اردشیر نجاتی جوارمی

The aim of this study was to identify Single Nucleotide Polymorphism (SNP) associated with selected reproductive traits in Holstein dairy cattle. The interval between calving and the first insemination, days open, the interval between the first and last insemination, and the number of inseminations per pregnancy were analyzed. For this purpose, the hair samples of 150 cattle, born between 2012-2014 in one of the cattle farms of Ferdous Pars company, were used for genotyping based on 30108 SNPs chip. The data were analyzed using the least square variance analysis method using the GLM. GWAS analysis was performed after controlling the quality of the data. The results identified that 2 and 12 SNPs had a significant correlation with calving to insemination interval and interval between first to last insemination traits(p<0.04), respectively. In addition, 11 SNPs and 5 SNPs showed significant correlation for days open and the number of insemination per conception traits (p<0.04), respectively. In the Post-GWAS stage, some Quantitative Trait Loci (QTL) and various genes were identified that affected or controlled the trait. Out of the related NUF2 gene on chromosome 3 affects the development of the oocyte, ANAPC1 gene on chromosome 11, which affects sperm motility, PITX2 gene in chromosome 6, affects milk production and ELOVL6 gene on chromosome 6 affects body weight. In general, it can be concluded that chromosomes 3, 6 and 11 have SNPs that are more strongly related to reproductive traits.

Genomic evaluation of crossbred progeny due to their limited pedigree and lack of genotyping and performance accessibility is inevitably based on the information from purebred parental populations to increase crossbred performance. Despite the fact that single-step genomic evaluation (ssGBLUP) method can use information from both genotyped and non-genotyped animals simultaneously, leading to more accurate genomic estimated breeding values, but due to the incompatibility of the genomic and pedigree relationship matrices, it might lead to dispersion (inflation/deflation) and bias in the estimated breeding values higher than that with the BLUP method. Therefore, in this study, the prediction ability of the genomic breeding value of crossbred progeny was investigated based on the ssGBLUP method and simulation data of the purebred parents and crossbred population, considering the different scaling factor of residual polygenic variance. Based on the results of this study, the use of different ratio of residual polygenic (β) variance to incorporate the genomic and pedigree relationship matrices did not considerably affect the accuracy, bias and dispersion of the predicted genomic breeding values in crossbred progeny. In addition, the effect of proportion of residual polygenic variance (β) in blending the genomic and pedigree relationship matrices does not significantly affect the convergence point. Therefore, to simplify the model, the default value of β (0.05) might be used in the inverse of the relationship matrix.

Improvement of reproductive traits, in addition to the effect on herd reproduction, can be effect on treatment and veterinary costs, animal welfare, and most importantly, profitability. While today, reproduction problems are one of the main reasons for the lack of profitability in dairy cattle herds. The purposes of this study was to Genome Wide association study (GWAS) of Age at First Insemination (AFI) and Age at First Calving (AFC) traits and the Number of Inseminations per Conception (NIPC) in Holstein heifers.In order to conduct this study, the record of 150 heifers born between 1390-1392 was used based on the breeding value of milk production. The results showed that 5 SNPs were significanteffect on age at first insemination (pValue<0.04). which was observed in BTA3(2), BTA5(2), BTA15(2), BTA21, BTA23, BTA28 and BTA30 regions respectively. For the age at first calving, 10 SNPs has a high correlation (pValue<0.04) which was located on BTA3(2), BTA5(2), BTA15(2), BTA21, BTA23, BTA28 and BTA30 regions respectively. 11 SNPs had a high correlation (pValue<0.04) for the Number of Inseminations per Conception and were able to be above the significant threshold line, which were located in BTA11, BTA8, BTA28, BTA6(5), BTA13, BTA18 and BTA14. QTLs identified in the margins of significant SNPs, with body weight trait; calving difficulty, calf weight and heifer maturity age were related. Finally, the QTLs identified in the margins of significant SNPs confirm the fact that the age of the first insemination and the age of the first calving can be effective on production traits, reproduction, longevity and finally on the profitability of the herd. In this situation, it can be said that herd management has a significant role in advancing breeding goals.

