سعید اسماعیل خانیان

Animal husbandry, as one of the important sub-sectors of the agricultural sector, requires the formulation of a strategic plan at the regional level. The purpose of the research is the necessity of scientific planning for the improvement and development of livestock production, in line with the optimal use of the existing capabilities and capacities of Sistan region. The data collection tool was a questionnaire, Data analysis was done in the descriptive statistics section in Excel software, and then multi-indicator decision making technique and gray method were used to estimate other results. The results of the study showed that the index of reducing the vulnerability caused by natural disasters through capacity building and water resources management has the greatest effect in determining the index of the vision, goals and strategies of sustainable development of the industry. The index of preventing severe market fluctuations has the most effective variable to improve the capacity of the existing economic activities of the industry. In addition, the results showed that in order to meet the energy and protein needs of this livestock population, about 1288274 tons of dry matter, 171666 tons of raw protein and 2430870955 megacalories of metabolizable energy are needed, and about 209 thousand tons of dry matter (33% protein and 1.41% energy) are needed annually. Metabolizable) is deficient.Based on the type of strategy obtained, Zahak and Hamon cities should include aggressive strategy, Hirmand and Nimroz cities, change direction strategy, and Zabul city should include diversity strategy in the work plan.

Although sperm cryopreservation seems to be an efficient technique for distributing competent sperm for artificial insemination, the process affects the quality of post-thawed sperm.

This study was designed to see how the novel mitochondria-targeted antioxidant “Mito-TEMPO” affected buck sperm quality during cryopreservation. 

After proper semen samples collection, they were diluted and divided into 5 equal groups and cryopreserved in liquid nitrogen with 0, 1, 10, 100, and 1000 µM Mito-TEMPO. Sperm motility, lipid peroxidation, abnormal morphology, acrosome integrity, membrane integrity, and viability were all evaluated after thawing. 

When the freezing extender was supplemented with 10 µM Mito-TEMPO, total motility, progressive motility, membrane integrity, acrosome integrity, and viability increased (P≤0.05), while lipid peroxidation decreased (P≤0.05). 

Finally, the novel mitochondria-targeted antioxidant “Mito-TEMPO” could be introduced as an effective cryo-additive to improve buck semen quality parameters during cryopreservation.

Sustainable use, development and conservation of poultry genetic resources are of particular importance for agriculture, food production, rural development and the environment (Besbes et al. 2007). Indigenous chickens are often considered as a support for low input backyard or free-range system of production in rural, semi-urban and nomadic areas (Haunshi et al. 2019). Native chickens have unique characteristics such as ability to adapt to adverse environments, hardiness, broodiness and aggressiveness to protect their chicks, and more. However, low genetic potential is one of the identified limitations for increasing the productivity of native chickens along with inadequate nutrition and disease prevalence (Magothe et al. 2012a). The inbreeding accumulation and the decline in genetic diversity that occurs due to the mating of related animals in closed populations negatively affect phenotypic values and additive genetic variance (Falconer and Mackay 1996). Inbreeding, which occurs because of mating of related animals in a population, often occurs in the closed and small populations. The negative consequence of inbreeding is referred to as inbreeding depression, which has become a major concern in research related to evolution, ecology, and conservation biology (Reed et al. 2012). In small populations in particular, the inbreeding depression is significant in reproduction issues and has important consequences for the population's ability to evolve and adapt to environmental changes and ultimately their longevity (Leroy 2014).Increasing the inbreeding rate in closed populations of indigenous chickens' farms may negatively affect the increase in population productivity following the selection process and have destructive effects on improving economic traits in the population. Therefore, considering the importance of the issue, it seems necessary to monitor the inbreeding rate as well as the resulting depression in the under selection closed population of breeding station of Khorasan Razavi indigenous fowl.

In order to estimate the inbreeding rate and evaluate its effects on some important economic traits the pedigree data of 38489 birds collected during 2006-2017 in breeding station of Khorasan Razavi indigenous fowl were used. First, the pedigree data of the studied traits were edited using Foxpro and Excell software and then the files required for data analysis were prepared. The eight traits including average egg weight (AEW), egg number (EN), egg weight at 1st day of laying (EW1), age at sexual maturity (ASM), weight at sexual maturity (WSM), body weight at 12 weeks of age (BW12), body weight at hatch (BW1) and body weight at 8 weeks of age (BW8) were studied. The inbreeding coefficients of all birds recorded in the pedigree were estimated using the CFC program (Sergolzai et al. 2006). The inbreeding coefficients of the birds were divided into different categories. Then, the mean changes of inbreeding during different generations were evaluated and the amount of inbreeding changes in each year was calculated using SPSS software by fitting linear regression of inbreeding per generation. Also in this study, regression coefficients of studied traits on individual and maternal inbreeding percentage were estimated with the REML procedure of WOMBAT software (Meyer 2007) through different models.

