sa rafat

The genome-wide association study (GWAS) is a powerful approach to identify genomic regions associated with fertility traits that explain a significant portion of the genetic variance associated with these traits and identify the relevant causal mutations. Evaluating the correlation between each genotyped marker and trait is an essential strategy for GWAS studies that examine the effects of all markers by considering their possible interactions, environmental factors, and even mutual effects between markers. Recently, machine learning methods have been introduced to genomic topics, and the basis of these methods is different from the common methods of genomic evaluation. The machine learning method is used to estimate the genomic breeding values of the candidate animals by considering the training data (genotypic and phenotypic information of the reference population). One of the key advantages of this method is the ability to analyze large data. Machine learning is a branch of artificial intelligence whose goal is to achieve machines that can extract knowledge (learning) from the environment. A variety of machine learning methods (random forest, boosting, and deep learning) are used to model genetic variance and environmental factors, study gene networks, GWAS, study epistasis effects, and genomic evaluation. Random forest is one of the machine learning methods that has been successfully used in various fields of science. This research was conducted to identify markers and genes related to reproductive traits such as calving interval (CI), days open (DO), daughter pregnancy rate (DPR), and age at first calving (AFC) in Iranian Holstein dairy cattle. These traits have already been investigated with the ssGBLUP method and using a smaller sample size. However, in the present research, by using more genotyped animals, a random forest algorithm was used to identify markers and genes related to reproductive traits.
The records used in this research were provided by the National Animal Breeding Center and Promotion of Animal Products of Iran and included AFC, DO, CI, and DPR related to the genotyped bulls' daughters. In this research, the pedigree information of 2774183 animals was used. The genotypic information of the markers related to 2419 Holstein bulls was used. Genomic data quality control was performed using factors such as the number of genotyped SNPs per animal (ACR), the number of genotyped animals per SNP (CR), Hardy-Weinberg equilibrium (HWE), and minor allele Frequency (MAF). When filtering genomic data, the markers whose MAF was less than 5% were removed, and then the samples whose genotyped frequency was less than 90% were identified and removed. Then, the markers whose genotyping rate was less than 95% in the samples were identified and removed. Finally, the SNPs that deviated from the HWE test (P<10-6) were excluded from the analysis as a measure of genotyping error. To control the quality of genomic data, PLINK 1.9 software was used. Then Ranfog software was used in the Linux environment to perform analysis through random forest algorithm.
By using the random forest algorithm, a total of 21 important SNPs were observed, then important fertility trait candidate genes were identified by the gene ontology method, and 62 genes were within 250 Kb of these SNPs. The most significant SNP was observed for AFC. The main SNP for AFC is in ARS-BFGL-NGS-22647 BTA3, for CI is in ARS-BFGL-NGS-114194 (BTA11), for DO is in BTA-74076 -no-rs (BTA5), and for DPR is in ARS-BFGL-NGS-32553 (BTA26). The researchers, who studied fertility traits in Nellore cattle using machine learning methods, identified MPZL1 and CD247 genes on chromosome number 3 and this gene was associated with age at first calving. Many pathways of cell biology affect the performance of reproductive traits. Research has reported the relationship between the CD247 gene and pathways of biology, including cell development and function. Research has shown that the IFFO2 gene plays an important role in the molecular structure of cells, as well as in the mechanism of blastocyst formation, embryos, and the length of gestation in cattle. In a study conducted on the mouse population on the structure of the flagellum and the sperm maturation process, the role of the ALDH4A1 gene in the sperm maturation process was reported. The association of the RPS6KC1 gene with pregnancy rate and antral follicle number in Nellore heifers has been reported. The KAT2B gene is a transcriptional activator that plays an essential role in regulating the correction of histone acetylation and plays an important role in improving carcass quality, muscle and fat development, and metabolism in native Chinese cattle. In addition, they play a key role in regulating biological processes and are related to cell growth, metabolism and immune system function.
  According to the objectives of this research, new information on markers and candidate genes related to reproductive traits in Iranian Holstein dairy cattle was reported. The markers and candidate genes identified in the present research can be used in genomic selection to improve the reproductive traits of Holstein dairy cattle.

Copy number variation (CNV) consist of deletion, insertion, and duplications. It is an important source of genetic variation in organisms and thus influences on the gene expression and phenotypic variation. Copy number variation (CNV) is one of the structural variant with an intermediate size class larger than 50bp which involves unbalanced rearrangements that increase or decrease the amount of DNA (Pirooznia et al 2015, Alkan et al 2011). The size of CNVs is larger than 50bp, while smaller segments are known as insertions or deletions (indels). Thereupon these structural variations comprise more polymorphic than SNPs because of enormity, detection of them and their effect on phenotype has caught the attention of many researchers recently. It has been reported that CNVs changes in gene dosage and regulation as well as in transcript structure, and thus contribute to phenotypic variability (Pirooznia et al 2015, Alkan et al 2011). The pea-comb phenotype is caused by a CNV mapping to intron 1 of the SRY (sex determining region Y)-box 5 (SOX5) gene (Wright et al. 2009). Late feathering in chickens is due to incomplete duplication in PRLR and SPEF2 genes (Elfrink et al. 2008). In swine, dominant white colour has been related with a duplication of a 450-kb fragment of the KIT gene (Giuffra et al. 1999) and a splice mutation causing the skipping of exon 17 (Giuffra et al. 1999). In sheep, doubling in the ASIP gene results in the regulation of pigment in body coat (Norris et al. 2008). Doubling the 4.6 k base pair into the six introns of the STX17 gene results in a gray body color in the horse with age. Deletion of the intergenic region with a length of 11.7 kbp in the goat genome leads to the removal of horns (Clop et al. 2012). Chicken is the most intensively farmed animal on earth and is a major food source with billions of birds used in meat and egg production each year. A big share of chicken CNVs involves protein coding or regulatory sequences. A comprehensive study of chicken CNV can provide valuable information on genetic diversity and assist future analyses of associations between CNV and economically important traits in chickens. Unique chicken genome with macro and micro chromosomes and its biology make it an ideal organism for studies in development and evolution, as well as applications in agriculture and medicine (Burt 2005). In the last several years, There has been an increasing interest in the study of CNVs in the chicken. This study focuses on comparison of CNV between the broilers and layers chicken to find evidence of domestication on the genome using whole genome sequencing.

we used n=90 female birds of two commercial broiler (n=40) and layer (n=50) chicken. The broilers (BRs) were represented by 20 DNA samples of each of two lines (BRA and BRB) established independently and previously collected as part of the AVIANDIV project. In the layer group (LRs), data from 25 birds each from purebred white (WL) and brown (BL) egg laying populations, sequenced in the frame of the SYNBREED project (http://www.synbreed.tum.de/index.php?id=2 ,(were included. The paired-end reads with a read length of 101bp were mapped against the current reference genome assembly Galgal6 using the Burrows-Wheeler aligner (bwa, 0.6.2-r126 Version, with default parameters. Duplicate reads were masked during post-processing using the Picard tool set (version 2.9.2, http://picard.sourceforge.net). Finally, Genome Analysis Toolkit-3.3.0 was used to realign reads for correcting errors caused by InDels. Using GATK software package and Depth Of Coverage function (McKenna et al 2010), the depth of readings was calculated for each sample. Then filter out reads with mapping quality below 20. Because comparing the genomes of individuals in different groups was time consuming and computationally difficult for all parts of the genome, the genomes of each individual were divided into 1000 bp non-overlapping windows and the average reading depth per window was calculated. Then the results were normalized against the BL sample that showed highest average depth. In short, we created a correction factor per population and applied it on the depth of coverage value for each window. For all the contrasts, we performed an analysis of variance (ANOVA) as described (Carneiro et al 2014). For the Broilers-Layers contrast we scanned 935247 windows. 70372 windows showed significant by FDR with P < 0.001, with ANOVA using the Benjamini-Hochberg FDR method for multiple corrections (Benjamini and Hochberg 1995).

