سید حسن حافظیان

Milk production and reproductive traits are important economic traits in goat. The different approaches including candidate gene mapping and genome-wide association studies (GWAS) are now implemented in goats in an attempt to identify the molecular mechanisms affecting these economically important traits. The gene ontology (GO) analysis gives a controlled vocabulary for describing attributes of genes and gene products. Kyoto Encyclopedia of Genes and Genomes (KEGG) provides the mythology for the careful examination of gene functions in respect of networks of genes and molecules. Gene network analysis can also identify paths and processes shared by candidate genes. The purpose of the present study was to bioinformatics analysis (GO, path enrichment, and network analysis of the effects of protein-protein interaction) of genes effective in litter size and milk production in goat.

Candidate genes associated with studied traits were retrieved from literature review, review of candidate gene studies, GWAS and NCBI database. GO analysis and enrichment analysis of the signaling pathways of KEGG were performed using online database of G: Profiler. The String database was used to infer the network of protein-protein interactions (PPI) and the selection of performance module. Cytoscape software was used to draw the resultant networks of protein-protein interactions. Finally, cytoHubba was used to identify Hub genes.

GO analysis for litter size showed that, for molecular function the candidates genes enriched in signaling receptor binding, signaling receptor active activity, hormone activity, protein binding and transforming growth factor beta receptor activity. The effect of the transforming growth factor β (TGF-β) family on fertility and reproduction, embryonic development, organogenesis, and uterine growth and function is remarkable in a wide range of organisms. In mammals, even early stages of reproductive development, including male and female germline specification, are controlled by TGF-β-related proteins. Hormone binding play an important role in fertility and reproduction. Sex hormone-binding globulin (SHBG), specifically bound to the biologically active androgens and estrogens that are key regulators of the reproductive organs as well as other sex-differentiated tissues such as muscle, adipose tissue, and bone. KEGG analysis also identified some signaling pathways including ، PI3K-Akt signaling pathway، TGF-beta signaling pathway and ovarian steroidogenesis which are significantly associated with litter size. GO analysis for 33 candidate genes related to milk production traits identified only one GO category for biological process namely linoleic acid metabolic process.

In this study, we identified several significant biological and signaling pathways that can be used to better understand the biological processes associated with litter size and milk production in goats.

Horses have played an important role in the history of Iranians during different centuries. They kept horses for various aims such as agriculture, transportation, sport, food sources. Iran has a suitable climatic, social and economic potential for keeping and breeding horses, that is why it has been created different breeds using the selection and breeding. But due to problems such as mechanization, lack of government support, export ban, high costs of breeding and maintenance, import of foreign horses, lack of proper planning, interest in keeping horses has decreased. So, unfortunately, only a few native Iranian breeds remain. Additional investigation of the equine genomic architecture is critical for a better understanding of the equine genome, as well as for expanded comparisons across diverse mammalian species. Turkmen and Caspian horses are well-known breeds of Iranian horse breeds. These breeds were historically selected to perform distinct tasks and therefore may harbor a wealth of unique variation at the genome level. Copy number variation (CNV) along with single nonucleotide polymorphisms (SNPs) play a key role in genetic diversity in livestock species. CNVs, a term that refers to a change in the number of copies of a genomic segment, are responsible for more sequence differences between individuals than SNPs and are considered to be a major source of genetic variation contributing to differences in phenotypes (Beckmann et al, 2007). Several studies identified copy number variations in horses using different techniques (Doan et al, 2012). Part of these studies tried to establish associations between CNVs and a specific trait, a disease or even gene expression (Schurink et al, 2017). Most of these studies found either no association or inconclusive associations as the number of horses with phenotypic information or with specific CNVs were limited. For example, a 62 kb duplication on Equus caballus (ECA) chromosome 10 seemed to be related to recurrent laryngeal neuropathy (Dupuis et al, 2013). However, little is known about CNV in Iranian horses.

In this study, detection of CNVs and CNVRs were performed based on SNP data from Caspian and Turkman horse breeds were genotyped via Equine70k SNP beadchip. PennCNV software was only used to detect CNV on autosomes. The PennCNV algorithm was only applied to autosomes (command: -lastchr 26) to identify individual-based CNVs. To increase the confidence of the detected CNVs, quality control was performed by employing standard exclusions of the LRR (standard deviation of LRR) <0.3, a BAF drift <0.01 and a waviness factor <0.05. We classified the status of these CNV into two categories: “loss” (CNV containing a deletion) and “gain” (CNV containing a duplication). The CNVRs were determined by aggregating the overlapping CNVs with CNVRuler. BioMart in the Ensembl database and DAVID was employed to identify genes located in CNVRs and GO terms and KEGG pathway analyses respectively. Quantitative real-time PCR (qPCR) was applied to validate the CNVRs that were detected in this study.