This study was conducted to compare the morphological characteristics of wild and farmed common carp. In total 70 samples of common carp, including 25 samples of wild from Torkaman port and 45 samples of farmed common carp from Silver carp center in Gilan province were collected. Morphometric results were standardized using Elliott formula, and then principal component analysis (PCA) and discriminant function analysis (DFA) were used. Independent t-test was used to evaluate the significance of traits between these two populations. The results of this study revealed that the two populations of wild and farmed common craps were completely separated from each other, using PCA and individuals were assigned to their true population with high accuracy (98%) based on DFA. Among the 33 truss distances that were analyzed, 16 distances showed a significant difference between two populations (p<0.05). The results showed that the studied populations can be distinguished by many morphological differences, especially by dorsal fin length, pectoral fin length, pelvic fin length, anal fin length, dorsal fin width, body width, tail stem width, distance between pectoral and pelvic fin, distance from mouth to dorsal fin and the distance from the mouth to the anal fin. Overall, the results showed that the population of wild carp was significantly different from the population of farmed common carp from the morphological point of view.

Morphological characteristics of fish, including phenotypic diversity in scale pattern, anal fin, and spine shape, play an important role in their viability and economic value. The aim of this study was to investigate the scale patterns and deformities in wild common carp (Cyprinus carpio) and breeder’s common carp (Cyprinus carpio) of Iranian hatchery centers. In total, 219 samples including 40 wild and 179 farmed common carp (From Silver Carp center in Guilan Province, Cooperative center of 12 in Guilan Province, Shahid Maleki Center in Khuzestan Province) were collected. All farmed and wild Common carp samples were photographed and their other morphological characteristics were examined. The results of this study show different scale patterns in farmed common craps. We observed three different scale patterns in farmed common carp including full scales (Normal), large scales along the lateral line of the body (Line) and a small number of large scales (Mirror). Furthermore, we found a wild common carp with spinal deformation and one farmed common carp missing anal fin. We also found a different scale pattern in farmed common carp that was covered with a disordered full scale. In general, the results of the present research which examines the possible variation in the scale pattern and types of deformities in the appearance of wild and farmed common carp for the first time in Iran, can provide valuable information for further researches in the field of molecular identification of the genetic basis of the variation observed in Common carp.

In this study the cis and trans regulatory effect of long non-coding genes (lncRNA) on the expression of genes in fish infected by Viral hemorrhagic septicemia virus (VHS) was investigated using RNA-seq technology. At the end of experimental period (the thirty fifth day), total RNA was extracted from spleen tissue (group treated with virus) and physiological serum (control group) was used to prepare the library for RNA-seq. After library preparation, sequencing was carried out by Illumina High Seq 2500 platform. The results of RNA-seq analysis showed that 63 lncRNA genes had differential expression that were associated with 92 cis coding genes in the range of 20k up and downstream sites of the target genes. Among the pairs of coding and non-coding genes, those with both more than 90% and less than 90% expression correlations were considered as positive and negative co-expression genes, respectively. The coding genes such as Interlukin10, BHLHE41, RBP47, gastrotropin, synaptopodin, OX2, and SMC2 were associated with cis and trans with 8 and 13 lncRNA genes, respectively. Interlukin10, gastrotropin, synaptopodin, OX2, and SMC2 genes had higher expression in the virus-treated group. The two genes RBP47 and BHLHE41 were more expressed in the control group. Gene ontology analysis showed the activity of cytokine genes, including interleukin 10 gene, which plays an important role in inflammatory responses in the immune system.

Reducing the population size of Sistani cattle due to the multi various reasons during the last years, was the motivation of the current study. Therefore, the aim of this study was to investigate the factors of population decline and strategies to increase the population and revive this breed. For this purpose, a questionnaire was developed using the Delphi method. Questionnaire was included 21 reasons and 18 strategies related to the situation of Sistani cattle population. Based on the breeders’ insight, drought in the Sistan region during last three decades was considered as the most important factor in reducing the population of Sistani cattle, and for both groups, the least important factor affecting population decline is the uneconomic importance of Sistani cattle (P < 0.05). Both groups were agreed that climatic factors are the most important in reducing the population of Sistani cattle and almost no differences in this regard were observed between the two groups (P > 0.05). From the breeders' point of view, economic support for Sistani cattle breeders is the most important way to support the Sistani cattle population, while experts believe that the most important way is to rehabilitate Hamoun Wetland. In general, the results of this study showed that due to the changing and varying climate of Sistan region, attention to economic issues and support for breeders can largely compensate for the problems caused by unfavorable climatic conditions in the rehabilitation of Sistani cattle population.