Mapping sequencing data to galGal6 assembly showed an average 98.61% mapping rate and 11.51 depth. Manhattan plot was plotted for regions of the genome that differed significantly between the two groups (FDR = 0.001). The points above the hypothetical line were identified and examined in a 25 Kbp confidence interval to identify possible genes. 39 regions were identified that half of them dose not contain any genes. Although Long noncoding RNAs are under lower selective pressure than protein-coding genes (Batista and Chang 2013), The other 11 regions contained 16 genes related to long non-coding RNAs. Long noncoding RNAs (lncRNAs) play a critical role in organizing the 3-dimensional genome architecture and regulating gene activity in cis or in trans through multiple mechanisms (Zhang et al 2019, Batista and Chang 2013). 6 othere regions also contained 12 coding genes. Most of the identified genes were somehow linked to the immune system disease or cancer. Genes such as DEDs and TNFAIP8 are involved in programmed cell death (apoptosis) and two genes NPAL3 and RCAN, which are involved in the immune system, had a copy number variation in the studied samples. In addition RCAN is involved in Down syndrome. The PFDN gene, located on chromosome 25, is also involved in Alzheimer's and Parkinson's disease.

Ghezel is an Iranian medium-sized and fat-tailed sheep breed and is native in the East and West Azarbaijan provinces. Ghezel sheep plays an important role in supplying meat and milk in the region of Azerbaijan (Ghasemi-Panahi et al. 2016). Also, an important source of farmer's income is lambs production (Nabavi et al. 2015). Therefore, one of the prospects for improving the region's production is improving reproductive performance of sheep flocks. In order to suggest a proper approach to improve reproductive performance, there should be a comprehensive information from the livestock farms of these two provinces. Therefore, the present study was conducted with the aim of evaluating reproductive performance of Ghezel ewes in a couple of sheep farms in the East and West Azarbaijan provinces.

After designing questionnaire in this study, 30 Ghezel sheep flocks were randomly selected from different regions of East and West Azarbaijan provinces (15 flocks in each province). Then, livestock farmers of the region were interviewed using questionnaire and information on reproductive performance of flocks were collected including: pregnancy rate, multiparty, lambs' birth weight, age at the first parturition, weaning age, lambs weaning weight, number of unfertile and fertile ewes, flock surface area, farmers' education, and etc. The flocks were divided into four flock sizes. The breeding systems were also studied based on the three groups of nomadic, rural, and industrial breeding systems. The results of the questionnaires were reported as percentages (for classified data) and mean ± SD (for other data). Also, correlation coefficients between important traits were calculated using Spearman’s rank-order correlation of SAS 9.2 (2008) software.

Based on the results of this experiment, 87% of the breeding systems of two provinces were rural. Other reproductive indexes of two provinces included 65% lambing rate, 79% pregnancy rate, 24% ewes' fecundity rate, 20% estrus synchronization usage, 5% flock mortality rate, 9% ewe's infertility rate, 0.1 ram to ewe ratio, and 17 months of age for ewes at the first mating. Seifi et al. (2014), with evaluating Ghezel and Afshari sheep breeds, reported low reproductive performance in these two breeds. Khodayi-Motlagh et al. (2014) reported low knowledge of farmers about the methods of estrus synchronization. However, a number of studies reported an extraordinary improvement in the reproductive performance of Ghezel ewes using different methods of estrus synchronization or using flushing rations (Najafi et al. 2014; Ghasemi-Panahi et al. 2016; Hasani Dash Tapeh et al. 2017; Ahmadzadeh et al. 2018). Therefore, it seems that improving knowledge and skill of farmers about estrus synchronization methods and/or proper rationing can improve reproductive performance of Ghezel sheep in the region. According to the correlation results, there was a negative correlation between the breeding system and the flock size (correlation coefficient: -0.6) and between the flock size and estrus synchronization usage (correlation coefficient: -0.51), (P<0.05). These results indicated that the breeding system has been changed into the nomadic system in the larger breeding flocks and there is a less interest in the use of new methods of estrus synchronization in this kind of breeding system. Also, results indicated a significantly negative correlation (correlation coefficient: -0.42) between ram to ewe ratio and lambing rate (P <0.05). So, regardless of the role of rams on flock fertility, asymmetrical increase in ram to ewe ratio causes a negative impact on lambing rate by reducing the ewe population (which are the animals whom produce lambs). The results showed a significant positive correlation (P <0.05) between lambing rate and the age of ewes at the first mating (correlation coefficient: 0.54) and also the age of ewes at the first delivery (correlation coefficient: 0.66). These positive correlations indicate poor rearing condition of young ewes and are consistent with the general believe of farmers, which they breed ewes at the second year (age 16-18 months) to obtain optimum fertility rate. Results showed a negative correlation between the age of ewes at the first mating and birth weight of lamb (correlation coefficient: -0.60), while indicating a positive correlation between the age of ewes at the first mating and age of weaned lambs (correlation coefficient was 0.49), (P <0.05). These results can be explained by higher fecundity rate in older ewes, which reduces lamb birth weight, while it increases weaning age of lambs. The negative correlation (correlation coefficient: -0.41) between weaning age of lambs and estrus synchronization use (P <0.05) can be due to the fact that lambs from the synchronized ewes born and weaned at the same time and then, reared under better nutritional and management conditions.

The overall results of the present study showed low reproductive performance in the Ghezel sheep flocks of East and West Azarbaijan provinces due to the low use of estrus synchronization methods and poor management. Therefore, it seems that by informing the farmers about the new methods of estrus synchronization, raising their level of knowledge in this field, ration training, and management of synchronized animals can improve reproductive performance and increase profitability in the region.

Cashmere is a very fine fiber that is produced by secondary hair follicles in cashmere goat. Based on American test and material association description, cashmere is fine fiber in Asian Indian goat hair follicles with diameter lower than 30 microns. Cashmere is growing as “under coat” in cold season and it shedds during the time from late winter until early spring. It is estimated that 68 goat breeds produce cashmere fibers in the world. Cashmere goats are originated from Asia. The important countries that can produce a large amount of cashmere are China, Mongolia, Iran, Turkey, and India. Total production of cashmere is estimated to be 5mt. During the last decades, due to the economic importance of cashmere, USA, Australia, and NewZealand joined to the cashmere producing countries. Many researchers reported that cold climate is suitable for production of quality cashmere. In this research, effects of nutrition and age on histological characteristics of Raeini Cashmere goat were studied in Tabriz, East Azerbaijan.

For this research, 24 female Raeini cashmere goats were selected. The goats were selected from Baft Raeini cashmere goat breeding and husbandry station. Goats were fed individually   and were treated for 8 months of study based on feeding levels (Maintenance, 0.7 M, 1.4 M, and 1.8M) and age (6 months and 18 months) on fleece growth. The trial was conducted at the khalat-Pushan Research Station, University of Tabriz. The goats allocated to four feeding levels: M (goats fed to maintain live weight, 0.7M (goats fed to lose 3Kg live weight from February to September), 1.4M, and 1.8M (goats fed to gain live weight). Patches of fleece from defined areas were repeatedly shorn at 4 weekly intervals from the right mid side of each goat. For follicle study, in the fist, 120cm2 of left side of animals was marked firstly; then, these region fibers shaved by electrical shaver. Shaving was repeated monthly (for four weeks). Skin biopsy was taken monthly from left mid side of skin of abdomen. samples were fixed in 10% formalin. Paraffinized block were prepared and then, they are sectioned as serial section in 8-micron thickness. Histological sections were stained by sak pic method (reference ????). Results were analyzed by analyses variance and paired t-test.   