A total of 202 and 105 CNVs and CNVRs were identified in the studied horses, respectively, which cover 1.08% of the horse genome. The number CNVs in Caspian breed were 1.6 times more than Turkmen. Also, the average size of CNVs in Caspian breed was longer than Turkmen. In both breeds, the genetic event of gain was higher than the genetic event of deletion. In Caspian breed, chromosomes 1, 3, 12, and in the Turkmen breed, chromosomes 1, 6 and 12 showed the most changes in CNVs, respectively. Functional analysis showed that the identified CNVRs overlapped with 434 genes and the most of these genes were common between the two horse breeds (more than 60%). Among these genes, PPARG and GALR have potential related with breed-specific traits. The KEGG pathway analysis also identified several pathways that are significantly enriched in olfactory sensory perception, chemical stimulus sensory perception, antigen processing, and G protein signaling pathway. Also, 60% of successfully detected CNVRs were confirmed by Real-time qPCR. The results of this study were compared with the results of eight other studies. For example, we concluded that the average size of the CNVRs detected by the 70k arrays and the 50K arrays were significantly larger than obtained by the CGH and NGS arrays. This may be due to the relatively low coverage and non-uniform distribution of SNP in the equine genome in SNP arrays. Possible reasons for the differences between our results and some CNV studies can be related to different parameters such as sample size and genetic background, different detection platforms and CNV retrieval algorithms, CNV definitions and CNVRs, as well as random error estimation methods (Pinto et al. 2011).

CNVs can describe part of the phenotypic diversity and adaptation evidence in Iranian horses. With regard to Genes identified in a number of cellular components, biological processes and molecular functions within CNVRs, the importance of such CNVRs and the possible effect needs to be studied and may interest insight into the functional and adaptive consequence of CNVs in horse. In total, the number of CNVs in the Caspian breed was greater than in the Turkmen breed, and also the CNV length in the number of copies in the Caspian breed was greater than in the Turkmen breed. In both breeds, there were overlapping genes with CNVRs that were significantly enriched in biological pathways, including sensory perception, immunity, and metabolism. This is the first CNV report on Turkmen and Caspian horses and the findings of this study could provide valuable information for better understanding of the horse genome and also the important performance traits with CNVRs and associated genes for the future studies in horse breeds.

Identification of single nucleotide markers and different methods of genomic evaluation in the form of marker assisted selection at the genome level has led to considerable genetic progress in the economic traits of domestic animals. The success of genomic prediction is measured by its accuracy. Deterministic formulas determine the relationship between prediction accuracy and factors affecting prediction accuracy and therefore before running into genomic selection, it is possible to design an optimal program such as the appropriate size of the reference population to achieve the optimum level of selection accuracy. The aim of the present study was to evaluate the prediction of the accuracy of deterministic formulas and compare it with the accuracy of prediction of genomic breeding values in the simulated study.

Four deterministic formulas including Daetwyler et al formula, Goddard formula, Goddard et al formula and Rabier et al formula were used to predict the accuracy of genomic evaluation in different genetic architectures including different levels for heritability, reference population size and number of independent chromosome segments. The ShinyGPAS program was used to compare and plot the accuracy of prediction. In order to compare the performance of deterministic formulas with the accuracy of predictions in the simulated population, population simulations were performed using QMSIM software. For this purpose, in genome simulation, three levels of heritability of 0.1, 0.3 and 0.5 and two levels of reference population size of 1000 and 2000 individuals were considered and estimation of genomic breeding values was performed using Bayesian method A and Bayesian B using BGLR package in R medium

In low heritability, the highest prediction accuracy was observed in Goddard formula, which had the closest prediction accuracy (0.56) to the accuracy of genomic evaluation of simulated data estimated by Bayes A method (0.56). With moderate heritability (0.3), Goddard (0.74) and Rabier et al. (0.73) had the closest and most similarity to the accuracy of the simulated data. With population size increased from 1000 to 2000 individuals along with increasing heritability, the performance of deterministic formulas was closer to the accuracy estimated from simulation data by Bayesian methods and the most agreement was obtained in Goddard and Rabier methods. In the lower independent chromosome segments, the highest accuracy obtained by Rabier et al (0.860). With increasing chromosomal independent segments, the highest value of accuracy obtained by Goddard predictive formula.

