فصلنامه پژوهشهای تولیدات دامی
پیاپی 39 (بهار 1402)

Antibiotics reduce the microbial population of the gastrointestinal tract, increase the available nutrients, and improve the feed conversion ratio (FCR) and body weight gain (BWG) of broilers. Due to the persistence of antibiotics in manufactured products and their transmission to humans, and the emergence of resistance, their use has been banned in many countries. Therefore, the use of antibiotic alternatives in the livestock and poultry industry has been considered, including organic acids. Organic acids modulate the intestinal microbial and improve animal performance by destroying harmful bacteria and providing nutritional conditions for beneficial bacteria. This study was performed to compare the effects of citric acid-based acidifiers with the commercial samples in drinking water on performance, serum biochemical parameters, pH, and intestinal morphology of broilers.

In this experiment, 400 one-day-old Ross 308 male broiler chicks were allotted to 5 treatments with 4 replicates in a completely randomized design. Experimental treatments included control treatment receiving drinking water without an acidifier and groups receiving drinking water with 0.025, 0.05, and 0.075% of produced acidifier and 0.2% of commercial acidifier.

The results indicated that feed intake (FI) and FCR decreased during the growth period by adding 0.05% of produced acidifier to drinking water compared to the control group (p<0.05). The BWG of broiler chickens increased at the level of 0.075% of the produced acidifier at the stater period and in the groups treated with the commercial sample in the total period compared to the control group (p<0.05). A numerically and significantly decrease in serum triglyceride was observed at treatments containing 0.05 and levels of 0.025 and 0.075% acidifiers respectively. The serum HDL was increased at treatments containing commercial acidifier than the control group (p<0.05). Groups receiving acidifiers had lower serum alkaline phosphatase compared to the control group (p<0.05). A decrease in the pH of the duodenum and jejunum in 42 days, as well as a decrease in the crypt depth and an increase in the villus height were observed in treatments containing 0.2 and 0.05% of commercial and produced acidifiers respectively (p<0.05).

According to the results, the level of 0.05% of produced acidifier in drinking water is recommended to improve the performance, intestinal morphology, and reduce the pH of the gastrointestinal tract in broilers.

The use of antibiotics in poultry nutrition, in addition to their importance in preventing diseases, causes an increase in congenital anomalies, chronic diseases, increased microbial resistance and hundreds of other small and large complications, which is attributed to the current health problems of human society. The focus has always been on animal welfare, environmental care, limited use of medicines and the production of a healthy product without chemical residues that do not endanger human health. One of the suitable alternatives to antibiotics is bioactive peptides.

This experiment was used in a completely randomized design with 240 one-day old male commercial Ross 308 broilers in six treatments, five replications (eight chickens per replication). Experimental treatments include: basal diet, basal diet + 0.1% of vitamin E and 0.05% of maduramicin, basal diet + 0.05% of maduramicin, basal diet + 200 mg / kg superworm peptide, basal diet +400 mg / kg were superworm peptide and the basal diet was + 600 mg / kg superworm peptide. The effect of treatments on performance, microbial population, intestinal morphology and immune system response of broilers was investigated.

Addition of maduramicin (treatment 3) and superworm peptide at the levels of 200, 400 and 600 mg to the diet compared to the control group was able to reduce feed intake in the final period. On the other hand, treatments that used antibiotics, compared to treatment 5, which contained 400 mg of superworm peptide, were able to reduce the total bacterial population. Adding all levels of bioactive superworm peptide to the diet reduced the crypt diameter compared to the control group and also the diet containing 400 mg of the superworm peptide reduced the crypt depth compared to the control group. The results obtained in relation to immune factors can be stated that by adding antibiotics to the diet, it can increase immune factors such as immunoglobulin G at the age of 35 days compared to the control group, as well as the superworm peptide. At a concentration of 400 and 600 mg per diet, it was able to improve the total SRBC titer at 42 days of age compared to the control group.