This research results, showed that there was no significant effect of feeding level or age on weight of cashmere and hair per area, secondary follicle activity, cashmere length, and yield (P<0.05). Fleece and live weight for young goats were significantly less than that of old goats (P<0.05). Result were appeared that mean cashmere diameters of patch shorn in September of goats fed M, 1.4M and 1.8M were significantly greater than that of goats fed 0.7M (P<0.05). In group feeding more than maintenance requirements, results indicated no increase in cashmere production. Average fiber diameter of cashmere in June was higher than in May. Results of this research indicated that there are not any significant differences between different levels of feeding and age on fiber growth rate (P<0.05). The highest fiber production and the maximum mean of fiber growth rates (1.64 and 1.48 g/120cm2 / 28 days) were observed in June and July. Secondary to primary follicle ratio of all goats was 12.60. Study of secondary follicles ratio showed that different levels of feeding cannot reduce number of secondary follicles. Many researchers reported that increase in feeding levels to over maintenance rate cannot increase cashmere growth rate. This research results confirmed by previous studies. it was reported that feeding limitation can reduce diameter of cashmere, but there is not any increasable effect during over maintenance feeding and an increase in dietary protein. This research indicated that cashmere diameter was more in two-years old goat than one-year old goat cashmere diameter. These   results were similar with reports of Klor et al. (1993), Rafat (1997), and Salehi (1997). Increase in diameter of wool fibers with increasing in the age of animals was reported in sheep and goat. In other studies, it is shown that effect of age on diameter of Norway cashmere goats was significant (P<0.05). Results of our research show that diameter of cashmere in Raeini goats increases at June. Similar results are illustrated in Kerman (with the same age and sex). The weight of produced fibers / body surface was the same in four feeding treatment groups, but diameter of cashmere was different. Numbers of secondary follicles   increased in April. Minimum weight of fibers was observed in April in all of the treatments, which may be because of low activity of follicles in this month. Variation of cashmere diameter and cashmere growth rate can explain differences in total cashmere production. Changes of feeding level from under maintenance to high levels cause increase in cashmere diameter. This study appeared that diameter of cashmere fibers can have reaction to feeding rate. Accordingly, energy has important effect on growth of hair and cashmere. The animals with low energy diet produce low amount of cashmere, Other researchers have opposite idea. According to their statement, there are not any difference in partition for nutrient between primary and secondary follicles. This research result showed that increase feeding cannot increase cashmere production. Jia et al (1995) reported that increase of diet net protein has not any important effect on cashmere goats production in Spain. In other study using unpregnant goat it has been indicated follicular activity and fiber growth is not under influence of pregnancy and milking. However, some researches showed that reproduction condition of animal, as pregnancy and milking, has effect on cashmere fiber growth.  

Generally, results of this study showed Raeini cashmere goats in East – Azarbayjan climate did not show any fundamental changes in diameter and length of cashmere in comparison with Raeini cashmere goats which reared in Kerman province.

Arkharmerino sheep breed is a fine wool type. Crossbreeding can lead to combination of favorable characteristics from the breeds involved. The greatest part of the wool produced by the indigenous sheep breeds in Iran is used in the hand woven carpets. It is estimated that 5.1 million m2 hand woven carpets is produced in Iran annually; therefore, the country needs 28 thousand tons of washed wool. Approximately 8 thousand tons of wool is imported as merino wool from Australia and New Zealand. Iranian wool is suitable for use in coarse-carpet industry, but it has some difficulties for use in the fine carpets. Fine carpet makers usually utilize imported wool, which has more uniformity of diameter. For finding suitable sheep breed to produce more uniform wool, we interest to Arkhar-Merino breed at University of Tabriz. The Kazakh Arkhar-Merino breed was produced at Kurmektinski experiment station of the Academy of Sciences of the Kazakh.  The purpose of research was to introduce a new breed of fine wool sheep which would combine the good production characteristics of the Merino with adaptability of local Arkhar. The breed is based on crossbreeding of wild Arkhar rams with ewes of the Novocaucasian Merino, Précoce and Rambouillet breeds. Crossbreeding between Iranian wool sheep and foreign wool breeds can lead to the production of a genetic combination with the better wool fibers. In order to evaluate fleece characteristics, wool samples of 451 yearlings of Arkharmerinos×Ghezel (ArGh) were collected by Mokhber et al. (2008). At first generation of ArGh, mean (± standard error) of fiber diameter, fiber diameter variability, staple length and percentage of true wool, medulla and kemp percentage were 27.10 ± 3.36 μ, 36.60 ± 7.84 %, 11.81 ± 4.06 cm, 91.31 ± 9.32%, 7.27 ± 6.90%, and 1.40 ± 3.03 %, respectively. At second generation of ArGh, the same traits were 26.33 ± 3.41μ, 34.64 ± 9.36 %, 10.15 ± 3.99 cm, and 95.41 ± 4.70 %, 3.39 ± 5.85 % and 2.01 ± 2.65 %, respectively.  The main aim of this work was to study the morphological and structural properties of breed wools of first and second generation of Arkharmerino ×Ghezel with breed Arkharmerino as a father's base and comparing with their parent's wool characteristics. The aim was to obtain information about crossbreeding of local fat tail rams with Arkhar-Merino ewes regarding the wool traits. Arkhamerino breed has been imported from Kazakhstan. For this purpose, the wool fibers were sampled from the middle region of the sheep's body. The physical properties of the wool fibers, such as fiber diameter, staple length, Kemp fiber percentage and modulation fiber percentage were measured. For study the morphological properties of fibers, surface image of the fibers was prepared using a scanning electron microscope. In order to measure the structural properties of the fibers, which is one of the important factors in the production of textile products, the infrared spectrum of each fiber was obtained according to the relevant standards. The chemical structure (such as the components of the main and side chains, functional groups, various linking bonds, etc.) and the chain conformation in wool fiber play a crucial role in its mechanical, other physical, and service properties. The effect of wool breeding on the chemical structure and chain conformation of wool samples, which were from Ghezel sheep and Arkharmerino Sheep in first and second generations, were investigated by employing an FT-IR spectrometer (IR Affinity-1s ATR-FTIR, Shimadzu, Japan) in a spectral range from 500 to 4000 cm-2. The infrared spectra of the control sample of wool in Fig. 1 indicate that the strong peak with absorption band at 3399.5 cm-1 was assigned to the combined stretching vibrations of N-H and O-H (νN-H, νO-H), and the absorption bands at 2960.2 cm-1, 2930.0 cm-1, 2870.0 cm-1were assigned to the asymmetrical and symmetrical stretching vibrations of C-H in CH3 and -CH2- groups, respectively. Moreover, the strong peak with absorption band at 1639.8 cm-1was due to the stretching vibration of C=O from amide Ι (νC = O), which was essentially relative and indicative to the α-helix conformation of the main chains of wool (Wojciechowska et al. 2002). The medium peaks with absorption bands at 1540.1 cm-1 and 1239.9 cm-1 were attributed to the bending vibration of N-H (δN-H) from amide ΙΙ and the stretching vibration of C-N (δC-N) from amide ΙΙΙ, respectively. Moreover, the stretching vibration of C-N (δC-N) from amide ΙΙΙ was considered to be relative and indicative to the β-sheet conformation in wool fiber (Cai and Singh 1999). The peak at 1079.3 cm-1 was due to the vibration of sulfur-containing group of cystine in wool. Table 2 shows the average and standard deviation of absorption band of the functional groups in the wool fibers. The results showed that the fiber scales in crossbreed and Arkharmerino fibers have a telescopic and regular state that are different from the irregular structure of the Ghezel fiber scales. The measurement of structural properties showed that the wave number of amide, amine, hydroxyl and C-N bonds in the second generation was more similar to Arkharmerino and it can be concluded that in the second generation of Arkharmerino × Ghezel, genetic structure of fibers has the most similarity to Arkarmerino breed. In general, the results show that the second-generation fibers of the Arkharmerino × Ghezel have a good structural and superficial quality for usingin textile products.