The results showed that about 57% (21892 birds) of all birds registered in the pedigree were inbred. The mean of individual and maternal inbreeding varied relatively little over 12 generations. The mean inbreeding of all birds and inbred birds was estimated to be two and three percent, respectively. The highest and lowest inbreeding rates were three and 0%, respectively. As the results show, despite the closed raising and selection of the population and also the increase in the probability of inbreeding in the population, the inbreeding rate has been increased with a relatively low slope over the generations. In general, during the studied generations, the average coefficient of individual and maternal inbreeding in the whole population showed an increasing trend, so that by fitting the linear regression of inbreeding to the generation, the rate of changes in individual and maternal inbreeding was estimated to be about 0.005± 0.03 and 0.004± 0.02 per generation, respectively. In a study conducted on the Isfahan improved native chicken population (Jelokhani et al. 1400), researchers estimated the rate of individual and maternal inbreeding changes per year for the all population by fitting linear regression of inbreeding per generation to 0.006± 0.05 and 0.005± 0.04, respectively, which is approximately consistent with the results of the present study. In this study, 43.12% of the birds were non-inbred and the rest of the birds (47.68%) were grouped in six different inbred groups. The results showed that among the inbred groups, the most inbred birds (47.68%) were birds with inbreeding coefficients between 0 and 5%, which indicates that the population inbreeding is relatively low. Various studies have been performed on the inbreeding rate of domestic chickens in the country; the results are consistent with the results of the present study. For example, the results of a study on 26 generations of genetically improved domestic chickens of Mazandaran showed that, the rate of inbreeding for this population is relatively low (Ghorbani and Omrani 1399). In another study to estimate the inbreeding rate of Indigenous Kokok balenggek chicken (KBC) population in Indonesia, the researchers estimated the inbreeding coefficient to be 0.0031 (0.31%) and concluded that considering the inbreeding rate of herd is less than one percent, and inbreeding less than one percent indicates that one percent of heterozygosity is lost in one generation, the population is not endangered (Rusfidra et al. 2014). In another study on the population size of 37 protected local chicken breeds in five European countries, the relatively low inbreeding rates (0.02 to 0.71%) was reported (Spalona et al. 2007). In our study, the highest effect of individual inbreeding was shown on BW12. In this trait, for a one percent increase in inbreeding rate, the body weight decreases by 1.17 grams. Based on the another study performed on the Isfahan improved native chicken population (Jelokhani et al. 1400), it was shown that for every one percent increase in individual and maternal inbreeding, the WSM is reduced to 3.97 and 1.38 grams, respectively. In another study conducted on Mazandaran native fowls, the results showed that for every one percent increase in individual inbreeding, body weight decreased for the traits including BW12, BW8 and WSM (Ghorbani and Emrani 1399). The results of another study on the improved Fars native fowl revealed the greatest effect of inbreeding on body weight traits (8 and 12 weeks). In this study, for every one percent increase in individual inbreeding, body weight at 12 and 8 weeks decreased by 2.14 and 1.07, respectively (Jelokhani and Ghorbani, in press).

According to the findings in the present study, since the population is closed and under selection, the probability of inbreeding in the population is high. However, because there are controlled matings in the population of breeding station of Khorasan Razavi indigenous fowl, the inbreeding rate in each generation has increased slightly, which shows the appropriate management practices are running in selecting the best birds. Best management practices such as controlling the matings between birds can prevent an increase in population inbreeding as well as its possible negative effects on the traits.

The aim of this study was to evaluate the effects of vitamin E with glycerol as cryoprotectant on freezability of Alpine goat semen. Semen was collected from Alpine male Goat (3-4 years), twice a week for five weeks at the Animal Science Research Institute of IRAN (ASRI). Different concentrations of vitamin E (0, 0.5, 0.75 and 1 mM) in 5% glycerol as a cryoprotectant were evaluated to improve the quality parameters of goat semen. After ejaculation, semen equilibrated at 5 ºC for 2 h, and aspirated into 0.25 mL straws. After equilibration, straws were frozen in liquid nitrogen vapor and plunged into liquid nitrogen for storage. Sperm parameters, including motility and progressive motility by CASA, viability, membrane integrity and total abnormality sperm, were assessed. The results show that addition, different levels of vitamin E to the extender for freezing of goat semen can improve motility (P>0.05). Also, 1 mM vitamin E showed higher progressive motility, VSL, VCL and ALH than the other treatment groups (P>0.05). Addition 1 mM antioxidant significantly improved the viability and membrane integrity of sperm than the control group (P>0.05). Addition different levels of vitamin E to goat semen extender showed no significant difference in abnormal sperm and lipid peroxidation than the control group (P>0.05). Therefore, addition of 1 mM of vitamin E to extender improves the freezability of goat semen.