The results of this experiment showed that the experimental treatments were able to improve the performance indices at the age of 11 to 42 days and some morphological features of the jejunum such as: crypt depth and diameter. Also, it can be said that the effect of experimental treatments on the total bacterial and lactobacilli population and the level of immunoglobulin G (day 35) and total SRBC titer (day 42) was significant.

Egg is a complete food for feeding different age groups, which has a wide range of required nutrients, contains chemical compounds sensitive to adverse environmental factors such as temperature, shelf life and storage conditions. In the present experiment, the duration, location and storage status of edible eggs in home refrigerators and their effects on quality traits, shell traits and biochemical characteristics of egg yolks were evaluated.

In this experiment, 216 healthy eggs produced one day of hens of W36 line strains, aged 77 weeks, were prepared and in the form of 2 * 3 * 3 factorial arrangement, including 3 weeks, 3 floors and two egg storage conditions (sharp to Bottom or vice versa) in 18 treatments, 72 replications and 3 eggs per replication were used in a completely randomized design.

Duration of storage, location and storage of eggs in the refrigerator had significant effects on internal quality, shell traits and biochemical parameters of egg yolks (p<0.05). Storage of eggs in the upper floors of the refrigerator compared to the lower floor increased the yolk index and yolk color (p<0.05). With increasing the storage time of eggs to three weeks in the refrigerator, the percentage of yolk, units, egg shell thickness and yolk cholesterol concentration decreased, while the percentage of white and yolk color increased (p<0.05). Egg storage conditions in the refrigerator (bottom sharp or vice versa) did not have significant effects on internal quality, shell traits and biochemical characteristics of egg yolks (p<0.05).

Due to the nutritional value of various compounds and the nature of some nutrients in eggs and especially egg yolks (such as unsaturated fatty acids), as a concern for nutritionists and housewives, duration, location and the storage status of the eggs in the refrigerator is imortant. In the present experiment, it was observed that, firstly, the lower floor of the refrigerator is not a suitable place for storing eggs, and secondly, by increasing the the duration of keeping eggs to more than two weeks, the internal quality, the quality of the shell and the yolk content of the eggs will decrease, but the storage condition of eddible eggs in the refrigerator (sharp egg point down or vice versa) had no significant effects on the aforementioned traits. According to the above findings, it is recommended, that the eggs needed by households not to be purchased in large quantities and not to be stored for more than 2 weeks, as well as in the lower floors of home refrigerators.

In recent years, application of natural and safe feed additives such as herbs and herbal products has been increased, due to their beneficial concequences on health and thereby animal production. One of the natural important compounds present in plants, is phenolic compounds which has been recived high interest and many investigations have been conducted about their different effects on broilers. This study was conducted to investigate the effect of dietary inclusion of Iranian oak acorn (Quercus brantii L.) (OA), as a phenolic cmpounds-rich feedstuff, on some breast meat traits of broilers at different refrigerated (4 °C) storage times.

A total of 160 one-day-old mix of male and female broiler chicks were distributed between 2 experimental treatments (with 4 replicates of 20 birds) in a completely randomized design and fed a control diet (without OA) or a diet containing 20% ​​OA. During the rearing period, birds were fed with starter (d 1-10), grower (d 11-24) and finisher (d 25-42) diets, respectively. At the end of the rearing period, two birds were slaughtered from each replicate and samples were taken from breast muscle and kept in refrigerator. Different parameters (population of  Lactobacillus, Psychrotriph bacteria, Enterobacteriaceae, total aerobic bacteria, lipid oxidation, water holding capacity, cooking loss) were measured at 2, 4, 6, 8, 10 and 12 d of storage.

The results showed that using OA decreased population of Lactobacillus at 6 and population of total aerobic bacteria at 6 and 8 d of storage (p <0.05). At 2 d of storage, the rate of lipid oxidation in breast meat of OA-recieved group was higher than the control group (p <0.05) but in other days no significant difference was observed between two treatments. Feeding birds with OA had no significant effect on water holding capacity of breast meat at different storage days. In birds fed with OA, breast meat cooking loss was lower than the control group at 4 d of storage, but it was higher than the control group at 10 d of storage (p<0.05).