About 6 million heads of cows in Iran are native cattle, but their characteristics and production potential remains unknown. Inbreeding is one of the important factors which must be considered in the herd and can be of considerable economic loss to producers. In this research, we tried to investigate the occurrence of inbreeding and its effects on the production traits of Serabi native cattle in a breeding center related to agricultural ministry located in Sarab. The aim of this study was to evaluate inbreeding effects on milk yield, fat percentage, protein percentage, and birth weight of Sarabi dairy cattle. In this research, the effects of inbreeding and environmental factors on production traits and birth weight of Sarabi cows have been studied. The data were collected from 1250 Sarabi cows during 1992- 2012 years by Sarabi Breed Center in East Azerbaijan province. In the present study, a pedigree file containing 1250 head (764 females and 486 males) of dairy cows was used, including data about the registration number of the livestock, date of birth, gender, father's registration number, and registration number of the mother, date of birth, parity, and production records. After the removal of animals with unknown and unregistered parents in the flock, the pedigree was arranged using pedigree software. Pedigree software was used to calculate the inbreeding coefficient for each animal. The principles of this software in the calculation of inbreeding coefficient is based on the formation of a kinship matrix among the individuals. The inbreeding coefficients of animals were considered as a discrete trait in 4 groups. In this herd, inbreeding coefficient was estimated between 0- 0.28. Average inbreeding coefficients of all cows and inbred cows are 0.0109 and 0.0574, respectively. Totally, 19% of all animals were inbred. In this study, inbreeding coefficient has been included in the model either as a continuous variable or as a classification variable. When inbreeding factor considered as continuous variable in the model, its effect on milk yield, fat and protein percentage, and birth weight was significant (P<0.01). When inbreeding considered as a continuous trait, 1% increase in inbreeding coefficient had an effect equal to -2.69 kg, 1.59%, and +18.1% on milk yield, fat, and protein percentage, respectively. Miglior et al. (1995a) reported a 1% increase in inbreeding coefficient in Holstein cows reduced calf weaning by 0.44 kg and reduced milk production by 25 kg. Mohammadkarim (2006) using a univariate model reported for 1% increase in inbreeding coefficient, changes in milk yield, fat yield, open days and length of first lactation equal to -14.02, -0.349 kg, + 0.4839 and + 0.148 days, respectively. Inbreeding has a negative effect on production traits and birth weight. Results showed that the effects of year-season of calving and parity on production traits and birth weight were significant (P<0.01). The regression coefficient of milk, fat and protein percentages and birth weight on inbreeding, when inbreeding considered as a discrete variable, were -0.129kg, +0.093%, +0.072% and -0.564 kg, respectively. In this study, when inbreeding traits considered as a continuous variable, did not show any linear or nonlinear relation with birth weight trait of Sarabi cows. It can be concluded that in order to maintain the genetic reserves of Sarabi cattle breed, it is necessary to carefully monitor the reproduction breedings in this native cattle population. In the case of endangered breeds, such as Sarabi breed, these breeds have beneficial properties, particularly in relation to resistance to diseases, and tolerance to stressful environments. These desirable traits can be transferred to future genetic composition cattle breeds. Preserving the genetic resources of the country's livestock and pay attention to similar breeds of Sarabi should be taken into consideration by decision makers at livestock breeding centers. In Holstein cows it has been found that high milk production is associated with a genetic susceptibility to disease (Khaleghi & Rafat 2018), so the desirable characteristics of the Sarabi breed should be studied in this regard of susceptibility to diseases. The existence of a complete family tree in computer registrations is the first step in controlling inbreeding. The existence of this pedigree will help breeders to avoid breeding between close-up animals, like a brother-sister and a father -daughter, which will increase the incidence of inbreeding in the population. For this purpose, it is recommended to use optimal mixing softwares that controls inbreeding. There are programs for managing the breeding to identify animals as soon as possible and calculate their relativeness in the herd. By this method, it is possible to prevent the occurrence of high inbreeding in the herd and produce calves with high profitability. The prospect of this research is to carry out further research on the issue of inbreeding and effective population size on local breeds of dairy cattle to prevent the replacement of these breeds with Holstein. It is imperative to prevent the replacement of the foreigner breeds (Holstein generally) instead of Sarabi breed and its extinction as much as possible.

Average daily gain (ADG) is the most economically important trait in sheep industry.
In genome wide association study and genomic selection, determining of extent and level of linkage
disequilibrium (LD) and haplotype block structure are critical in sample size and marker density. Haplotype blocks are defined as long stretches of SNPs along a chromosome that have low recombination rates, which characterized by relatively few haplotypes. Understanding haplotype structure in genome can greatly facilitate LD analysis. Haplotype-based association analysis can offer a powerful approach for mapping functional genes (Gabriel et al., 2002). Therefore, the objective of this research were to study LD pattern, determine haplotype block structure and genome wide haplotype association study in Zandi sheep for identifying the genomic region associated with pre-weaning (AGW) and post-weaning daily gain (PWG). A total of 96 Iranian Zandi sheep were used in the study. The following two traits were analyzed: pre-weaning daily gain and post-weaning daily gain. Animals were genotyped using 50 K SNPChip panel. Quality control of the genotype data consisted in removing SNPs with a call rate less than 95 %, SNPs with a minor allele frequency (MAF) less than 5 %, individual with more than 10 % missing genotypes, and SNPs that deviated strongly from Hardy–Weinberg equilibrium (P < 10−6). LD between all pairs were calculated with r2 by PLINK v1.07. Haplotype blocks were identified on base algorithm Gabriel et al. (2002) for all autosomes, using Haploview software (Barrett et al. 2005), based on estimates of D' for all pairwise combinations of SNPs within each chromosome. Following Gabriel et al. (2002), a pair of SNPs is defined to be in “strong LD” if the upper 95% confidence bound of D' is > 0.98 (consistent with no historical recombination) and the lower bound is > 0.7. Using the Haploview default values for blocks (Gabriel et al. 2002), a haplotype block is defined as a region over which 95 % of informative SNP pairs show “strong LD”. The PLINK was used to generate the matrix using the GLM algorithm. In this analysis, because of the previous selection history of the flock, it was important to identify and correct for population stratification. To evaluate whether estimates were overinflated, we used the genomic inflation factor λ using the PLINK software (Purcell et al., 2007). We also assessed their deviation from the expected distribution of no SNPs being associated with the trait of interest using a quantile-quantile (Q-Q) plot, which is commonly used to analyze population stratification in GWAS. We use SNPEVG tool to show the (Q-Q) plot. The Bonferroni method was used to adjust for multiple testing from the number of SNP loci detected. We declared a significant SNP at the genome-wide significance level if the raw P-value was, 0.05/N, here N is the number of SNP loci tested in the analyses. Therefore, for each trait, the threshold P-value for declaring genome-wide significance was (0.05)/40,879=1.2×10-6. The exact positions of the annotated genes were extracted from the latest sheep genome Oar_v4.0 assembly along with the NCBI annotation release 102 of the sheep genome. To investigate whether the
significant SNPs detected in this study were within the range of previously identified QTL for relevant traits, we searched for meat or production QTL in the Animal QTLdb within a 1-Mb region on both sides of each significant haplotype. After quality control, 2 individuals were excluded, leaving 94 sheep for the association analysis. Additionally, we removed 1070 SNPs with call rates less than 95% and 7717 SNPs with MAF less than 0.05. A total of 40,879 SNPs passed these quality-control filters and were retained in the dataset. These SNPs were distributed across 26 autosomes, with the number of SNPs per chromosome ranging from 747 to 5694, and with a mean distance between adjacent SNPs ranging from 50.4 to 68.7 kb. Also, in this study, the extent of LD was 40 kb with r2=0.2. Overally, 1472 blocks were observed in the 7.58% of all SNPs were classified into haplotype blocks, covering 1.45% of the total autosomal genome size. The results showed a reduction in LD level with the increase in distance between markers. The average pre-weaning daily gain was 0.197±0.04 kg with an individual sheep range of 0.08-0.34 kg. Average post-weaning daily gain was 0.126±0.07 kg with an individual sheep range of 0.03-0.41 kg. The result from genomic control showed weak population stratification for AGW and PGW in between population of Zandi sheep. The genomic inflation factors (λgc) for the two traits were equal to 1.039 and 1.073, for AGW and PGW, respectively. However, as the Q-Q plots clearly show, there is no evidence of any systematic bias (λgc˂1.1) due to population structure or analytical approach in our case. Considering the significant fixed effects in the genomic wide association analysis, four haplotypes on chromosomes 3, 5, 6 and 7 identified to affect significantly AGW and PWG traits. The results of this study could provide a suite of novel SNP markers and candidate genes associated with growth traits and hence, may play an important role for understanding the biology of average daily gain in sheep.