Sistani cows are generally restless animals; therefore, controlling, treating, and weighing them is difficult. On the other hand, recording the weight of domestic animals, including Sistani cows, is inevitable, because it provides a good scale for management decisions in the herd such as balancing the diet, changing environmental conditions, or determining the time of slaughter of fattening animals. In addition to scales, various methods are commonly used to measure the body weight of large animals. Some of these methods include the use of weight-meters, appraisal assessments, and the use of mathematical models. One of the new methods for predicting livestock weight is artificial intelligence. Because some reports are indicating that artificial intelligence could facilitate the weighing process of animals, this study was performed to predict the body weight of Sistani cows using computer vision technology. The data required for this study were recorded in the Zahak breeding station located in Sistan and Baluchestan province of Iran. The recording operation involved the weighing and biometric measurement of about 190 Sistani cattle, including calves, heifers, and male and female animals, every three months during a year. At the time of weighing, images of the lateral view of each animal were taken and recorded using the CANON SX150IS digital camera. During this period, a total of 358 weight records of Sistani cows at different ages were recorded. The digital images were initially preprocessed using MATLAB software, and then some morphological features were extracted from each image. For predicting the weight of Sistani cows via the Artificial Neural Network (ANN), the extracted features of images were introduced to the ANN model as input and the weight of cows as output. The "feed-forward neural network", which was trained by the "error propagation" algorithm, was used to predict the weight of cows. The function used in the hidden layer of the ANN model was sigmoidal and in the output layer was linear. An ANN model which had the highest precision and lowest error was selected as the final model for predicting the animal weights. The criteria for selecting the best model were the highest determination coefficient (R2) and the lowest mean square error (MSE) compared to other available models. Out of 22 features extracted from each image, only 15 of them, which had a higher correlation with the body weight of cows at different ages, were selected as effective features. As result, equivalent diameter, major axis length, minor axis length, bounding box, convex area, filled area, area, perimeter, and the number of non-zero pixels of the image (NNZ) had the highest correlation with the cattle weights (P<0.01) and used as effective features to train the ANN model. The final ANN model had 15 neurons in the input layer including selected image features, 11 neurons in the hidden layer, and one neuron in the output layer including the weight of the cows. The precisions of the artificial neural network in the training, validation, and test phase were 0.974, 0.970, and 0.981, respectively. The results showed that the final ANN model had acceptable precision in all light, medium, and heavy-weight cows, and the size and the age of animals did not have a significant effect on the precision of the artificial neural network model. A correlation between the actual weight of Sistani cows and the weights predicted by the ANN model was 98.3%. The average error of the model in predicting the weight of cows was 1.11%. In the practical test, a 2.32 kg deviation was observed between the predictions of the ANN model and actual weights in Sistani cows. The accuracy of the ANN model for predicting the weight of Sistani cows in the present study is acceptable and within the range of the other reports. The proposed method based on image processing and ANN, had acceptable results in predicting the weight of Sistani cows. Given the difficulties of weighing Sistani cows as heavy livestock and sometimes the time-consuming process, it seems that the use of new technologies such as computer vision methods can be a good alternative to conventional weighing methods and facilitate and reduce recording costs of Sistani cows.

This research was conducted to investigate the possibility of using visual machine technology in measuring the body dimensions of Sistani cows. For this purpose, the record of body dimensions including length, shoulder height, hip height and chest circumference of 179 heads of livestock in Zahak Sistani cow breeding station, were measured at different time points, using a tape meter. At recording time, digital images were taken using the canon camera from the lateral view of cattle from distance of 2 meters. Digital image processing and feature extraction were performed using Graphical Unit Interference of MATLAB software. The feature of digital images as input and different body dimensions of cows as output of Artificial Neural Network(ANN) were used in the training and modeling phase. The results showed that, out of 22 features extracted from the images of Sistani cows, the 15 effective features, such as Equivalent Diameter, Major Axis Length, Minor Axis Length, Bounding Box, Convex Area, Filled Area, Area, Perimeter, and the number of white pixels of image (NNZ) had a significant correlation with the body dimensions of the Sistani cow(p<0.01). Body dimensions of Sistani cows including body length, shoulder height, hip height, and chest girths were estimated with accuracy of 0.98, 0.97, 0.97and 0.98%, by the ANNs model, respectively. The results of the present research showed that Artificial Intelligence Technology can act as a suitable alternative to biometric evaluation of Sistani cows and save time and relevant costs.

Breeding between Indus cows and Taurus cows in the Sistan region of Iran has been done in recent years through the use of liquid sperm, frozen sperm, or foreign bulls. There are few studies in Iran on the effects of interbreeding programs on Sistani cattle. The present study was performed to identify mononucleotide polymorphisms (SNPs) based on RNA-Seq data in purebred Sistani cows and its crosses with three foreign breeds of Holstein, Simmental, and MonteBilliarde cows.

In this study, RNA-Seq data were used for pure Sistani, Sistani and Holstein, Sistani and Montebeliarde, Sistani and Simmental cattle. For this purpose, first of the tail vein of purebred cattle mixed with Holstein, Simmental, and MonteBilliarde. (4 treatments and for each treatment two biological replications) in the same environmental, nutritional, and managerial conditions located in the breeding center of Sistani cattle in Zabol. blood was drawn.

SNP discovery analysis was performed on transcriptome using SAMtools software package, which led to the discovery of 152496, 177042, 134285, and 163362 SNPs in pure Sistani breeds and its crosses with three foreign breeds of Holstein, Simmental, and Montebeliarde bulls. In this study, there was no direct relationship between the number of SNPs identified and the length of chromosomes. Also, 12 types of SNPs were identified, of which four types were transition and eight types were transversion. The most common known SNPs were transition which was 71.84% in pure Sistani, 72.65% in Sistani and Holstein, 72.60% in Sistani and Simmental, and 71.94% in Sistani and MonteBilliarde.

Overall, the results of this study confirmed that RNA-Seq technology is an effective, economical, and efficient method for identifying SNP loci. Factors influencing RNA-Seq evaluation are such as the number of samples.

Monitoring the inbreeding rate of native chickens in breeding stations is of significant importance because of planned matings and lack of gene flow inthe population. This study was undertaken to estimate the inbreeding coefficient, investigate the trend of inbreeding changes and evaluate the effects ofinbreeding depression on the economic traits in Isfahan improved native chicken population. The studied traits were body weight, age at sexualmaturity, weight at sexual maturity, egg number, mean egg weight and egg weight at first day. In the present study, data of 97272 birds recordedduring 21 generations were included. In order to estimate the inbreeding coefficient of each bird and the effect of inbreeding on the traits, CFC andWOMBAT software were used, respectively. Pedigree analysis indicated that 79.48 percent of population were inbred. The estimated averageindividual and maternal inbreeding coefficients were 4.3 and 3.5 percent, respectively. According to results, for every one percent increase ininbreeding, rate of inbreeding depression for the traits including the body weight in 1 day, 8 weeks and 12 weeks, age at sexual maturity, weight atsexual maturity, egg number, average weight of eggs and egg weight at first day was -0.008, -2.52, -3.51, 0.23, -3/97, -0.13, 0/02 and 0.06,respectively. Based on the results of the present study, although in closed populations under genetic selection, the absence of inbred bird is almostimpossible, but, the reduction of inbreeding can be achieved by controlling the matings, which prevents the adverse effects of inbreeding in thepopulation.