The native species of Caspian brown trout (Salmo trutta caspius, Kessler1877) is an important candidate for introducing to the aquaculture industry because of carcass quality and marketing in Iran. In introducing any species, it is necessary to complete the domestication stages. The most important advantages of domestication are controlling the costs and the biological and non-biological factors include environmental and social aspects in order to economize this activity and interaction between genetics and environment in breeding program, must be considered. A survey of the activity duration of the 43 Caspian brown trout farms showed the biggest challenge is the lack of sustainability. For this research, two questionnaires were designed. In first questionnaire, 16 professionals and experienced people were asked to determine the most important environmental and management factors affecting on the sustainability of this activity who completed the list and rated each of the factors. Water temperature factor with 13.15% and water debi with 7.03% obtained highest and lowest scores. Then second questionnaire was prepared including farm characteristics based on the first questionnaire results and was sent to 43 farms. Finally, 26 completed forms were received from the farmers. For scientific evaluation of the results, the variance multivariate analysis, Pillai,s Trace, LambadaWilk,s, Hotelling,s Trace, Roy,s largest root and  Helmert Contrast tests were performed using spss16 software. The result showed, there was significant reciprocal correlation (p<0.01) between all groups of dependent variables, except for water debi and the weight of fry at the beginning of aquaculture (p>0.01), Also minimum temperature and aeriation system factors had significant main effect on activity duration (p<0.01). In the Helmert Contrast comparison statistic, there was significant correlation between 4 years of experiences group and rest groups for minimum temperature factor (p<0.01). The results of this study can be used by aquaculture planners to select appropriate environmental and management conditions for sustainable production of this activity.

The agriculture contribute to 50-60 % of global methane emission and ruminants have a key role in this contribution. Methane has an important role in global warming and it's global warming potential is 25 times greater than CO2. Furthermore, methane is the second most abundant global anthropogenic greenhouse gas after carbon dioxide. The present study aimed to perform genome wide association study to identify genome regions affecting the predicated methane production based on the concentrations of volatile fatty acids of rumen in Iranian Holstein cattle. One-hundred and fifty hair and rumen digesta samples were sampled using the two-tailed strategy based on breeding values of milk. After the measurement of the concentration of volatile fatty acids of rumen, methane emission of each animal was predicated according to these acids. DNA of animals was genotyped using GGP-LD v4 SNP panel (contains 30108 SNPs). Fourteen significant SNPs associated with methane emission trait located on 1, 2, 6, 10, 15, 17 and 18 chromosome were identified. Using annotating some quantitative trait locus (QTLs) were discovered around some of these SNPs. The results showed a genetic selection potential to mitigate methane emission per animal. Since genetic improvements are heritable, cumulative, and permanent, this improvement would be permanent and beneficial.

Nowadays one of the major challenges facing herders, dog owners, or working dog training centers is canine parvovirus (CPV-2). The virus has split into several types over the years since it discovered and resulted to genetic and amino acid changes that threaten a wide range of carnivorous around the world. The best way to avoiding the consequences of this disease is vaccination. This study were designed, due to the lack of sufficient studies on the distribution and prevalence of different types of this virus, which may be a prominent cause of vaccine errors, also because of high involvement of Iranian dogs with CPV. Molecular study and phylogenetic comparison of Iranian types compared to other types through the world showed that the dominant type of CPV-2 existed in Iran is CPV-2a with a prevalence of 24% and genetic differences in several points of VP2 gene with other types. We are probably facing to a new version of this virus in our country. In addition, based on the drawn phylogenetic tree, it was found that Iranian isolates on the other side have a relatively high topological difference compared to the origin types and conventional vaccines strain, which supports the initial hypothesis of this study.