Identifying of genes with large effects on economically important traits, has been one of the important goals in sheep breeding. Over the last decade, by the advent of genome-wide panels of single nucleotide polymorphisms (SNPs), it has become possible to identify and localize QTLs for complex traits in many livestock species. One important obstacle in association studies is the confounding effect of population structure. Because this effect generally increases in proportion to population size, population structure remains a major concern in association analyses. To date, 98 QTLs for wool traits have been reported via genome scan based on marker-QTL linkage analyses (http://cn.animalgenome.org/cgi-bin/QTLdb/OA/index, 27 Aug, 2017). Compared with traditional QTL mapping strategies, a GWAS has major advantages both in its power to detect causal variants with modest effects and in defining narrower genomic regions harboring causal variants for economically important traits. In this study, we assessed population stratification and performed a genome-wide association study (GWAS) of wool quality traits in Zandi sheep. Material and

A total of 96 Iranian Zandi sheep was used in the study. The following four traits were analyzed: staple length (SL), mean fiber diameter (MFD), fiber diameter coefficient of variation (FDCV), and the proportion of fiber that was equal or more than 30 µm (F≥30). Animals were genotyped using 50 K SNPChip panel. Quality control of the genotype data consisted in removing SNPs with a call rate less than 95 %, SNPs with a minor allele frequency (MAF) less than 5 %, SNPs with more than x % missing genotypes, and SNPs that deviated strongly from Hardy– Weinberg equilibrium (P < 10−6). The PLINK was used to generate the matrix using the GLM algorithm. In this study, although the resources of this breed were very clear, we still examined the distribution of the test statistics obtained from the numerous association tests. We also assessed their deviation from the expected distribution of no SNPs being associated with the trait of interest using a quantile-quantile (Q-Q) plot, which is commonly used to analyze population stratification in GWAS. We use SNPEVG tool to show the (Q-Q) plot. The Bonferroni method was used to adjust for multiple testing from the number of SNP loci detected. We declared a significant SNP at the genomewide significance level if the raw P-value was0.05/N, here N is the number of SNP loci tested in the analysis. The exact positions of the annotated genes were extracted from the latest sheep genome Oar_v4.0 assembly along with the NCBI annotation release 102 of the sheep genome. To investigate if the significant SNPs detected in this study were within the range of previously identified QTL for relevant traits, we searched for meat or production QTL in the Animal QTLdb within a 1-Mb region on both sides of each significant haplotype.

After quality control, 2 individuals were excluded, leaving 94 sheep for the association analysis. Additionally, we removed 1070 SNPs with call rates less than 95% and 7717 SNPs with MAF less than 0.05. A total of 40,879 SNPs passed these quality-control filters and were retained in the dataset. These SNPs were distributed across 26 autosomes, with the number of SNPs per chromosome ranging from 747 to 5694, and with a mean distance between adjacent SNPs ranging from 50.4 to 68.7 kb. Wool MFD was 29.85±0.03 µm with an individual sheep range of 22.4-39.04 µm. The overall coefficient of variation of fiber diameter was 43.12%±0.7% with an individual sheep range of 19.7%–68.0%. The average percentages of fiber that had equal or more than 30 µm were 27.04±0.03% with an individual sheep range of 12.04-43.10%. Average wool staple length was 11.25±0.03 cm with an individual sheep range of 6-19 cm. The result from genomic control showed weak population stratification for SL, MDF, FDCV and F≥30 between populations of Zandi sheep. The genomic inflation factors (λgc) for the four traits were equal to 1.127, 1.101, 1.059, and 1.009 for MDF, FDCV, FD≥30 and SL, respectively. However, the Q-Q plots clearly showed there was no evidence of any systematic bias due to population structure or analytical approach in our case. Overally, two significant SNPs at the genome-wise level were identified for FD, and FDCV. No significant SNPs was identified for SLor FD≥30. Two Haplotype region within ERBB2 and GNAS genes previously reported in human growth and development hair and skin. Haplotypes were located with previously QTL reported to affect fiber diameter and fiber diameter coefficient of variation in Merino and INRA401 breed sheep. The functions of all of the above genes are directly or indirectly related to skin and hair development. Hair follicles are skin appendages and produce hair; therefore, we hypothesize that these genes control hair follicle development and fiber diameter trait.

The results of this study could provide a suite of novel SNP markers and candidate genes associated with wool traits and hence, may play an important role in understanding the biology of wool traits in fat-tailed sheep.

In some studies, it has been reported that high milk production has a negative effect on animal health and longevity and affects the herd's profitability. Decreased cow health can affect herd profitability through increased rates of involuntary culling and decreased or lost milk sales. Common diseases in dairy cows include mastitis, abomasum displacement, lameness and reproductive disorders such as ovarian cysts and metritis. The objectives of this study were to provide a report on the reasons for culling in dairy herds, estimate the genetic parameters of production traits, diseases and to calculate the spearmen correlation between the breeding value of bulls for the traits and their breeding value for resistance for risk of culling.
Material and In this study, 31550 calving records from 17476 Holstein cows were used. In this study production data and culling reasons for diseases of 47 herds in East Azerbaijan from 1995 to 2012 has been analyzed. For genetic analysis ASReml software has been used. The investigated culling reasons for diseases were including of: mastitis, displaced abomasum, lameness, ovarian cysts and metritis. Estimation of disorders heritability has been obtained using univariate animal model. It has been presented a description statistics of culling reasons for diseases, estimation of genetic parameters of diseases and production traits in the studied dairy herds. Furthermore, correlation between bulls breeding value for culling reason for diseases traits and their breeding value for production traits has been calculated.
The average culling rates of dairy herds in this study was 7.05% (with a range from 2.04% to 26.98%). Results of this study showed that 55.24 % of animals in the herd were culling because of diseases and 44.76% for other reasons such as other diseases, physical injuries, non-economic and financial needs. In the other studies the average culling rate of Holstein dairy cows in northeastern Iran was reported as13.1% (4.4 to 25.3% per herd). Lameness and metritis's culling reasons had the highest heritability among studied traits with values of 0.28 ± 0.010 and 0.21 ± 0.045, respectively. A positive correlation (0.37) between mastitis and milk production was reported (Urib et al. 1995) suggesting that high milk production cows have a high genetic capacity for mastitis occurrence. The highest and lowest estimated repeatability in our study were for the traits of 305-day milk yield (0.47 ± 0.009) and fat percentage (0.25 ± 0.009), respectively. The spearman correlation showed positive correlation between breeding value for milk production and ones for displaced abomasum, lameness and metritis that were 0.197, 0.121 and 0.116, respectively. In the present study, there was a positive and significant correlation between the breeding value of bulls for culling due to displaced abomasum and ones due to lameness and ovarian cysts. So it seems the selection of bulls to resist against the risk of culling due to displaced abomasum helps them to resist against lameness and ovarian cysts diseases. Logistic regression results showed that all studied factors affecting culling due to mastitis. Logistic regression of culling risk factors due to displaced abomasum showed that age and season of parturition are important. Fleischer et al. (2001) reported a significant correlation between 305-day milk production and displaced abomasum disease. Logistic regression results showed that culling due to lameness is related to parity and 305- milk production. The selection of cows based on high milk production, milk fat percentage or body type characteristics could have adverse effects on the occurrence of diseases and resistance to health difficulties. So ignoring these negative correlations among traits in the selection process in the long term affects the dairy herd's profitability. The results of this study showed that about half of the culling percentages in the studied herds was unpredictable and due to diseases. Therefore, with considering of the resistance to diseases in selection strategies, it can be achieving to more survivability of the profitable herds.
The results indicate that most of the studied traits have positive genetic correlation with 305-day milk yield, so probably the cows with high potential for milk production are less resistant to culling for diseases. It is suggested that mastitis and metritis be taken into account in the breeding programs of Holstein dairy cows in the country.