One of the major challenges in camel husbandry is the lack of records and registration. The camel breeding system in the country is Extensive and dependent on rangelands and the long distances and high dispersal of herds have added to the problems of recording and the establishment of net. On the other hand, recording, especially in weights of camels, is very difficult and it is necessary to use statistical models and estimation of body weight by body measurements. Networking to communicate camel breeders with each other and education and research centers can provide camel productivity in the country. therefore, it is necessary to use ICT in camel husbandry. In camel breeder assisted system, by communicating through the SARBANYAR app, in addition to communicating and providing skill training, camel breeder knowledge in the mobile platform will be enhanced. The camel herd is also tracked online using the GPS hardware and this APP.

The aim of this study was to investigate the effects of adding betaine to diets of Ross and Arian strains that received drinking water with total concentration of TDS. 720 single-day broiler chicks, Ross and Arian strains were distributed in 12 experimental units for six weeks. The experiment was conducted in a completely randomized design with factorial arrangement (2 × 2 × 3) containing two levels of additive betaine (0 and 0.2% diet) and three levels of TDS (400, 2000 and 3500 mg / l) with four replicates and 15 chicks in Every repetition was done on the seventh day. . With the increase in TDS water content, the body weight of the chicks decreased, and the conversion factor of food and water consumption increased. Additive betaine had a significant effect on the increase in weight and water consumption during the durability period. The percent mortality and moisture content of the waste was higher in treated water with higher TDS. The amount of moisture was reduced by the addition of betaine. The effect of adding betaine and increasing TDS on the concentration of sodium chloride in chicks was significant at 28 days of age (P <0.05). By increasing TDS in drinking water, the BHMT enzyme gene expression in the liver of the chicks also decreased in the Arian strain relative to the Ross strain. The gene expression increased with the addition of betaine to the ration of chicks.

In this study, direct methylation was compared with two conventional extraction methods (Soxhlet and Folch) in terms of extraction yield, the stability of configuration of fatty acids chemical structures and their effect on saturated and unsaturated fatty acids profile. Also, by evaluating and comparing fat extraction methods for fish, egg yolk and milk samples, the efficiency of these methods was determined according to the sample tissue. After extraction and esterification procedures, fatty acids were determined by gas chromatography method. The statistical method of ANOVA using GLM technique was applied to compare the mean of data. The fatty acid profile was subjected to analysis similarities based on cluster analysis to check how the methods would affect the fatty acid profile and to evaluate how much differences are between the methods. The obtained results indicated that the Soxhlet had the lowest efficiency for the extraction of fatty acids, especially in a sample of dry milk, but it was the highest precision compared with the Folch and direct methylation methods. It was also found that the methods have different ability to extract fatty acids based on their unsaturation degree. In general, extraction methods, in addition to affecting the fatty acid profile, have a different effect rate, depending on the sample tissue. Therefore, in order to select an effective method for extracting fat, it is necessary to consider the sample tissue.

Due to the importance of conservation and preserving indigenous breeds, Baluchi sheep as the most populous breed of Iranian sheep with reliable pedigree was selected. In this study genetic variations were analyzed with 15 microsatellites markers (BM737, BM1815, BMS332, BMS995, BMS2721, KD101, LSCV36, LSCV38, McM63, McM139, McM214, McMA1, McMA10, OarVH110, TGLA231) in a population of Baluchi sheep. Whole blood samples were randomly collected from 140 sheep at Abbas Abad Breeding Station (Mashhad). After PCR reactions, McM139 locus wasn't amplified and LSCV38 locus was ignored for many null Alleles. Thirteen microsatellites loci were %100 polymorphic. Number of alleles, observed and expected heterozygosity, polymorphic information content (PIC) and Shannon index were calculated. Highest and lowest allele numbers was observed in OarVH110 locus with 12 alleles and 6 alleles in BM737, BMS332, McMA10, respectively. Effective number of allele was between 3.51 (LSCV36) to 8.66 (OarVH110). The highest and the lowest heterozygosity belonged to 0.89 (OarVH110) and 0.71 (LSCV36), respectively. OarVH110 locus indicated the highest PIC (0.873) and LSCV36 locus indicated the lowest PIC (0.669). The highest and lowest Shannon index were belonged to 2.21 (OarVH110) and 0.66 (LSCV36), respectively. These results verify high efficiency of microsatellites marker for screening of population's structure in Iranian native sheep and in future study for QTL mapping. So, presence of new alleles and allele range indicates difference between Baluchi sheep population structure with foreign Sheep breeds.