Accurate genomic evaluation depend on large reference population with reliable performance information such as predicted breeding value (PBVs). The aim of this study was to identify the most appropriate reference population to predict the genomic breeding value for Iran Holstein dairy breeding programs. Phenotypes and genotypes were simulated based on the dairy cattle Iran population program (open breeding nucleus with gene flows between the nucleus and the commercial population). Medium (0.3) and low (0.05) heritability levels were considered independently. All simulations were performed with 10 replications and the results were evaluated. In the first study, female cows were selected for genotyping in four scenarios: random selection, individuals with upper and lower extremities of phenotypic value, highest phenotypic value and highest breeding value with maximum accuracy; and these females are added to the reference population. Single Step BLUP (SSBLUP) was used to predict the genomic breeding value for individuals in the population. The accuracy and unbiased coefficient of predicted breeding value were investigated. The results showed that when female animals with the highest and lowest phenotypic values were selected (the second scenario of determining females), the highest accuracy of prediction of breeding value was observed compared to other scenarios. Determination of substances with high phenotypic value (third scenario of female selection) showed the least bias. The use of imported males with genotype and their use alone as a reference population showed the least accuracy and the most bias. The combination of males and females showed an increase in accuracy and a decrease in bias compared to the scenarios for males or females alone. However, in relation to the size of the population similar to females, no improvement in the prediction of the breeding value was observed. Therefore, in terms of economic conditions (genotyping costs), the use of only female cows in the reference population (2000 females genotyped), according to the second scenario of female selection, is the best strategy to form a reference population and genomic evaluation at the lowest cost, in Iran.

Establishment and maintenance of pregnancy are essential for product persistency in ruminants, and especially in dairy cattle. Embryo implantation into the uterus is an essential process for the maintenance of pregnancy, and involves complex interactions between the embryo and maternal endometrium. Examination of genes and mechanisms regulating the initiation of implantation is necessary to understand implantation process. In this study, in order to better understand the molecular basis of implantation, we undertook the transcriptome profiling of endometrial cells of pregnant with non-pregnant cows, during this period. In total differentially expressed genes were identified with the comparison of the endometrial profiles. Thus, after preprocessing and analysis of data and meta-analysis, gene interactions were investigated using data mining approach. Also with the reconstruction of network and search for important and functional modules, we found 4 main modules. The most important genes contained CLU, ACTA2, MX1, MX2, C1S, COL3A1, S100A11, NID1, SELL, PTN and CDH13. The results of this study suggest that identified modules can be used as markers for uterus receptivity, and embryo implantation.

To evaluate the influence of VHS disease on rainbow trout biometric traits, this research was conducted. Two hundred eighty-one rainbow trout (88±3.38 g initial weight ) were collected, and after 18 days of adaptation period were randomly divided into five groups. All experimental groups were fed by commercial ration. The first group was selected as a control group (no injection), but the second to fifth groups were injected with 0.03 ml physiological serum, 0.06 ml physiological serum , 0.03 ml VHSV, and 0.06 ml VHSV with the concentration of 4.5x104 pfu.ml - respectively. To diagnose the disease, RT-PCR test was used. The research period was 35 days, and records of body weight, and fish length (standard length, fork length and, total length) were collected on days 28, and 35 of rearing. Mean comparisons of these traits between different groups were conducted using the Tukey test (HSD) and R software. In the results of body weight in the first week after challenge (day 28) significant differences were observed between the control group with VHSV injected groups (p < 0.001) and also between physiological serum with VHSV injected groups (p < 0.05). In the second week after challenge (day 35), there were significant differences (p < 0.001) for body weight between VHSV injected groups with control and physiological injected groups (p < 0.001). In the second week after the challenge for traits related to fish length (standard length, fork length, and total length), there were significant differences between all experimental groups (p < 0.05). Based on the observed results, VHS disease will reduce fish growth, and it will cause economic losses.