The indigenous stocks play an important role in villager economy in developing countries, especially in Iran. Indigenous breeds could maintain higher level of performance under Incompatible environment compared to commercial strains. In classic breeding programs for poultry, selection of birds was based on phenotypic and pedigree information. The development of genomic selection prefers new strategies in animal breeding. Genomic selection has a major limitation for implementation. This method need genotyping of large numbers of markers for implementation and the costs of genotyping for these markers is high, especially for developing countries. To overcome this problem, before applying genomic selection, different scenarios have to be compared using computer simulation. The objective of this study was comparison of results in genomic selection and classic selection method in Iranian native fowls by using ZPLAN software (Täubert 2010). ZPLAN software is a very useful tool to optimize conventional and genomic breeding programs this software allows modeling of all relevant breeding structures, while taking all relevant biological, technological and economic parameters for complex breeding programs into account (Sitzenstock et al. 2013). This software then generates results such as the annual genetic gain for the breeding objective using a pure deterministic approach (Dekkers 2007). This program has been based on the discounted gene flow-method (Hazel 1943) and selection index theory (Hazel and Lush 1942). This software calculates genetic gain, discounted return, profit and costs within and over selection paths. The results of monetary in ZPLAN are standardized to an animal unit and are given per year (Sitzenstock et al. 2013).
Material and A reference scenario and a genomic scenario were simulated on 3460 birds in both sexes. Reference scenario was simulated based on phenotypic information and genomic scenario was simulated based on combination of phenotypic and genomic data with two reference populations of 500 and 1000 birds. Genomic data was based on the information of 4000 hens and variable numbers of cocks (800 to 4000). Studied traits included egg number, body weight at 8 weeks, mean of egg weight and age at sexual maturity. In this simulation, genetic and phenotypic parameters were used (Table 1). These parameters included: phenotypic standard deviation, heritability, genetic and phenotypic correlations and traits economic coefficients. Economic weights were based on the study of Kianimanesh et al. (2001) and the other parameters were extracted from the study of Yousefi 2012. The variable costs of rearing a cock or a hen were assumed to be 440000 Rial per animal (over a period of 20 weeks). During production, daily feeding costs resulted from a feed consumption of 0.11 kg per day at a price of 12000 Rial per kg. For each cock and hen, additional costs for the animal care (20000 Rial) were assumed. The costs of selection were assumed 40000 Rial per animal. The fixed costs were not considered in conventional scenario, because it was difficult to quantify them in breeding program. But these costs must reduce from profit. The interest rate was set to %7 for discounted costs and %2 for discounted returns (Sitzenstock et al. 2013).
The generation interval for both scenarios was 14.5 months. By adding genomic information to reference scenario, accuracy of estimations increased from 0.62 for chocks and 0.64 for hens in reference scenario to 0.77 for both sex in genomic scenario. Genetic development of traits increased with increase in the number of genotyped birds and the number of birds of reference population. Genetic development for traits egg number, body weight at 8 weeks, mean of egg weight and age at sexual maturity increased from 0.22, 2.57, 0.09 and -0.23 (Table 2) respectively in reference scenario to 0.30, 3.60, 0.11 and -0.27 respectively in genomic selection with 1000 reference population. The profit of breeding program was higher than reference scenario only in genomic scenario with reference population with 1000 birds (Figure 2). The discounted return per animal unit in the conventional scenario was 20102400 Rial per year. The variable costs for conventional scenario were 1057200 Rial per animal unit. This resulted in a profit of 19044800 Rial per animal unit. The accuracy of the genomic information and the size of the reference population have a large impact on the benefits from genomic selection. Dekkers 2007 showed that with increasing of marker information increased the benefits from genomic scenarios.
The use of genomic information caused increasing genetic development in all traits. Although in this study costs were not reduced, but genomic information increased the accuracy of selection of breeding program. This study showed that genomic selection can increase the genetic improvement rate of native chickens. However, the costs of genomic scenarios were higher than conventional scenario, but genomic information increased accuracy of selection and genetic gain of breeding goals traits. To overcome this problem, use of low density SNP chips is suggested.

Received: July 28, 2015 Accepted: July 12, 2017 1MSc Student, Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran 2Professor, Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran 3Professor, Department of Pathobiology, Faculty of Veterinary Medicine University of Tabriz, Tabriz, Iran *Corresponding author: rafata@tabrizu.ac.ir
Nowadays, beside of production traits, the characteristics of genetic resistance to diseases is considered as animal breeding aims in animal breeding. There is a growing interest by producers and consumers in the production of meat animals with minimal chemical input to reduce chemical residues in the meat and to increase the sustainability of livestock production. Selection of superior sires with identified resistance should be possible because parasite resistance that usually measured by fecal egg counts (FEC) or blood packed cell volume (PCV), is moderately heritable. One option to control helminth infections is to breed sheep that are resistant to these parasites. Genetic variation in response to parasite infection has been documented in the previous studies in some sheep breeds, mostly involving tropical and subtropical breeds, such as the Red Maasai, St. Croix, Florida Native, and Barbados Blackbelly. These breeds have consistently been more resistant to trichostrongyle infections than temperate breeds, such as Dorset and Rambouillet. The objective of this study was to evaluate differences between blood packed cell volume (PCV), parasitic nematode eggs per gram of feces (FEC) and FAMACHA scores of Ghezel breed and Ghezel-Baluchi crossbreds and determine that which group is more probable resistant to nematode parasites.
Material and Data were obtained from 24 one year-old lambs belonging to two genetic groups. Genetic groups including Ghezel (n= 12) and Ghezel-Baluchi (n=12) crossbreds. Ghezel × Baluchi group was containing 50% of Ghezel breed and 50% of Baluchi breed. Samples were collected at two different times on the 2012/2/19 and 2012/3/4 in the Khalat pooshan research station, Tabriz, East Azerbaijan. All lambs were born in the winter of 2011 and they were not given anthelmintic before and they were at the same environmental conditions. Fecal samples were collected directly from the rectum of animals and samples were tested by the method of Clayton Lane. The FEC were obtained for nematodes of Nematodirus (spp.), Marshallagia(spp.), Trichuris(spp.) and unknown nematode eggs. The other measured traits included body weight, PCV and Famacha test. All data except PCV were analyzed by the MIXED procedure of SAS software.Birth weight and blood packed cell volume were analyzed by the procedure of the GLM.
Results showed that the effect of the genetic group on nematodes eggs per gram of feces and Famacha test was significant (P The Ghezel-Baluchi crossbred ewes appeared to be more resistant to infection than the Ghezel breed in natural grazing condition. Crossbreeding of Ghezel and Baluchi sheep breeds increased resistance to internal parasites of the traits measured in this study. As a general conclusion, this research attempted to find resistance traits in relation to domestic parasites in the domestic environment. These characteristics have been investigated by veterinary parasitologists for many years, but animal breeders also need to consider the issue of improving the genetic resistance of sheep to nematodes, and more precisely how they measure the relevant traits and expressions to use in selection of breeder rams and ewes. It seems that crossbreeding of the Ghezel sheep breed with Baluchi breed increases the relative resistance to internal parasites in terms of Famacha, EPG and PCV as measured in this research. In the future there are two needed subjects in this area of animal science: a) to do more investigations to find exactly genetic explication for the relative superiority of crossbreds to pure breeds; and b) the discovery of the nature of the polygonal or non-additive nature of genetic resistance to nematodes in small ruminants.