The effect of addition of different concentrations of folic acid (vitamin B9) to the culture medium on in vitro maturation of bovine oocytes was investigated in two experiments. Optimization of bovine oocyte maturation medium is one of the strategies affecting quality of maturity and fertility, ultimately resulting in increasing the quality of produced bovine embryos. In the 1st experiment, to specify the concentrations of folic acid and homocysteine, ovarian follicles were divided into two categories including follicles with more or less than eight mm of diameter. Then, the concentrations were measured in both follicle groups as well as a commercial culture medium. In the second experiment, bovine ovaries were transferred to the laboratory immediately after slaughter and the cumulus-oocyte complexes were collected by aspiration from 2-8 mm diameter follicles. Oocytes were randomly divided into four groups and different levels of folic acid (0, 10, 100 and 1000 ng/ml) were added to maturation medium based on the results of the first experiment. Following incubation of oocytes, the percentage of mature oocytes was determined by Hoechst staining. The concentrations of folic acid and homocysteine in follicles with diameter of less than eight mm was higher than those with diameter of greater than eight mm, as well as the culture medium Supplementation of maturation medium with 100 ng/ml folic acid increased the percentage of metaphase-II oocytes compared to the control (P <0.05). Considering the concentrations of folic acid and homocysteine in the medium, results showed that the addition of folic acid improves in vitro maturation of bovine oocytes.

The aim of this study was to assess the impact of heat stress on production of dairy cows of National Research and Development Station for Dual-Purpose Cattle (Gavdasht, located in Babol city). In this order from 3876 test-day records which have been collected from 159 heads of Holstein cattle during the years 2015 to 2018 were used. Using meteorological data of the nearest synoptic station, two climate index with different weightings of dry bulb temperature and humidity were calculated and compared. Because longer periods of heat stress might have a more severe effect than shorter periods, 1-, 2-, and 3-d periods were also considered, by averaging the weather data measurements. Generally, regression analysis with a generalized linear mixed model was used to study the change in test day milk yield in response to climate conditions. Goodness of fit of models were determined using coefficient of determination (R2) and mean square error (MSE). Based on these results, the index with the temperature and relative humidity (THI) was determined as the best indicator for studying the climatic conditions of this study area. It was also observed that the average weather data 2 d before the test date (TD) explained more of the variability of milk yield than weather data 1 or 3 d before TD or on the TD itself. The starting point of heat stress for the Holstein cattle of Gavdasht Research Station was around 74 and their yield decreased by -0.12 kg per unit increase of THI ≥ 74.

Information theory is a branch of mathematics. Information theory is used in genetic and bioinformatics analyses and can be used for many analyses related to the biological structures and sequences. Bio-computational grouping of genes facilitates genetic analysis, sequencing and structural-based analyses. In this study, after retrieving gene and exon DNA sequences affecting milk yield in dairy cattle, the entropy in orders one to four for each gene and eta exons was calculated. In order to extract gene distances, mutual information method was calculated. The results of mutual information of DNA and exon sequences were entered as input into 7 general clustering algorithms. In order to aggregate the results of clustering, AdaBoost algorithm was used. Finally, the results of AdaBoost algorithm were investigated by GeneMANIA prediction server to explore the results from gene annotation point of view. Integrated result of each clustering algorithm due to AdaBoost algorithm, which implied as gene tree, indicated that proposed method biologically grouped set of genes as it was proved by their gene annotation using GeneMANI. We believe that the proposed method might be used with other DNA based clustering competitive methods and therefore, it can be used to group set of genes in other species.

In the past decade, many performance traits in chickens have greatly improved to meet the growing demand for chicken meat. On the other hand, due to the 70% share of feed costs in the total cost of livestock production, feed efficiency has become one of the most important genetic traits in livestock and poultry. Residual feed intake (RFI) is the difference between the actual absorption of animal feed and the expected of the animal absorption based on body weight and its level of performance. Selection to improve feed efficiency through RFI is suggested due to its phenotypic independence from body weight and body weight gain. There is evidence for the genetic basis of variation in productivity in all species. Previous studies have shown that some genes may play an important role in controlling RFI through effects on the digestive system and metabolic processes. It seems that changes in the amount of residual feed intake is the result of changes in the expression of the genes associated with it, and the study of transcript changes in chickens with high RFI helps to identify the mechanisms that affect it. Experiments were conducted on Commercial breeds (high production efficiency) and Isfahan Native Chickens (low production efficiency). From each breed, 60 chicks were harvested and caged from day 24 to 42 days for 19 days. The chicks of both groups were raised under the same management conditions. In order to measure the residual feed intake of each bird in individual cages and daily intake (FI) of the amount of feed consumed in 19 d (from day 24 to 42) divided by number of days, and daily gain (DG) of the weight difference 24. Using these figures, the amount of residual feed consumed will be calculated. Ten samples of liver tissue were then collected from each breed and immediately transferred to liquid nitrogen and transferred to the laboratory for total RNA extraction. Two pooled samples of every breed (each consisting of three extracted RNA sample) were prepared. Prior to Alignment, the quality of the raw readings sequence was evaluated using the Fastqc software. The reference genome for the chicken (Galgal4) and the annotated file were obtained from the Ensembl database. After controlling the quality and Trimming the reads, the Hisat2 software was used to mapping obtain reads from the genome of the reference. Analysis of differential gene expression was performed using Cufflinks.. To identify different isoform of the gene and to measure the expression of isoform, it is necessary to examine the position of microwave splicing between the exons. Cuff compare compares the transcripts that are assembled with a reference genome and categorizes each transcript into known, new, and potential new isoform. The phenotypic results showed that the difference in the mean RFI values between the native (+13.430±5.393 g/day) and commercial (-11.212±4.435g/day) chickens was highly significant (P<0.001). About 83% of the sequenced fragments were matched to the reference genome and Duplex analysis of gene expression was performed..Differential expression analysis for more than 45070 isoform Related to 19003 genes using Cuffdiff showed that 28949 and 16121 isoform were up- and down-regulated (adjusted P≤0.05) in the native breed, respectively. 206 Isoform was identified as a change in expression between the native and commercial chickens. Moreover 21081 novel isoform were identified which have not been included in the gene annotation so far. Moreover, the functional enrichment analysis showed that the down-regulated isoform in the native chickens were mainly involved in the different response to stress،response to oxygen-containing compound،response to cytokine،response to nutrient،response to lipid،animal organ development ،single-organism biosynthetic process،regulation of multi-organism process response to nutrient level and lipid biosynthetic process. The Differentially Expressed Genes and their isoform explored between the chickens of the two breeds led to the identification of some important candidate genes for further breed improvement programs, including RSAD2, IL15, EGR1, and DUSP16. These genes could be related to the higher RFI of the native. Our findings showed that a large number of related genes with metabolism (fat, amino acids, carbohydrates, and vitamins), growth, as well as oxidative stress and immunity, can make a difference in the RFI. Identification of the difference genes and their isoform between two breeds of chickens led to the identification of important candidate genes for breeding programs, including RSAD2, IL15, EGR1 and DUSP16.