The main objective of dairy farmers is to maximize their profit. Increased incidence of mastitis in farms is one of the health problems, causing in serious economic losses as a consequence of treatment costs and reduction of production and longevity. The objective of this study was to evaluate the genetic architecture and associated genomic regions with milk production and somatic cell score (SCS) as an indirect measure of mastitis and the quality of raw milk. Thus, an SNP data set from 1938 Holstein bulls were used in a single-step genome-wide association study. The proportion of additive genetic variance (agv) for each of 1.5-Mb genomic window (adjacent SNPs) was used to identify informative genomic regions, accounting for more than 1% of the agv. A total of 11 significant windows over 9 bovine autosomes were found for the SCS. A peak on BTA14 explained the largest proportion of variance (3.85%). These regions together, explained 20% of agv and harbored 94 candidate genes. For milk yield, we identified 6 informative windows across 6 chromosomes, and a peak on BTA10 explained 2.08% of agv. These regions, explained 8.8% of the agv and sheltered 89 candidate genes. For the fat yield, 9 significant windows were identified on 7 chromosomes and explained 15.6% of agv, and 9 windows contained 87 candidate genes on 8 bovine autosomes were associated with milk protein yield (10.6% of agv). Four genomic regions had a pleiotropic effect. These findings can be an important source of information in genomic evaluation of dairy cattle.

In order to evaluate the effect of genotype by environment interaction on production traits of Holstein cattle of Iran, first lactation test day records of 344170, 135000 and 156840 of milk, fat and protein yield on 34417, 13500 and 15684 cows and SNP markers of 1935 genotyped bulls were used. The production data were retrieved from the Animal Breeding Center and Productions Improvement of Iran’s database which were collected from 2013 to 2018. To consider the interaction of genotype and environment, mean of temperature-humidity index (THI) in three days before each test day records as continuous environmental effect were retrieved from the 35 closest meteorological stations in the vicinity of 139 Holstein herds from 13 provinces. Variance and covariance components were estimated through a single-trait random regression model with orthogonal Legendre polynomials of second order for days in milk and THI using AIREMLF90 software. The results showed that changes in THI across lactation led tofluctuations in additive genetic variance over time. The change in heritability of milk production traits over lactation followed the same trend as additive genetic variance. The results from cross-validation analysis showed that including genomic information into the predictive model, increased prediction accuracy and including THI information increased unbiasedness. Due to the changes in milk production of daughters of bulls across days and THI , genotype by environment interaction should be considered when selecting bulls under different conditions.

In this study, transcriptome data were used to identify the genes involved in embryo elongation of dairy cattle and the inter-gene interactions to evaluate the important functional modules during this process. The growth, successful development, and survival of the embryo are the most important needs of the dairy industry. The majority of pregnancy loss occurs during the first weeks, especially at the embryonic elongation stage. Thus,in order to better understanding of the molecular basis of this process, we undertook the transcriptome profiling of endometrial cells of pregnant versus non-pregnant cows, during this period. After preprocessing and analysis of microarray and RNA-Seq data and combining the results, gene interactions were investigated using data mining approach. Finally, by comparison of the endometrial profiles, reconstruction of the network and search for important modules, we found four significant functional modules. The most important genes contained ANKRD54, ADAMDEC1, PTN, MT1A, LIMS2, MT1E, CPA3 and MTPN. According to this study, we suggest that identified modules can be used as markers for embryonic growth, elongation, development, secretion of uterine luminal fluid, immune response and embryo survival.

Increased homozygosity resulted from mating of relatives is considered as one of the challenges faced in dairy farming industry which has attracted the attentions. This research has been conducted to measure homozygosity based on SNP and ROH in high- and low-producing Holstein cows. In current research, both random regression and pedigree index approaches were used to obtain candidate animals for genotyping process. The samples were obtained from 150 Holstein dairy cows (75 by high- and 75 by low-EBV for milk production). We proposed a suitable method, by integrating breeding value estimation calculated by random regression and pedigree index, to select the candidate animals for genotyping. The results showed that putting too much emphasis on production traits in high-producing dairy cows had negative impact on the traits associated with fertility (DPR = -0.55) and productive life (PL = 0.1). The calculated homozygosity based on ROH showed different amount of variation in different chromosomes in the cows with high and low production which may be related to uneven distribution of genes influencing production traits in different chromosomes.