In conclusion, under the conditions of this study, feeding broilers with OA had no significant and constant effect on the most of investigated parameters.

Today, the poultry industry tends to increase production per unit area, at the same time, the increase in flock density is faced with management and health restrictions and obstacles. Consuming medicinal plants can be an effective nutritional solution to overcome the challenge of high density. Therefore, an experiment was designed and conducted in order to investigate the effects of the essential oils of medicinal plants in two un-capsulated and microencapsulated forms in the diet on the performance, intestinal morphology and acidity of the digestive system of broiler chickens.

In this research, out of 250 broiler chickens of the Ross 308 strain in the form of a completely randomized design with a factorial arrangement of 2x2, with 4 treatments and 5 repetitions, and in each repetition, normal density of 10 chickens and high density of 15 chickens with a similar weighted average was used. Microcapsules containing essential medicinal plants containing effective compounds of thyme leaf, savory leaf, peppermint leaf and black pepper seeds developed in the Agricultural Biotechnology Research Institute of East and North-East region of Iran. The tested treatments were; The first treatment: normal density (10 chickens per square meter) + no plant essential oil (control), the second treatment: high density (15 chickens per square meter) + no plant essential oil, the third treatment: normal density (10 chickens per square meter) + 500 mg/kg of un-capsulated essential oil mixture, fourth treatment: high density (15 chicks per square meter) + 500 mg/kg of encapsulated essential oil mixture. The number of casualties, the weight of the casualties and the weight of the eliminated chickens were recorded separately. The amount of feed consumed and weight gain were measured weekly and the food conversion ratio was calculated. At the end of the experiment, 2 birds were randomly selected from each repetition and slaughtered after blood sampling. To study the structure of small intestine villi, samples were obtained from duodenum, jejunum and ileum. A microscope with 40 times magnification was used to measure the height and width of the villus, and a 100 times magnification was used to measure the depth of the crypt. The acidity of the caecum was measured by a pH meter.

The results showed that the addition of microcapsules led to a decrease in the percentage of losses, an increase in weight at high density compared to the absence of microcapsules. The use of microcapsules in conditions of high concentration led to a decrease in the oral conversion factor. Treatments using microcapsules in normal and high density conditions had significantly higher gastrointestinal acidity compared to treatments that did not receive microcapsules. Consumption of microcapsules in normal and high concentrations led to an increase in the length of intestinal villi.

It can be concluded that the addition of encapsulated essential oil improved the weight gain, feed conversion ratio, intestinal morphostructural characteristics.

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.

In Suckling calves, due to the low development of rumen, the digestibility of food may decrease, so the energy of the diet can be increased by adding fat sources. The present experiment was conducted to investigate the effect of omega-3 and omega-6 fatty acids on feed intake and growth parameters of Holstein calves.

A total of 40 newborn calves (average age 3 days), for 60 days, in the form of a repeated design to 4 treatments including: (1) no supplemented fat source (control; CON), (2) 3% calcium-salts of soybean oil (Ca-SBO), (3) 3% calcium-salts of flaxseed oil (Ca-CO), and (4) 3% mixture of Ca-SBO and Ca-CO (1.5% each, DM basis; MIX). The study continued 66 days and the calves were gradually weaned during 61-65 days of age.

The starter intake during the period of 31 to 60 days for the control treatment was higher than the other treatments (p=0.05), but no differences were observed among the treatments in the entire experimental period. The daily weight gain in the periods of 31 to 60 days and the whole period for the treatment containing soybean oil supplement was better than the control treatment (p<0.05). Regarding body weight, soybean oil treatment had the highest weight at the end of the experiment. In terms of feed efficiency, mixed oil treatment had better performance than the control and flaxseed oil treatment, and it was not significantly difference with soybean oil treatment (p<0.05). Regarding blood metabolites, a significant differences were observed between experimental treatments in terms of glucose, total protein, cholesterol and other metabolites. Also, the liver enzyme concentration of aspartate aminotransferase for the treatment containing soybean oil on the 60th day of the experiment was the lowest compared to other treatments (p<0.01).