The results showed that deterministic formulas have a good ability to predict the accuracy of genomic evaluation and their performance is linked to the genetic architecture. The results suggest that the predictions of accuracy, in general, using Goddard and Rabier formulas are more consistent with genomic estimation accuracy in the simulated data.

The bias in the selection of superior animals and accurate prediction of hereditary values of animal offspring selected in future generations is one of the important topics of breeding; therefore, the study of oblique trends in successive generations can be effective in the method of unbiased selective animals in the future. The statistical distribution of the effects of single nucleotide markers can be different in different traits and occupy a range from the normal distribution to the gamma distribution; therefore, the study of the amount of bias caused by pre-selection for different traits can be different according to their genetic structure. The purpose of this study was to investigate the effect of statistical distribution of the effects of SNPs on the biased process of estimating breeding values resulting from pre-selection of animals by genomic selection method. The statistical distributions studied included two distributions of normal and gamma, the biased trend of each of which was studied during consecutive generations. The bias criterion includes the regression of actual correction values on the estimated correction values. Initial Simulation and historical population in the form of two selection scenarios in three different traits with different heritability in 10 consecutive generations by two selection scenarios of 10% and 50% and the number of three QTL species were simulated accurately to estimate genomic breeding values using QMSim software. The need for calculations was analyzed using R software. The regression of TBVs on their GEBVs in the first generation whose genotyping was random was about one and unbiased; But by making choices based on superior breeding values from the second generation onwards it created a bias. As the number of consecutive selection generations increases so does the amount of bias but the rate of change in this bias decreased dramatically after the second generation and remained almost constant in the fourth generation which could be due to a reduction in genetic and phenotypic variance as a result of continuous selection known as the Bolmer effect. The results showed that in both statistical distributions, the amount and intensity of bias and its trend are almost the same and the difference in the statistical distribution of effects will not cause a difference in the amount and trend of bias. Moreover, due to the stabilization of the amount of bias in the 4th generation onwards, it is possible to correct the amount of bias from the 4th generation onwards by using a scale corrector.

Ascites syndrome is one of the most important causes of death in the poultry industry, in which various tissues of the body, including the kidneys, are involved. This syndrome occurs with different frequencies in males and females, and different mechanisms of ascites in the two sexes have not been studied to date. In this study, the gene expression profile of kidney tissue of male and female chickens with ascites syndrome from the paternal line (B) of the Arian commercial line was compared using RNA-Seq data. Due to severe cold stress applied, the mortality rate was high and about 59%, which was higher in males (63.4%) than females (54.1%). The results of transcriptome analysis showed that 240 genes were significantly different in comparison between ascites male and female birds. The annotation analysis of these genes showed that the metabolic pathways of antibiotic biosynthesis and amino acids, carbon metabolism, cell adhesion, receptor-extracellular matrix interaction (ECM) were involved in this process. The body's response to ascites-induced damage to kidney tissue is the development of renal fibrosis (to repair the damage) and reduced activity of the glycolysis pathways and increased gluconeogenesis to reduce energy and oxygen consumption in these pathways. Furthermore, an increase of the STAT-JAK2 signaling pathway activity (due to the high expression of JAK2 and STAT3 genes) was observed. This signal stimulates cell growth, angiogenesis, differentiation, migration, and apoptosis. It is expected that the results of the present study to provide new insights into understanding the molecular mechanism of ascites incidence and also differences in its occurrence in males compared to female broiler chickens.

Chicken major histocompatibility complex region (MHC) is important in the productive traits, immune responses, resistance to infectious diseases and phylogenetic relationships.

This study was investigated for single nucleotide polymorphisms of MHC region related to the immune system in commercial broiler and layer chickens.

One hundred blood samples were taken from commercial broiler and layer chickens and genomic DNA was extracted by salting out method. The allelic polymorphisms were investigated in B-L, B-F and B-G loci using PCR-RFLP and MspI enzyme.

For two commercial broiler and laying populations, in the 374 bp locus of B-L, only BB genotype was detected but in the 1048 bp locus of B-F, two genotypes of CG and GG were identified in broiler chickens. The C allele contained four bands of 515, 410, 75 and 47 bp, and the G allele with five bands of 410, 302, 213, 75 and 47 bp. In B-G (401 bp) locus, three genotypes of MM, MN and NN and two alleles of M with one band (401 bp) and N with two bands (350 and 51 bp) were identified. In total populations, the Shannon information index was calculated to be 0.45 and 0.73 in markers loci of B-F and B-G, and the fixation index values were -0.20 and 0.34, respectively. The highest observed heterozygosity index for B-F and B-G loci was 0.34 and 0.23, respectively.