In present study, Analytical Hierarchy Process method was used for  determining  most important traits in the breeding program of Caspian Sea trout and two questionnaires were prepared in two stages. The first questionnaire was sent to the 43 Caspian Sea trout farms that were previously identified. In this questionnaire, farmers based on their knowledge and experience were asked to select and rank the six most preferred out of 15 economic traits that they should be included in genetic improvement of this species in the breeding objectives with the aim of making more profit on their aquaculture. In this phase, 26 completed questionnaires were received. Six selective traits for compiling second questionnaire were determined as: Thermal growth coefficient (TGC), Feed Conversion Ratio (FCR), Late maturation, Survival at harvest, Fillet percentage and Flesh color (redness).According   to analytical instruction, 15 pairwise comparison questions were constructed which genetic parameters based on previous studies. The second questionnaire was sent to 26 farmers who had completed the first questionnaire.Finally, 21 farmers (81%) completed  pairwise comparisons. The Analytical Hierarchy Process was used to estimate the vector of individual preference values and Inconsistency Ratio using Super Decisions software. A judgment is commonly reliable when Inconsistency Ratio is less than 0.10. After modification of   the matrix of 19 observation that have Inconsistency Ratio<0.1 , the final ranged from  0.107 to 0.027. The median of the preferences obtained from AHP showed in both cases, before and after correction of Inconsistency Ratio, the highest preferences of genetic improvement were for survival (0.252,0.191) and  FCR (0.201,0.275). Late maturation (0.152,0.142) was third in both cases. Also, after correction of the matrixes, TGC (0.112, 0.133) was fourth and the percentage of fillets (0.132 , 0.094) and Flesh redness (0.073, 0.057) were in the end of  ranking. The results of present research can be used in the national breeding program of the Caspian Sea trout as a unique endemic species for development of aquaculture industries.

The objective of this study was the detection of polymorphism in ATP1A1 gene and its association with conception rates in Holstein and Sarabi cows by PCR-SSCP method. For this purpose, blood samples were taken from 124 cows. DNA was extracted from whole blood using modified salting-out method and polymerase chain reactions were performed for amplification of 330bp fragment of the bovine ATP1A1gene. The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method was used to scan for the mutations within the amplified regions. Subsequently, a numbers of samples per each band pattern were sequenced for identification of Single Nucleotide Polymorphism (SNP). The results of the sequencing and alignment using available sequences in NCBI two SNPs in the ATP1A1 gene that one of those was located in exon14 and another one in intron14 area and the mutation located in exon area was along with no changes in amino acid and obtained protein of this gene. For evaluating of association between this locations and conception rate trait, the band pattern (haplotype) were considered in the model. The results showed that the observed haplotypes in the ATP1A1 gene is not significantly correlated with conception rate.

The methane production from ruminant production system was estimated to reach 250-500 L per animal per day which has been reported to contribute up to 8-10 % of global warming during the next 50-100 years. The aim of this study was to investigate the correlation among methane emission (predicted by volatile fatty acids) with milk production traits, its components and breeding values (BV) of these traits in Iranian Holstein cattle. The rumen digesta was obtained from 150 cattle through stomach tubing and this population divided into 2 groups with 75 cattle in each (the groups have different milk production BV). Data were analyzed by R.3.3.0. The results showed that methane emission per unit of milk and fat were different in the two groups (P<0.0001). Also, the BVs of milk production, fat and protein traits and daily production of milk, fat and protein had weak to moderate negative correlation with methane emission per unit(P<0.05). The highest correlation was observed between daily production of fat with methane emission per unit of fat (-0.79) as well as daily milk production with methane emission per unit of milk (-0.62). These results showed that methane emission may be reduced by indirect selection per generation for the traits had a high correlation with the gas (daily production of milk and fat).