Nowadays, in ovo injection is being used for increasing hatchability and growth, while reducing mortality rates and disease prevalence in poultry (Moran 2007). Methionine is the first limiting amino acid (Dilger and Baker 2007) and lysine is the second limiting amino acid in broilers (Tessseraud et al. 1996). Lysine has been used as a standard in ideal relationships of other amino acids (Baker 2009). Paradox results were observed using different ratios of methionine to lysine during the growth period in a way that some reported no effect (Lee et al. 1991; Si et al. 2004), while others reported positive effect on growth (Hickling et al. 1990; Mehri et al. 2012). Al-Murrani (1982) reported that the optimal methionine to lysine ratio for 7 d old chick embryo is 50.5%. Therefore, the aim of this study was to evaluate the effect of in ovo injection with different ratios of D-L methionine to L- lysine at 14th d of incubation on body weight parameters and blood metabolite concentrations in a day-old Ross 308 broiler chicks.
In this experiment, 210 fertile Ross 308 broiler breeder eggs were randomly assigned into 7 experimental groups with 30 individual eggs per each group. Experimental treatments including control (non-injected), sham-control (injected sterile water), and 40.5, 45.5, 50.5, 55.5 and 60.5 D-L methionine to L-lysine ratios were injected into the amniotic fluid at 14 d of incubation through the broad end of eggs. On day 22 (one day post hatch), 4 chickens per replicate were selected, bled, and then slaughtered to measure internal organ weights.
Hatchability rate was not affected by treatments (P>0.05), though the highest hatchability was observed in 45.5% D-L methionine to L-lysine ratio (Fig 1). In other studies, no effect (Mottaghitalab and Shafiymanesh 2015) or reducing effect (Coşkun et al. 2014) of in ovo injection with D-L methionine was observed. All the treatment groups showed higher chick weight in comparison with control groups (P0.05), while reduced sera triglyceride (P The overall results of the present experiment indicated that in ovo injection of different ratios of D-L methionine to L- lysine up to 55.5% ratio had an increasing effect on carcass efficiency, muscle production, and protein, while a decreasing effect on triglyceride and urea concentration in a day old Ross broiler chicks.

Reproductive system is affected by hormones so we can control livestock reproduction process by using synthetic hormones and use maximum of their reproductive capacity.
The aim of this study was to evaluate the effect of hCG injection on serum and seminal plasma testosterone.
In this study, six 3-4 years old Ghezel rams were used. Rams was studied with an injection of 500 IU hCG hormone in reproductive season and hCG injection were repeated every seven days for 9 weeks. Blood samples were taken before injections and 30, 60 and 90 minutes after intramuscular injection of hCG from jugular vein. Ejaculate samples were collected at a distance of zero, 1 and 7 days after injection of hCG and serum and seminal plasma testosterone were determined by using ELISA kits.
The results showed that hCG injections increased testosterone levels in seminal plasma and serum that serum testosterone levels at 90 minutes after injection of hCG reached to peak, but between 30 and 60 minutes after injection had the greatest increase. Seminal plasma testosterone levels reached the peak value 1 day after injection but 7 days after injection was reduced and close to the base.
As a result, hCG injections can improve reproductive traits by increasing serum testosterone.

Main objective of this research was production of high fat yoghurt by partial or complete substitution of milk fat with palm oil. Three different types of high fat yoghurts, including yoghurt containing only 8% milk fat (control) yoghurt containing 4% milk fat and 4% palm oil, yoghurt containing 8% palm oil were produced. Samples kept in 4°C for 28 days and their physicochemical properties determined at the interval of 7 days. The results of statistical analysis showed that the treatment and the storage had significant difference (P0.05). Substitution of milk fat with palm oil reduced the levels of saturated fatty acids and short chain fatty acids while the amount of saturated fatty acid of Palmitic acid and unsaturated fatty acids of oleic acid and Linoleic acid showed a significant increase (p

Ram semen has proven to be more difficult to cryopreserve than semen of other farm animals. Cryopreservation, adversely the cryosurvive of spermatozoa, leads to reduction of sperms fertile life. The aim of this study was to investigate the effect of supplementation of diluent with different raffinose concentrations in the cryopreservation of three breeds of ram semen during reproductive season. Ejaculate samples were collected from 3Ghezel,2Ghezel-Merinos and 2Merinos-Moghani rams using artificial vagina. Samples immediately were transported to the laboratory and a primary evaluation was done at 37°C. Semen samples were diluted with a Tris-based extender complemented with 50, 75, 100 mM raffinose and an extender containing no raffinose as a control group. Semen samples were aspirated into 0.25 ml straws, cooled to 5°C and after frozen finally stored in liquid nitrogen. Achievedresultsshowed thatthe highest percentage of alive sperms belonged to 75 mMraffinose (75.47±0.83) and the lowest to control groups(70.76±0.88).The highest percentage of motilityandprogressive motility were observed in raffinose 50 mM(52.84±1.33and45.98±1.33 respectively), while the control grouphad the lowest percentage of motile sperm andprogressive motility (41.18±1.38 and 35.41±1.38 respectively). Percentage of abnormal sperm in100 and 75 mM Mraffinose (8.58±0.32 and 8.93±0.31) was thelowest andthe control group (9.78±0.32) had the highest percentage of abnormal sperm (P<0.05). This study showed that raffinose improved cryopreservation of ram semen. Also the highest percentage of alive sperms, motility and progressive motility were observed in the Ghezel rams and the lowest percentage of abnormal sperm recorded in Ghezel-merinos rams. This study showed that raffinose improved cryopreservation of ram semen. Also preservation capacity of Ghezel rams were better than the other breeds.

Traditionally, pot (Kope) cheese produced from raw milk in the Northwestern provinces of country and nowadays some of the Kope cheese producers have been used of plastic or metal container as a pot. The aim of this study was to determine the effect of pasteurization and packaging on the physicochemical and sensory properties of Kope cheeses during 120 days of ripening. The results revealed that before filling of cheese in pot and plastic container, pasteurized cheeses had higher salt and pH, and pasteurization process increased acidity in pot cheese and pH in cheese which ripened in plastic container at 120th day of ripening. Although usage of pot as a container increased pH, total solid, salt, ash, fat, protein and also overall taste, where plastic container increased acidity and lipolysis of cheese.

Lighvan cheese has large market acceptability due to its excellent sensory atributes. Since Lighvan cheese is made of raw sheep milk that was always warring for health with respect of pathogenic bacteria such as brucella, Listeria monocytogenes and others pathogens. The present research was done to, produced cheese from pasteurized sheep milk by adding microbial starter culture of lactobacillus casei and lactobacillus plantarum isolated from Lighvan cheese were used as starter in cheese for producing Lighvan special aroma and taste. In this reaserch the physicochemical and sensory properties of the white brine cheese made of pasteurized sheep milk using lactobacillus and plantarum was studied. Results revealed type of that treatment, ripening time and their interactions had significant (P < 0.05) increase and decrease effects on the physicochemical properties such as ash, dry matter, pH, acidity, fat, protein, lipolysis content. Pasteurization for cheese samples on day 60 ripening 41% had less dry matter than control samples had not been pasteurized. The rate of lipolysis pasteurized treatments cheese was 15 meq/100g oil. Ash samples pasteurized at about % 0/5, most of the samples had not been pasteurized. Pasteurization treatment with Lactobacillus plantarum strains have the highest of soluble nitrogen to total nitrogen was among treatments. Sensory assessment of cheese samples showed the highest sensory scores obtained from pasteurized cheese made with starter lactobacillus plantarum at the end of 60 day of ripening. It can be concluded that, while reducing the amount of chemical properties of pasteurized cheeses such as dry matter, but the risk of pathogenic bacteria were eliminated. According to sensory evaluation and physicochemical results obtained can be said of Lactobacillus plantarum strains isolated from Lighvan cheese capable of can be used as a starter in the pasteurized cheeses for flavor and desirability to consumers than Lactobacillus casei strain.

Semen collection and sperm evaluation are essential for successful artificial insemination. This study was conducted on 4 rams. Average age of rams was 2-3 years old (2 Ghezel Merino and 2 Merino Moghani). The aim of the present study was to evaluate seasonal variation in semen characteristics. After rams were trained to serve the artificial insemination، semen samples were collected weekly from august 2011 to June 2012. Semen ejaculates were evaluated for volume، color، non- microscopic mass motility، wave motion، pH، sperm progressive motility، percentage of live and dead sperm and concentration. Regarding to semen production، it was found that semen collecting time affected in all seminal characteristics during the breeding and non-breeding seasons. Differences in genetic effect were observed significantly on almost seminal characteristics (P<0. 05) except volume and pH during in breeding season. Merino Moghani performance was better than Ghezel Merinos during breeding season. Ghezel Merino ram only had reproductive activity during non-breeding season.