Considering the confirmation of the presence of polymorphism in two loci of the B-F (in commercial broiler population) and B-G (in commercial broiler and layer populations), these sites can be used as genetic marker in breeding programs to increase resistance to diseases.

 Chicken major histocompatibility complex (MHC) region are important in immune responses, resistance to diseases, and relationships with evolution processes. The chicken major histocompatibility complex is composed of two gene regions: the B and Y (Rfp-Y) loci, both located on micro chromosome 16. The B locus includes three gene classes, I (B-F), II (B-L) and IV (B-G). The chicken major histocompatibility complex, consists of several clusters of highly polymorphic genes, some of which are associated with disease resistance. The class I and class II antigens resemble their mammalian counterparts in the encoded protein structure. The class IV region encodes the B blood group antigens, which are readily identified by serological blood-typing. The class III region appears to be divided in chickens, with some elements that are MHC-linked and others that map elsewhere. In addition the Rfp-Y system, which bears a strong similarity to the MHC, maps to the opposite side of the nucleolar organizer region on the same micro chromosome as the MHC. Each class of MHC genes is a potential candidate for a role in disease resistance. The MHC genes show associations with response to diseases as diverse as virally induced neoplasia, bacterial, parasitic and auto-immune diseases.

 In this study, allelic polymorphism in B-L, B-F and B-G loci involved in the immune system in four Iranian indigenous chickens were examined using PCR-RFLP technique. Two hundred birds including common, West Azerbaijan, Marandi, Mazandarani indigenous chicken breeds were selected. As much as 1-2 ml of blood was taken from each of the chicken. Blood samples were transferred to the anticoagulant (Ethylene diamine tetra acetic acid) tubes in the vicinity of the ice to the genetic and biotechnological laboratory of Islamic Azad University, Maragheh branch and until the onset of genomic DNA extraction and subsequent experiments were kept at -20°C. In the extraction of the genomic DNA of blood samples, the salting out method and for amplify of each locus, a pair of specific primers was used. For detection of mutation in the loci the Msp I enzyme was used. For genetic analysis of data derived from digestive enzymes in indigenous chickens, POPGENE software version 1.32 was used. This software is used to estimate the allele and genotypic frequencies, observed and expected heterozygosity, mean heterozygosity, Hardy-Weinberg equilibrium, Fixation index, Shannon information index, and other genetic parameters.

 According to this study results, in the 374-bp locus of B-L, after enzymatic digestion, only BB genotype and monomorphic was detected. In the 1048 bp locus of B-F, two genotypes CG and GG were identified and the C allele included 515, 410, 75 and 47 bp bands, and the G allele also included bands of 410, 302, 213, 75 and 47 bp and the χ2 calculated in this locus was not significant for all populations (P < 0.05), and all populations were in Hardy-Weinberg equilibrium. Three Genotype MM, MN and NN genotypes were identified for the locus of B-G (401 bp), M allele included a 401 bp band and N allele included bands of 350 and 51 bp. The χ2 calculated in this locus was not significant for the indigenous chicken population of Mazandarani (P < 0.05) and this population was in Hardy-Weinberg equilibrium. The Shannon information index was calculated to be 0.37 and 0.59 in markers loci of B-F and B-G, respectively, and the fixation index values were -0.13 and -0.17, respectively. The highest observed heterozygosity index for B-L and B-G loci was 0.24 and 0.57, respectively. Estimation of the negative fixation index values in the studied chickens populations could be due to the high selection rate in the populations. The fixation index values is always variable in range -1 to 1, and its negativity indicates a decrease in heterozygosity and increase in homozygosity or increased inbreeding, as well as a deviation from the Hardy-Weinberg equilibrium in the populations. Shannon's information index is an estimate of genetic diversity in populations. In all of the populations studied, the B-G locus has a relatively high genetic diversity.

 Regarding the polymorphism in the two gene sites (B-F and B-G) studied and the heterozygosity reduction in the populations studied, can be prevented from occurrence of non-random crosses in populations and prevented the reduction of heterozygosity and thus reduced genetic diversity. Also, by studying the immune responses associated with these two gene sites, from these genes can be used as marker for genetic breeding in indigenous chickens for increase of resistance to diseases.

Chicken major histocompatibility complex region (MHC) is important in the productive traits, immune responses, resistance to infectious diseases and phylogenetic relationships.

This study was investigated for single nucleotide polymorphisms of MHC region related to the immune system in commercial broiler and layer chickens.