Precise prediction of milk yield is essential for management and modeling of farmer’s income in analysis of cost-benefit. Such that, accurate prediction of future records can decrease recording time. Early estimation of bull breeding value using partly records of parity can lower generation interval and increase selection intensity and genetic progress. Linear model is the most commonly used modeling method in research on different field of science. Artificial Neural Network (ANN) is based on artificial intelligent that uses working principles of human brain. Ease of application and power to model complex functions and relationships is factor of wide use of Artificial Neural Network. Revolutionized use of artificial neural network modeling in different aspects of science in the last two decades, is indication of successful application of this powerful technique to solve wide range of problems in different scientific issues. Therefore, object of current research is prediction milk yield of different parity milk production of dairy cattle using production of first recorded parity and artificial neural networks modeling. Furthermore, results of artificial neural network model compared with linear model. In current research, two sequential records of 2460 dairy cattle of a herd were investigated. Pedigree of used data set contained 2517 individuals. Data divided into two sub data of training and testing, to fitting Artificial Neural Network model. Artificial Network model learned the relationship between output and inputs of training data set. Adequacy parameters of the model investigated using model predicted outputs of testing data set and original outputs of the data. Network structure with the beast adequacy parameters were used for Artificial Neural Network model. Finally, linear model was fitted and compared with artificial neural network model. The best structure of Neural Network had 8 inputs, 4 neuron at first hidden layer, 2 neuron at second hidden layer and output of milk production that inputs were breeding value of average milk yield of first recorded parity, parity, sire group, age at first registered parturition, number of records for each parity and mean, minimum and maximum of recorded days in milk for each parity. The used artificial neural network model, predicted the parity milk production with RMSE and R2 of 7.94 and 0.625, respectively. R2 and RMSE of considered linear model was 0.39 and 26.63, respectively. The applied model of artificial neural network appropriately predicted the subsequent parity production using precedent parity data. This research indicated that use of artificial network model can be beneficial for decreasing recording period for dairy cattle genetic evaluation specially in sire evaluation and will decrease generation interval. The results showed that incomplete data can be used for genetic evaluation using artificial neural network model. Comparison of the results with past reports indicated that use of effective inputs for milk production can increase accuracy and precision of the ANN model.

Introduction Native chicken breeds are important genetic resource and well adapted to the local environmental conditions. However, growth rate and feed efficiency of these breeds are not appropriate. On the other hand modern broilers grow faster and offer a higher nutritional efficiency than the indigenous chicken breeds. This advantage is the result of the severe genetic selection programs, which were designed to increase production. In this study, a systematic identification of mitoProteome genes and new pathways related to growth rate of pectoralis muscle in chicken has been made using gene expression profiles of two distinct breeds: Isfahan native, a slow-growing Iranian breed possessing low growth rate and Ross 708, a commercial fast-growing broiler line.
Materials and Methods All the birds were reared under the same management, environmental and nutritional conditions. The diet was the same throughout the whole experiment and formulated to contain 20% CP and 3000 kcal ME/kg. The birds received feed and water freely (ad libitum). On day 28 post-hatch, six birds were randomly selected from each breed, weighed and sacrificed. From each bird, 1 to 2 g of tissue was excised from the posterior region of the left pectoralis major muscle. Total RNA was isolated from breast muscle samples. Using Truseq Stranded RNA Prep kit (Illumina), each sample was converted to a uniquely indexed cDNA library, and the resulting cDNA libraries were pooled and sequenced on an Illumina Hiseq 2000 sequencer. An average of 70 million paired end reads (150 bp) were produced from all sample, 70% of which were properly mapped to the reference genome (EnsemblGalgal4). We analyzed the sequence data using bioinformatics tools Hisat2 and Cufflinks. Using Hisat2 aligner, more than 72% of clean reads (in average) were mapped back to the Galgal4 reference genome. In addition, about 90% of reads were aligned concordantly.
Results and Discussion On the first day after hatching, the weight of commercial chicks were heavier than native. This process continued until the end of the test, 28 days. The commercial chickens have a heavier weight, higher growth rate, and lower feed conversion rates than native chickens. The RNA-Seq of four muscle samples yielded around 131, 590, 636 million of raw 150 bp paired end reads, of which 94, 483, 431 and 37, 107, 205 reads were for native and commercial breeds, respectively. We identified 606 differentially expressed genes (DEGs) between two breeds with at least 2-fold differences (P-adjusted (Benjamini) ≤ 0. 05, log2FC ≥ 2). Of these, 249 and 357 genes were up-regulated in native and commercial broilers, respectively. In the native chickens, FoxO3 transcription factor activated the atrophy pathway related to E3 ubiquitin ligases and led to increased proteolysis and reduced the skeletal muscle size as compared to the commercial broilers. Hypoxia and regulation of the metabolic process of the reactive oxygen species (ROS) were among the most important significant biological processes in native chickens. The analysis of the genes associated with the mitoProteome revealed significant changes in the expression of many genes involved in transcription regulation and growth. Also the increased expression of FoxO3 gene and the releasing of amino acids caused by the degradation of proteins, increased the expression of amino acid catabolism enzyme's (such as MCCC2 and TDH), as well increased expression of pyruvate dehydrogenase kinases (PDK4 and PDK3). This led to reducing of the aerobic oxidation of pyruvate and increasing gluconeogenesis. Increasing the UCP3 gene expression in native chickens can partly reduce mitochondrial efficiency and inappropriate feed conversion ratio compared to commercial chickens. These changes were also reflective of a complicated adaptation program that facilitates proteolysis and reduces oxidative metabolism of glucose and pyruvate in the muscles. These metabolic pathways have evolved to reduce the requirements of indigenous chickens and increase the ability of these strains to overcome the circumstances and environmental stress and resist nutritional deficits.
Conclusion Our results suggested that different expression patterns of some genes including SGK1, FBXO32, FBX030, IRS2 ، SP3, CUL, PIK3IP1 and FoxO3 in native breed might represent a cause for the poor growth performance for this breed than commercial breed. Hence, evaluation of native chicken based on these candidate genes would accelerate the efficient native chicken breed in near future. These results expand our knowledge of the genes transcribed in the breast muscle of two breeds and provide a basis for future research of the molecular mechanisms underlying the chicken breed differences.