The purpose of this study was to investigate the effect of different doses of trehalose and cysteine on bull frozen-thawed sperm quality. In this study, semen samples were collected from three healthy mature Holstein bulls by an artificial vagina. After primary evaluations, the samples were pooled to eliminate individual effects. Then, semen samples were divided into six equal parts and each part was extended and frozen with one of the following extenders. 1) without cysteine and trehalose (T0C0), 2) Five mM cysteine without trehalose (T0C5), 3) Ten mM cysteine without trehalose (T0C10), 4) A hundred mM trehalose without cysteine (T100C0), 5) Five mM cysteine with 100 mM trehalose (T100C5), 6) Ten mM cysteine with 100 mM trehalose (T100C10). Motility parameters, acrosome and membrane integrity and phosphatidylserine translocation assay were evaluated after thawing. All data were analyzed using a 2×3 factorial trail following data collection. The results of this study showed that cysteine had no effect on motion characteristics, apoptotic status, acrosome integrity and viability (P≥0.05). Also motion parameters, viability, acrosome and membrane integrity, in group without trehalose was higher than group containing that (P≤0.05). Regarding to interactive effects, the T0C10 group had higher amount of viability (P≤0.05) and lower necrotic sperms compared to rest of the groups. Based on the results, it can be concluded that cysteine had no remarkable effect and addition of Trehalose could negatively affects post-thawed bull sperm quality.

The Arab horses are famous for endurance riding, jumping and beauty. Kurdish horses are native to hilly regions of west of Iran and they are suitable for Polo tournament. Kurdish horses are shorter and heavier than Arabian horses. In this study, we use the linkage disequilibrium-based method, XP-EHH statistic, for Identification of regions that have undergone selection in the genome of Arabian and Kurdish horses. For this purpose, genomic DNA from blood and hair samples from 38 Arabian and 58 Kurdish horses were extracted. All DNA samples genotyped by the Axiom MNEC670 array. After data pruning, XP-EHH statistic was calculated. We identified 51 genomic regions (85 genes) in Iranian Arab horses and 7 genomic regions (13 genes) in Kurdish horses showing signatures of selection. We found positively selected genomic regions in the Iranian Arab horses associated with immune system related pathways, milk protein formation, muscle growth and development, vision, nervous system and body size whereas in the Kurdish horses associated with G protein–coupled receptors, growth and maturation of muscle fibers, cellular oxygen homeostasis and skin and hair pigmentation.

In this research the causal structure among calving traits of 29950 first-parity Holstein cattles of Iran including calving difficulty (CD), birth weight of calves (BW) and gestation length (GL) was revealed applying data collected by Iranian Animal Breeding in 131 herds from 1995 to 2004 by Inductive Causation (IC) searching algorithm. Significant structural coefficients were found for causal effects of BW on CD (0.060±0.002) and of GL on CD (0.007±0.002). Furthermore, the causal effect of GL on BW was significant (0.219±0.005). Considering the revealed causal structure, standard and recursive multivariate models were compared applying deviance Information criterion (DIC) and predictive ability of models in terms of two measures including mean square of error and correlation between observed and predicted values. The obtained results revealed the causal effect of BW and GL on CD and the plausibility of recursive multivariate model over standard multivariate one. Therefore, considering the causal structure among calving traits is of crucial importance.

Using SNP markers information and genomic evaluation approach, predicting the genetic merit of individuals without phenotypic records is now possible. However, using high-density panels for genomic evaluation of all individuals is not economically feasible. To achieve high genomic prediction accuracy with reasonable price, it is possible to genotype a proportion of animals with high-density panels and the rest of animals with low-density panels then impute them to high-density genotypes. In this study, the effect of three low-density panels (1k, 2k and 4k), genotype imputation to 10k panel and the relationship between reference and validation populations on the accuracy of genomic predictions and also the correlation between the estimated breeding values using panels with different densities in simulated data were assessed. The low density panels genotypes were actually consisting of 10, 20 and 40 percent of 10k markers selected randomly and FImpute was used for genotype imputation. As a general trend, by increasing the density of markers, the correlation between the estimated breeding values was increased using different panels. So, the accuracy of genomic predictions was similar using 4k and 10k genotypes. Moreover, imputing 4k to 10k genotypes, did not improve the accuracy of genomic prediction. However, the accuracy of estimated breeding values was increased after imputation from 1k or 2k to 10k. The accuracy of imputation was decreased when the reference and validation populations were more distant.