In general, the results showed that the use of soybean oil as a source of omega-3 fatty acids has more positive effects on the growth performance of Holstein suckling calves than flaxseed oil.

High concentrated diets are rapidly degraded in the rumen and lower ruminal pH by rapid and high lactic acid production. The use of chemical or biological buffers improves digestion and fermentation conditions in a high concentrate diet. The aim of this study was to compare the effect of using acid-consuming bacteria as pH regulator (biological buffer) and chemical buffer to improve digestibility and fermentation of high concentrate diets.

In the present experiment, 21 fattening Arabi male lambs with an average weight of 34.35±2.50 kg and an average age of 8±1 months old were used in a completely randomized design with 3 treatments and 7 replications for 50 days. Experimental treatments were included: 1- control diet (70% concentrate and 30% forage, without buffer and bacteria), 2- control diet + 1% sodium bicarbonate buffer, 3- control diet + 3 ml of Megasphaera elsdenii bacteria with 2 gram yeasts of Saccharomyces cerevisiae (bacterial-yeast).

Nutrient digestibility and growth performance parameters were not affected by experimental treatments. Rumen protozoa population was significantly higher in bacterial-yeast treatment than control (p<0.05). Ammonia nitrogen concentration and ruminal pH were affected by experimental treatments, and compared to control treatment, in treatments containing chemical or biological buffer, ruminal pH increased and ammonia nitrogen decreased. But blood and liver parameters, carcass characteristics such as size and weight of carcass parts, meat colorimetric characteristics were not affected by experimental treatments (p<0.05).

Overall, the results of the present experiment showed that the use of acid-consuming bacteria as pH regulators has competitive effects with bicarbonate buffer and even better in some cases.

The administration of Flaxseed as a source of energy supplementation can affect the growth of lambs. The purpose of this study was to investigate the effect of feeding different levels (0, 8 and 15%) of whole and ground Flaxseed on performance, nutrient digestibility, some blood parameters, and microbial protein production of Kabodeh Shirazi lambs.

30 male lambs (60 ± 4 days old and weighing 23.7 ± 2.5 kg) were allocated to 5 experimental groups with 6 replications in a completely randomized design. Treatments include 1- Diet without Flaxseed (control), 2- Diet containing 8% whole Flaxseed, 3- Diet containing 15% whole Flaxseed, 4- Diet containing 8% ground Flaxseed, and 5- Diet containing 15% of Flaxseed was ground (based on dry matter).

The addition of Flaxseed (whole and ground) had no significant effect on the performance of lambs and digestibility of nutrients in the whole gastrointestinal tract, but In comparison with the control group, crude fat digestibility has greatly improved in treatments using Flaxseed (p=0.001). As compared to the control treatments, the Flaxseed treatments raised plasma triglycerides (p=0.03) and cholesterol levels significantly (p=0.04). No difference was seen in glucose and albumin levels among lambs receiving different amounts or forms of Flaxseed. Purine derivatives, microbial nitrogen, and microbial protein production were also not affected by experimental treatments.

Flaxseed in various levels and forms improved the digestibility of crude fat and also increased triglycerides and blood cholesterol.

The most important problem of the animal industry is the supply of needed feeds, and identifying the new sources of feeds is of particular importance. This study was conducted to determine chemical composition of whole basil (Ocimum basilicum) forage after seeding and to investigate the effect of different levels of this forage replacing with straw and a part of alfalfa in the diet of fattening lambs on performance, blood parameters and the nutrients digestibility.

18 male Zandi lambs with initial body weight of 28.8±2.03 kg were used in a completely randomized design with 3 treatments and 6 lambs in each group. Experimental treatments were: 1) control (basal diet without whole basil forage) 2) basal diet + 12.5 % basil forage and 3) basal diet + 25 % basil forage. Chemical composition of basil forage was determined. Also, nutrients digestibility of experimental diets, blood parameters and performance of experimental lambs were determined. 