Native chicken breeds are important genetic resource and well adapted to the local environmental conditions. However, growth rate and feed efficiency of these breeds are not appropriate. Comparative studies of commercial and native chickens provide an opportunity to characterize the biological basis of differences between them. Here, RNA-Seq technology was used to investigate differences in the transcriptomes of breast muscle-related genes and associated pathways between Ross and Isfahani's native breed. In this study, 200 birds of the Ross 708 strain and 200 native chicks of Isfahani native were reared in a similar standard management and feeding manner. We extracted total RNA from two native and two commercial breast muscle samples of the 28 days old chickens. Compared with native breed, 606 significantly DEGs (differentially expressed genes) (357 up regulated and 249 down-regulated, P-adjusted ≤ 0.05) were obtained in commercial breed. PPI (Protein-protein interaction) network of DEGs (up regulated in commercial) was constructed and 267 genes were included in the resulted PPI network of which 75 genes were identified in the form of three modules with a maximum level of significance. Gene ontology studies showed that all three modules played an effective role in the growth of breast muscle and their hub genes with maximum degree were JUN, EGR1, THBS1, ITGA4 and ACTA2.

Information theory is a branch of mathematics that overlaps with communications, biology. The aim of the current study was to provide a method for clustering a number of Milk Governing Genes in Dairy Cattle using an algorithm based on Kullback-Leibler divergence. In this study, after retrieving gene and exon DNA sequences affecting milk yield in dairy cattle, the entropy in orders one to four was calculated. In order to extract gene distances, Kullback-Leibler divergence over three different methods was calculated. The first and second methods were based on the genes alignment but the third method was based on non-alignment and the relative entropy of the genes. The results of each method of Kullback-Leibler divergence over DNA and exon sequences were entered as input into 7 general clustering algorithms: Single, Complete, Average, Weighted, Centroid, Median and K-Means. Integrated result of each clustering algorithm due to AdaBoost algorithm, which implied as gene tree, indicated that the third method was based on the relative entropy of the genes, biologically grouped set of genes as it was proved by their gene annotation using GeneMANIA. We believe that the proposed method might be used with other DNA based clustering competitive methods and therefore, it can be used to group set of genes in other species.

In this study 429 smallholder dairy farms in 44 villages of the Zabol county included 1728 lactating cows and 3759 head of total herd during February 2015 to March 2016 were recorded to assess the estimate economic opportunities per cow. A questionnaire survey was used to collect data from last year information, direct recording during visit the farm and interview with the smallholder farmer. The number of 5 economic indices calculated using revenue and expense for each farm. The economic opportunity is the amount of additional revenue that could be obtained if farmers could improve various productivity indexes to meet reasonable targets. The economic opportunity estimated as the amount of difference between average herd and reasonable target multiplied by the value of one unit change in the variable in Rials. The sum of economic opportunities per cow per year estimated as 19.68 million Rails included 8.13 million Rails (37.73%) for average daily milk production per cow, 6.47 million Rails (32.51%) for average age at first calving, 3.58 million Rails (20.58%) for average lactation length, 0.82 million Rails (5.33%) for average calf production interval and 0.67 million Rails (3.85%) for average calf mortality, respectively. There was significant variation between different levels of season, breed, rearing system and herd size for the performance of economic opportunities indices. The results obtained in this study can be used in planning to improve the performance economic indices to improve productivity and economic efficiency in smallholder cattle farms.