In this study 103 ewes belonged to the sheep station in Ardabil, Jafarabad were selected for wool sampling. Image analysis method was used to measure the fiber diameter, coefficient of variation of diameter of fibers, medulated fibres percentage and kemp fibres percentage. The environmental factors including the year of birth, type of birth and age of ewes were considered as fixed effects in statistical analysis with GLM procedure of SAS software. Results showed that the effect of year of birth had a significant effect on the characteristics of fiber diameter (P<0.05). Characteristics of mean fiber diameter (micro-meter), coefficient of variation (%), medulated and kemp fibre percentage were 30.9 ±3.11, 36.14 ±5.81, 11.6 ±2.66 and 5.28 ±2.16, respectively. In the measured samples, coefficient of variation and percentage of kemp fibres were high, so it is necessary that breeding programs planned to improve these traits in Moghani sheep. Image analysis can be considered as an easy technique for measurement of most important traits in sheep breeding programs for fiber traits.

The main aim of this research was comparison of random regression animal and sire models for estimation of the genetic parameters for production traits of Iranian Holstein dairy cattle. For this purpose, were used the test day records 928513, 788577 and 653317 regarding milk, fat and protein yields, respectively, belonged to first of lactation of cows collected from 2003 to2010, by the animal breeding center of Iran.Number of Cows 108873, 96511 and 79501 and number of herd 1483, 1400 and 1227 for milk, fat and protein yields, respectively. The genetic parameters were estimated using restricted maximum likelihood algorithm by random regression model with legend repolynomials. For comparison of models, -2logL, Akaike’s information criterion, Bayesian information criterion and Residual variances criteria were used. Homogeneous residual variance was assumed throughout lactation. According to that used the records of all animals in the random regression animal model, therefore is high accuracy. Additive genetic variance and permanent environmental variance was higher in end lactation and beginning lactation, respectively. Estimates of heritability milk, fat and protein yields traits for both animal and siremodels were found to be lowest during early lactation. Estimates of heritability in the randomregression animal model for milk yield, fat yield and protein yield ranged from 0.05 to 0.25, 0.04 to 0.13 and 0.07 to 0.21 and in the random regression sire model 0.08 to 0.21, 0.05 to 0.12 and 0.5 to 0.23 in the during lactation were estimated, respectively. Phenotypic variance of the considered traits during lactation was not constant for both random regression animal and sire models, it was higher at the beginning and the end of lactation. Additive genetic correlation between adjacent test days was higher than between distant test days.The random regression animal model, purposed for estimation of the genetic parameters for production traitsof Iranian Holstein dairy cattle.

For the comparing the growth potency of crossbred and Ghezel lambs by analysis the univariate and repeated measures traits in period 40 male lambs of the same age were used. Genetic groups were included the 7 heads of pure Ghezel lambs and the 7 heads Baluchi×Ghezel crossbred lambs، 7 heads Arkharmerinoos×Ghezel and the 10 heads Arkharmerinoos×Moghani and the 9 heads Baluchi×Moghani lambs. The lambs in 90 days of age were fattened for 110 days in 5 groups. Birth weight، final weight، mean of average daily gain and mean of total average gain in 14 to 70 days of period were studied traits in this investigate. Total traits once analyzed by GLM procedure and mean of daily weight gain and mean of total weight gain in 14 to 70 days of period were analyzed by mixed procedure of SAS 9. 1 software again. In second method CS structure were used as the variance and covariance structure. Within traits the effect of genetic combination was significant on the daily weight gain and total weight gain in 14، 28 and 42 days of fattening period (P<0. 05). At the univariate analyze of traits Ghezel breed lambs have a high performance in 14 and 28 days of period، and Arkharmerinoos×Ghezel in 42 days and Baluchi×Moghani crossbred lambs in 56 days too. At the repeated measures analysis of traits Arkharmerinoos×Moghani crossbred lambs have a low performance، in 28 days Ghezel breed lambs have highly performance and in 42 days Ghezel breed lambs have lowly performance. With regard to obtained results and calculated standard errors for the comparing of least square means at the analysis of tow used methods، obtained results of repeated measurement traits were more accurate than univariate analysis of traits and using this method is recommended at the same researches.

(Co) variance components of milk, fat and protein yield of 11368 first lactation Iranian Holstein dairy cow were estimated by single trait random regression test-day models and restricted maximum likelihood (REML) method. In this study the homogeneous residual variance was assumed throughout lactation. Estimated heritability for 305-day production traits ranged from 0.25 to 0.31 and the highest genetic correlation between different days in milk was observed for protein yield. Persistency is one of the key factors determines the amount of total milk yield during a lactation period. Persistency is heritable economic trait and an important parameter of lactation curve in dairy cattle. In this research five different persistency measures were included: 1) different between estimated breeding values (EBVs) from d 290 and d 90; 2) different between EBVS from d 1 to 100 from d 101 to 200; 3) different average of EBVs from d 255 to d 305 from d 50 to d 70; 4) summation of different EBVS for d 61 to 280 from d 60; 5) summation of the EBVS from d 60 to 279 as a deviation from d 280, were used. Heritability’s as a function of time were calculated. Heritabilities estimated for persistency of protein yield (6-31 percentage) were slightly higher than this values for persistency of milk (7-28 percentage) and fat (3-25 percentage) yield, as well as genetic correlations between persistency and 305-day production were estimated slightly higher for protein and milk yield than thus for fat yield.

Flaxseed is a good source of omega-3 fatty acid، lignin، dietary fibre and natural anti-oxidants such as tocopherols. Having benefits for health with preventing disease is the major reason for fortification of functional food products with flaxseed. In this study، the effect of incorporating flaxseed mealinto wheat flour in proportion of 0 (control sample)، 5، 10، 15 and 20% (flour basis) on chemical properties of bread and flour including oil content، fatty acids profile، tocopherols، acidity and peroxide and their changes during baking were investigated. Moreover، bread sensory characteristics upon 5 days of storage were determined. The results showed incorporating flaxseed up to 20% substitution with flour increased fat content، linolenic acid and tocopherols. During baking، acidity and peroxide values increased. Linolenic acid was stable upon cooking temperatures، however، tocopherols were decreased. Bread containing 15% flaxseed received higher sensory scores compared to other treatments، but over the time، bread sensorial quality was diminished upon storage of bread at room temperature.

Bread is a perishable product which is best consumed when it is fresh. The loss of freshness is due to the microbial spoilage and complex processes known as staling. Sourdough is characterized by a complex microbial ecosystem, mainly represented by lactic acid bacteria and yeasts. The aim of this study was to investigate the application of L. plantarum, L. reuteri and their combination in sourdough preparation. In this study, control breads showed higher pH (5.63), lower TTA, higher loaf volume and height than those prepared from sourdough. Results showed that sourdough bread prepared by L. reuteri received better sensory scores, had lower staling rate and higher shelf-life than those prepared from L. plantarum.

The purpose of this study was to evaluate concentrations of some metabolites and hormones and their effects on the incidence of ovarian cyst at postpartum in dairy cows. Blood samples were obtained from 93 dairy cows. The concentration of glucose, urea, total protein, phosphorus, zinc and beta-hydroxy butyric acid as well as estrogen and insulin hormones in blood serum were measured. The results revealed that the Zinc concentration in cystic primiparous cows was significantly lower than the control and cystic multiparous cows (P<0.05). Serum glucose concentration showed significant differences between cold and warm seasons (P<0.05). Phosphorus concentration in the warm season was higher than that of the cold season (P<0.05). Serum urea concentrations in control and cystic primiparous cows showed significant differences compared with serum urea concentrations of all multiparous cows (P<0.01). Beta-hydroxy butyrate concentrations of serum of cows with healthy low milk production were lower in comparison to cystic cows (P<0.05). Serum insulin concentrations had significant difference among the higher milk producing cystic cows compared to the higher milk producing normal cows (P<0.05). No significant differences were observed among the cows considering their serum concentrations of total protein and estrogen hormone. The results showed that the Zinc concentration, level of milk production and calving season affected the incidence of ovarian cyst significantly.