Average amount of dry matter, crude protein, crude fat, NDF and ash of basil forage were 92.69±1.2, 6.65±0.06, 1.35±0.01, 54.26±0.33 and 11.09±0.44, respectively. Replacing of basil with wheat straw and alfalfa hay in finishing experimental lambs resulted in improvement in DMI, ADG and FCR (p<0.05). Blood glucose, BUN, cholesterol, triglycerides and hepatic enzymes were not significantly affect by experimental groups. Blood total protein concentration was higher in lambs fed by 25 % basil forage compared to other experimental groups (p<0.05). Feeding whole basil increased digestibility of crude protein, crude fat and NDF (p<0.05), but had no any effect on carcass traits and tail fat weight of experimental lambs.

Results of this study showed that whole basil can be used replacing with wheat straw and alfalfa hay up to 25 % in fattening lambs diet without negative effect on performance and digestibility of diets nutrients.

In conjunction with the increase in PoPulation and the need to Produce more food, Pesticides have been used to control and eliminate Pests in livestock and agricultural Products. Regrettably, the excessive use of Pesticides causes damage to the environment, Plants, animals, water, and soil. The Present study was conducted to investigate the effect of different concentrations of RounduP herbicide as a widely used and common agricultural Pesticide in in vitro maturation of goat oocytes.

To PrePare goat oocytes, ovaries were PrePared from a slaughterhouse and transPorted to the laboratory into the flask containing warm saline (30-34oC). Oocyte cumulus comPlexes (COC) were removed from small antral follicles (2-6 mm) with the slicing method and transferred to a maturation medium whit different concentration of RounduP. COC was Placed in a maturation medium for 24 hours and reached metaPhase stage II (nuclear maturation). The exPeriment was examined in a comPletely randomized design with 4 treatments included: control, 187.5 μM, 375 μM, and 750 μM of the rounduP.

This study showed that the addition of different concentrations of the herbicide RounduP significantly decreased the maturation rate of goat oocytes than the control treatment (P < 0.05). Also, the addition of different concentrations of RounduP in the goat maturation medium reduced the steroidogenic gene exPression in cumulus cells comPared to the control treatment. However, RounduP did not have a considerable influence on DNA methylation in the Promoter site of the StAR gene.

The efficacy of the treatment with a dose of 187.5 μM of the rounduP in reducing the relative exPression of StAR, CYP11A1 and CYP19 genes was higher than the 375 μM, which could be as a consequence of the fact that hormone disruPters (environmental Pollutants) have strong biological effects in low concentrations, but in high concentrations, they have weak or no biological effects.

The use of improved queens with desirable functional and behavioral traits is one of the most important factors of success in beekeeping. The current study was conducted with the aim of evaluating the performance of improved Iranian honey bee queens with control ones in the private apiaries of Kurdistan province during 2017 to 2021.

In this study, the queens of the third layer, which were the result of the improved queens of the Iranian honey bee breeding project, along with unimproved native queens (as control) were evaluated in six private apiaries of Kurdistan province based on honey production, calmness, aggressive, swarming, and overwintering traits. To evaluate the queens, special questionnaires were designed and provided to the beekeepers to evaluate the improved queens along with the control ones in their private apiary during the years of the study.

Variance analysis results showed that the effect of the queen was significant at the 1% probability level on all studied traits. The effect of year was significant at the 1% probability level on honey production and swarming traits and on calmness on the frame trait at the 5% probability level, but it had no effect on the overwintering trait. Also, the effect of the city was significant on swarming trait (p<0.01). The interactions effect of queen type – year and year- city were significant for the trait of swarming and honey production triats at the 1 and 5 % probability level, respectively. The results of the present study showed that the colonies with improved queens were significantly superior to the colonies with native queens in terms of calmness on the frame, aggressive, swarming and overwintering traits (p<0.05). An acceptable relative superiority and progress were observed in terms of honey production trait in the improved queens in all the studied years compared to native queens, but this superiority and progress was not significant due to the low heritability of this trait.

