WBG and BG could be accurately calculate pair breeds genomic relationships using sharing pair breeds genomic locations. Principal component analyses showed that WBG was let to strongly increase genomic relationship among animals that is led to improved power of WssGWAS.       According to recent studies, multibreed genomic evaluation with the WssGBLUP can improve the accuracy of multibreed genomic evaluation, and the results of our study showed that for multibreed genomic evaluation and WssGWAS with the WssGBLUP , instead of the genomic relationship matrix (G), BG or WBG genomic relationship matrices are the better to use.

When the urban population around the capitals or big cities increases, then need an intensive and modern dairy industrial farms or even mega dairy farm to support milk and dairy products demands. Therefore, many family farms shifted to big dairy farms which expecting more specializing and modern technology to be used towards reduction of the cost of milk production per cow. Management of these farms also completely different from housing, reproduction, nutrition and other technical points-of-view. In order to investigate true productive life and milk production during the last 15 years (2006-2020 years), in 20 industrial Holstein mega dairy farms this study was done. All the farms had a specialist in the fields of hygienic condition, calf rearing, balancing the diet, heat and Pregnancy detection and planed mating program for semen selection and breeding to control the production and type performance and preventing the inbreeding which help to use maximum inbreeding coefficient, if required.

The correlation between the lengths of true productive life (TPL), maximum lifetime milk production (MLMP305), and maximum lifetime peak of milk production (MLPMP) in 20 industrial Holstein mega dairy farms were investigated. The information recorded in the herd management software in the cattle breeding units, which included the information of the culled cows and all the existed cows in the herds from April 1385 to January 1400, were analyzed. The data includes 176,674 cattle records, of which 43,587 are related to existing cattle and 133,087 data are related to culled ones. The information of the existing cows was done in order to control the information of the herds and also monitor them. Finally, 133,087 data related to existing cows were edited and filled in the computerize program. To calculate the standard milk of 305 days, it is necessary to milk the animals three times a day and the animals have at least 4 monthly records of milk and also that the dryness of these animals has been recorded as the end of the milking period. The Data has been analyzed by univariate method of SAS software (Version 9.4). The Holstein-Friesian cow herds, on average, comprised 2069 cows, with a range from a minimum of 400 to a maximum of 5301 cows. These herds were distributed across 14 provinces throughout Iran. The average age at first calving was 750 days, and the standard 305-day milk yield averaged 12,342 kg during the third lactation. TPL records from 113584 cows and MLMP305 records from 78036 and MLPMP records of 111276 cows were used. The data were analyzed for the correlation between the characteristics of the true productive life, milk production of 305 days and the peak of milk production Also, the linear regression between the true productive life and milk production were analyzed.

The average TPL of the animals under investigation is 33.57 months and the standard deviation of the data is 20.77. The average MLMP305 by these animals is 12472 kg and their standard deviation is 2513 kg. The average MLPMP of the animals was 51.83 kg. The highest correlation was between MLMP305 and MLPMP, which is 74.66%. The correlation between TPL and LPMP was 47.88% (P<0.0001) and the correlation between TPL and LMP305 was 33.27 % (P<0.0001). Our results are in accordance with studies such as Van Vleck, 1964, Hudson Van Vleck, 1981, and Ducrocq et al. 1988, but were in contrast with the results of Hare et al. 2006, and Ajili et al. 2007, and Dallago et al. 2022. The highest level of correlation (as expected) is between305-day milk production and the peak of milk production.

The positive correlation between TPL, MLMP305, and MLPMP, shows that the animals with higher peaks also have higher milk production in one lactation period also have a higher true productive life. Considering the high significant positive correlation of this report, by selecting animals with a high production life span, not only can the productive life span be improved in the future generations, but contrary to the existing belief, milk production can also be increased in the future generations. It should be mentioned that the conclusion of this paper is extendable, when we can control all physiological and nutritional factors and have a proper pregnancy detection method which lead to perfect calving management and results that has been done exactly in the farms which we studied.