Apart from the fact that milk plays an important role in human nutrition, increasing milk production or changing its composition has attracted the attention of animal breeders, therefore, it is crucial to study and evaluate the genes underpinning milk production and its composition. Information theory is a branch of mathematics that overlaps with communications, biology, and medical engineering. Entropy is a measure of uncertainty in the set of information. In his famous article in 1948, Shannon introduced this concept and used its results in a number of basic issues of coding and data transferring theory, which forms the basis of new information theory. Information theory is used in genetic and bioinformatics analyses and can be used for many analyses related to the structures and sequences. Bio-computational grouping of genes facilitates genetic analysis, sequencing and structural-based analyses
DNA sequence of 30 genes involved with milk protein production were extracted ad hoc from NCBI genome database and stored in FASTA format. In this study, for each gene and its exons sets, the entropy was calculated in orders one to four. In this way, the Markov chain up to order 3 was used. Based on the relative entropy of genes and exons, kullback-Leibler divergence was calculated. After obtaining the kullback-Leibler distance for genes and exons sets, the results were entered as input into 7 clustering algorithms: Single, Complete, Average, Weighted, Centroid, Median and K-Means. In order to aggregate the results of clustering, AdaBoost algorithm was used. Finally, the results of AdaBoost algorithm were investigated by GeneMANIA prediction server to explore the results from gene annotation point of view. All calculations were performed using the MATLAB Engineering Software (2015)
By investigating the results of genes metabolic pathways based on their gene annotations, it was turned out that proposed clustering method, yielded correct, logical and fast results. This method at the same that that hadnt had the disadvantages of aligning allowed the genes with actual length and content to be considered and also didnt require high memory for large-length sequences.
It can be concluded that the performance of the proposed method could be used with other competitive gene clustering methods to group biologically relevant set of genes Also, the proposed method can be seen as a predictive method for those genes bearing up weak genomic annotations.

In this study 429 smallholder dairy farms in 44 villages of the Zabol county included 1728 lactating cows during February 2015 to March 2016 were used to assess the performance of smallholder farms. The performance of production traits were as 13.66, 7.82 and 7.24 kg for average total milk yield in farm, average milk sold in farm and average daily milk production per cow, respectively. The overall mean of reproductive traits and mortality rate were as 28.71 months for age at first calving, 14.17 months for calving interval, 232.66 days for average lactation length, 7.76% for calf mortality rate up to yearling age and 1.35% for mature cow mortality rate. The mean of daily feed consumption per cow was 13.36 kg, with 29.33% concentrate. The mean of daily feed intake expenses per cow and return from sale of daily milk per farm were 83 and 90 thousand rails, respectively. The value of milk income to daily feed intake expenses per cow, daily feed intake to average daily milk production and the kg milk price to kg feed intake ratio were 95.48%,2.20 and 1.97, respectively. The average total herd size was 8.76 head, included 30.57% lactating cows, 16.20% dry cows, 11.95% female milking calves, 11.79% male milking calves, 10.18% male growing calves, 10.03% female growing calves, 5.76% mature bulls and 3.52% pregnant heifer, respectively. There was significant variation between different levels of season, breed, rearing system and herd size all of the most traits.

In order to studying of genetic variation in Mazandaran and Esfahan native chickens، twenty microsatellite markers were evaluated. These microsatellite markers were MCW0014، MCW0081، MCW0183، MCW0067، MCW0104، MCW0123، MCW0330، MCW0165، MCW0069، MCW0020، MCW0222، LEI0094، MCW0295، MCW0034، MCW0216، ADL0268، ADL0112، ADL0278 and lEI0166. Blood samples of 90 and 150 native chickens of Mazandaran and Esfahan were randomly taken respectively. Genomic DNAs were isolated through optimized and modified salting-out procedure. The number of alleles varied from 1 to 6. In Mazandaran population one locus (MCW0216) and in Esfahan population three loci (MCW0216، MCW67 and MCW222) were monomorphic. The other loci were showed appropriate polymorphism. All the loci except MCW222 and MCW165 in Mazandaran population showed deviations from Hardy-Weinberg equilibrium (p)

This investigation was carried out on six populations of Silybum marianum (L.) Gaertn. in Isfahan Research Center for Agriculture and Natural Resources, 2009. Karyotype of mitotic cells in metaphase of root apical meristem was studied. The base number of chromosomes for all populations was x = 17 and all populations were diploid. Based on Stebbin's two- way table, all populations were located in class 2B indicating the same evolutionary status. Analysis of variance showed significant differences for the length of the smallest chromosome, asymmetric index, and coefficient variation of centromic index (p < 0.01), total chromosome length, sum of small arms, sum of long arms and the largest length of chromosome (p < 0.05). Factor analysis introduced two factors that justified more than 94 percent of total variation. In the first factor, total chromosome length (TL) and sum of long arms (SLa) were identified as the most important factors while asymmetric index (AI) and coefficient variation of centromic index (CVci) in the second factor were highly effective. All populations were classified in four groups by cluster analysis. The least Euclidean distance was between Ahvaz and Sary populations and the highest Euclidean distance was observed between Ahvaz and Amol. Analysis of variance showed significant differences for all traits among groups. Populations of Ahavaz, Sary and Esfahan in the first group were superiour in terms of TL, SSa, SLa, LC and SC compared to other goups. Population of Amol in the second group showed the lowest SC, Cvci, and AI. Maximum CVci and AI were observed in population of Kordestan while TL, SSa, SLa and LC were the least in this population. Population distribution diagram was drawn based on the first and the second component values that would confirm the results of the cluster analysis.