In general, the results of this study showed the progress and improvement of the target traits and the superiority of improved Iranian honey bee queens compared to unimproved native queens in the climate conditions of Kurdistan province. Considering the superiority and significant improvements in the majority of studied traits in the improved queens of the Iranian honey bee breeding project, it can be concluded that the Iranian honey bee can improve genetically. Therefore, in the continuation of this research, it is suggested to deal with the new problems of the beekeeping industry through more efforts towards the genetic stabilization of resulting improvements, preventing the homozygosity of sex alleles (which has a direct effect on reducing the performance of the colonies) and also using new breeding methods.

The scientists believe that human intervention has caused changes in climate conditions and these changes will be noteworthy in the future. Any significant change in climate variables can affect the milk production of industrial livestock farms.

In this research, the effect of temperature-humidity Index (THI) on milk production in Babolsar city was quantified, and then, using the SDSM model, the THI index was downscaled to the year 2100. Finally, the effect of climate change on milk production until the end of current century in three emission scenarios of RCP2.6, 4.5, and 8.5 were quantified.

The results showed that in the current situations, Babolsar station has been involved in temperature-humidity stress for 5 months of the year, which will increase to 7 months by the end of this century. Also, the results showed that in near future (before 2050) the stress condition is not much different from the base period, but after that, even in RCP2.6 scenario, the differences with the base period will increase significantly, and the most intensity of stress level will occur., As a result, on more days of the year, heavy livestocks will experience tempreture-humidity stress. Quantification of the effect of temperature-humidity stress on milk production showed that for increase of one unit of daily THI more than 70, the milk production of each animal decreases by 327 grams. The investigation of milk reduction trend in the future showed that until the year 2100, not only the milk production will decrease in more months of the year, moreover, the daily losses of livestock farmers also increase. so that in the stressful months, the daily milk reduction from 1 to 2 kg per animal in base period, will increase to 1.5 to 3.5 kg. So, the losses caused by climate change on milk producers will increase by at least 45 and at most more than 100 percent.

According to the results of this research, the stress level of emergency will occur in the last decades of this century, which will lead to a sharp decrease in milk production. Therefore, if adaptation policies to climate change are not considered in the future, there may be happens widespread deaths of heavy livestock especially in critical months of July and August, which is a serious alarm for livestock industry of the Mazandaran province.

Sheep are considered one of the essential livestock with the high ability to adapt to different climates, and a breed diversity was observed in Iran. As a result of different selections, some genomic regions have acquire high purity called Runs of Homozygosity (ROH). By examining these regions in the genome of sheep, the goals of selection in these breeds can be followed and the genes present in these regions can be identified.

For this purpose, the whole-genome sequencing data from 28 samples of Iranian sheep, including Afshar, Ghezel, Karakul, Moghani, Makui, Baluchi, Gray, and Shal breeds, were downloaded from the NCBI database. After quality checking and trimming, high-quality reads were aligned to the sheep reference genome by BWA software. Then the variants were identified and filtered using VCFtools software, a VCF file containing information related to SNPs was created for more analysis. At the end of the analysis, homozygous strands were extracted, and finally, the genes related to these regions were identified.

Based on the results of PCA, the samples related to Iranian sheep breeds were divided into three categories, the first group includes the Karakul and Baluchi breeds (KB), the second group includes the Moghani and Makui breeds (MM), and the third group includes the Shal, Ghezel, Afshari and Gray breeds (SGAG). According to the results of the analysis, ROH areas for KB, MM, and SGAG populations have 419 (52.375 areas per person), 139 (23.17 areas per person), and 876 (62.57 areas per person) ROH areas, respectively. Also, 6 and 17 common ROH (at least two samples) were identified in KB and SGAG populations, respectively. We could not find a common ROH for the MM population. Annotating the sharing ROHs leads to identifying 99 and 173 protein-coding genes within these genomic regions for the KB and SGAG populations, respectively. The results of gene ontology analysis showed that most of these genes are involved in processes such as energy and fat metabolism (FLCN, ELOVL3, STK3, SREBF1, and NCOR1) as well as the growth and development of muscle tissue and meat quality (MYL6 and TMOD1).

According to the results of this study, it could be concluded that there is a high level of diversity and crossbreeding in the native sheep breeds that could be used for different breeding goals and producing breeds with appropriate production. On the other hand, the candidate genes identified in this research also accelerate the time to achieve breeding goals in these breeds.

Due to the increasing use of next generation sequencing (NGS), it is necessary to use specialized algorithms and software to perform statistical analysis in order to identify functional genes. Alignment of reads with the reference genome is the first and most important step in most RNA-Seq data analysis programs, and the accuracy of downstream analyzes effectively depends on this step. Therefore, the aim of this research was to compare some different software for aligning the data obtained from total RNA sequencing on the reference genome.

RNA-Seq data related to 54 Holstein dairy cows raised in industrial conditions were used to identify genes effective in fertility. The quality of the reads was determined by FastQC software and editing of low quality sequences was done using Trimmomatic software. The edited data were aligned with bovine reference genome using Bowtie2, Tophat2 and Hisat2 softwares. The total percentage of mapped reads, the percentage of mapped reads on one location in the reference genome, and the percentage of mapped reads on more than one location were calculated.

The results showed that the most alignment was done on the cow reference genome using Tophat2 software. which mapped 94.197% of the From the total available reads, 94.197% and 92.526% were mapped on the reference genome by Tophat2 and Hisat2 software, respectively.  The Hisat2 software had more allocation function and mapped 89.202% of the data to a specific position, while this parameter was 87.812% of the total sequences  for Tophat2 software. From the total used sequences, only 3.324% and 6.385% of the sequences were aligned by Hisat2 and Tophat2 software respectively to more than one position of the reference genome. Bowtie2 software had low performance compared to  other two software.

The comparison of RNA-Seq data alignment software on the reference genome showed that although the Hisat2 swas the best read mapping software  but, Tophat2 software can also be used instead in RNA-seq data analysis. Meanwhile, Bowtie2 software is not very effective in relation to RNA-Seq data.

Complete information of relationship matrix is ​​an important principle to achieve reliable results in genetic evaluations. Two kinds of pedigree errors, including incorrect pedigree information and missing pedigree information, reduce the capability of the livestock model in traditional methods. The purpose of this study was to investigate the different levels of missing pedigree information such as sire, dam and both parents (sire and dam together) on heritability, accuracy of prediction and estimation of breeding value in threshold traits.

Sex-limited traits with heritability of 0.05, 0.1, and 0.2, were simulated. In order to create threshold phenotypes of litter size, 20% of the top-phenotypes were considered as two and the rest were considered as one. Different ratios of missing sire information (zero, 5, 10, 15 and 20), missing dam information (zeros, 5 and 10) and a combination of both missing information (sire and dam together) were created. A threshold model was considered. Heritability, breeding values ​​and accuracy of prediction were calculated by Bayesian statistical method.

With the introduction of different levels of missing pedigree information to the complete pedigree, the amount of heritability decreased. The lowest values ​​of heritability were 0.018, 0.084 and 0.16 for heritability of 0.05, 0.1 and 0.2, respectively. In the complete pedigree, the lowest and highest accuracy of prediction were 0.375 (h2 =0.05) and 0.521 (h2 =0.2), respectively. The lowest values of accuracy of prediction for heritability of 0.05, 0.1, and 0.2 were 0.309 (30% in paternal pedigree defects and 10% in maternal pedigree defects), 0.353 (paternal pedigree defects 20% and maternal pedigree defects 10%), and 0.459 (5% defect in paternal pedigree and 10% defect in maternal pedigree), respectively. Furthermore, missing pedigree information led to a decrease in the average breeding value.

The results showed that, compared to the paternal or maternal missing pedigree information separately, paternal and maternal missing pedigree information together, further reduces the estimation of genetic evaluations.

The review of published articles in the field of genomic selection shows that in the most of studies conducted in livestock and crop species, genomic evaluation and prediction of genomic breeding values ​​have been done without considering the dominance genetic effects. However, recent studies have shown that the dominance genetic effects contribute significantly to the phenotypic variation of productive traits of domestic animals. Therefore, it seems that ignoring the dominance genetic effects will affect the accuracy of the genomic evaluation. In this article, the consequences of not considering the dominance genetic effects in the genomic evaluation model on accuracy, mean square error, bias and reliability of genomic breeding values ​​were investigated.

A genome consisting of 5 chromosomes, each 1 Morgan length, containing 5000 bi-allelic single nucleotide polymorphism (SNP) was simulated at heritability level of 0.5. All quantitative trait loci (QTLs) were assigned additive genetic effects. Different distributions of QTL effects (uniform, normal and gamma) as well as three scenarios of the number of QTL as 5, 10 and 20% of the total number of SNPs (respectively 250, 500 and 1000 QTLs) were considered as simulation hypotheses. In different scenarios, dominance genetic effects were given to 0.00, 10, 25, 50 and 100% of QTLs. The genomic breeding values ​​were estimated using the genomic best linear unbiased prediction method (GBLUP) and the criteria of LR method such as prediction accuracy, mean square error of prediction, bias and reliability of the genomic breeding values ​​were used to analysis genomic breeding values ​​predicted by GBLUP.

The results showed that if the dominance genetic effects contribute to the phenotypic variation of the interested trait, but ignored from the genomic evaluation model and remain unseparated from the additive genetic effects, lead to a decrease in the accuracy of the genomic breeding values ​​by about 25%. Also, the mean square error of prediction of genomic breeding values ​​increased by 60% following increase in the percentage of QTLs with dominance effect from 0.00 to 100%. The bias of genomic breeding values ​​was also affected by ignoring dominance effects and increased by 36% following increase in the percentage of QTLs with dominance effect from 0.00 to 100%. Also, the reliability of genomic breeding values ​​was significantly reduced by about 40% with the increase in the percentage of QTLs with dominance effect from 0.00 to 100%.

In general, the results of this research showed that not separating the dominance genetic effects from additive genetic effects leads to low-accuracy, biased, and unreliable estimates of genomic breeding values, which will ultimately reduce the efficiency of genomic selection schemes. Therefore, it was suggested that in order to increase the efficiency of genomic selection, dominance genetic effects should be included in the genomic evaluation model.

 Selection in animal populations to increase the frequency of ideal alleles causes of remaining some signs in the animal genome, which are usually associated with important traits. Today, with developments in next-generation sequencing and easier access to animal genomic information, some models have been proposed to identify selective signatures based on allelic frequency and haplotype blocks. This research aimed to identify the selective signatures in two horse breeds of Caspian and Kurdish using a k70 SNP chip.

 In this research blood samples from 35 Caspian and 31 Kurdish horses were collected. After DNA extraction and sequencing (by Illumina company), Quality control of the data was performed for minimum allele frequency (PMAF<0.05), genotyping rate (PGENO < 0.5), and deviation from Hardy-Weinberg equilibrium (PH-W<1 ͯ 10-6). Then the theta (θ) test and ensemble site were used for identifying selective signatures and the positions of snaps respectively, and finally, the genes related to these positions were identified.

 After quality control of data and integration of genomic data of two populations based on R package protocols, 61 horses with 52,650 SNPs remained for the rest analysis. Finally, Fst statistical test based on unbiased estimator theta method 31 differentiating markers of the two studied horse breed were identified

The results showed that Caspian and Kurdish horse breeds belong to two separate groups. The Kurdish horse breed has more diversity and variety than the Caspian. The most important genes associated with significant SNPs were INPP5F, HPSE2, R3HCC1, DOCK3, ITGB6, GM6B, PHEX, WDR13, LRCH2, GRIA3 and THOC2. Most of the identified genes were associated with intercellular exchanges, muscle contractions, immunity, membrane support, DNA stability, and the nervous system.