One hundred blood samples were taken from commercial broiler and layer chickens and genomic DNA was extracted by salting out method. The allelic polymorphisms were investigated in B-L, B-F and B-G loci using PCR-RFLP and MspI enzyme.

For two commercial broiler and laying populations, in the 374 bp locus of B-L, only BB genotype was detected but in the 1048 bp locus of B-F, two genotypes of CG and GG were identified in broiler chickens. The C allele contained four bands of 515, 410, 75 and 47 bp, and the G allele with five bands of 410, 302, 213, 75 and 47 bp. In B-G (401 bp) locus, three genotypes of MM, MN and NN and two alleles of M with one band (401 bp) and N with two bands (350 and 51 bp) were identified. In total populations, the Shannon information index was calculated to be 0.45 and 0.73 in markers loci of B-F and B-G, and the fixation index values were -0.20 and 0.34, respectively. The highest observed heterozygosity index for B-F and B-G loci was 0.34 and 0.23, respectively.

Considering the confirmation of the presence of polymorphism in two loci of the B-F (in commercial broiler population) and B-G (in commercial broiler and layer populations), these sites can be used as genetic marker in breeding programs to increase resistance to diseases.

Baluchi sheep is one ofthe indigenous sheep breeds originating from the eastern part of Iran and it isadapted to the severe weather conditions. The economic efficiency of sheepbreeding is clearly related to the reproduction efficiency of the ewes. In thisstudy, twinning trait was studied as an important reproductive trait. Toidentify the genes associated with twinning trait, genome-wide association wasdone using 91 Baluchi ewes genotyped with 50k Illumina SNP chips. For thispurpose, the extended repeatability model was used. In the next step, a geneset enrichment analysis was implemented to identify the biological pathwaysassociated with the twinning. Six SNP markers on chromosomes 1, 3, 10, 15 and25 located in CTH, ANKRD13C, SRSF11, PTGER3, LDHB, LRRC40, and KCNMA1 geneswere identified. According to pathway analysis, 25 pathways were associatedwith the twinning trait. Among those pathways, the defense response biologicalpathway has an important role in the ovulation. Interferons and interleukinsare the main cytokine proteins in this pathway. These cytokines create aprocess such as inflammation that causes oocytes releasefrom the follicle into the oviductfor transport and fertilization. Cell adhesion andintercellular bridge pathways were other significant pathways. Cell junction pathwayvia the CX43 protein can affect the transfer of GDF9 effects togranulosa cells. To the best of our knowledge, this is the first study thatreports indirect effects of GDF9 on twinning trait in Iranian sheep.

Genetic resistance to diseases is very important in chickens. Determining the genetic diversity of the chicken immune system is one of the main options for examining differences in resistance to diseases. Two hundred blood samples were taken from indigenous chickens populations of Common, West Azarbaijan, Marandi and Mazandarani and genomic DNA was extracted by salting out method. The allelic polymorphisms were investigated in IgL and IFNɣ loci involved in the immune system using PCR-RFLP and the Sau96I and Tsp509I enzymes. After enzymatic digestion, for IgL marker site (354 bp), three genotypes of AA, AB and BB and allele A (with two bands of 173, 161 and two bands of 10 bp) and allele B (with three bands of 161, 103 and 70 and two bands of 10 bp) and for IFNγ marker site (129 bp), three genotypes of CC, CG, and GG and allele C (with one band of 129 bp) and allele G (with two bands of 90 and 39 bp) were identified. The total populations for loci were not in Hardy-Weinberg equilibrium. The Shannon information index for markers’ sites of IgL and IFNɣ (0.67 and 0.69, respectively), fixation index values (-0.24 and -0.18, respectively) and the highest observed heterozygosity index (0.61 and 0.59, respectively) was estimated. Regarding the presence of polymorphism in the studied loci, it is possible to use these candidate genes in selection programs to increase disease resistance.

The selection of useful mutations in some populations will leave footprints at the genome level. Because of the link between these regions and important economic traits, genomics is one of the important issues in animal genetic research. The aim of this research is to identify regions of the genome which carrier signature of selection in Kurd horse using 70kb SNP markers. 28 horses selected from the different area of Kurdistan and Kermanshah, after collected sample, DNA extracted, they were genotyping. To detect footprint of signal selection, extended haplotype homozygosity (EHH) and integrated Haplotype Score (iHS) was used. The using of iHS statistics, 9 genomic regions on chromosomes 5,7,11 and 15 as regions candidate of footprint selection, identified. For the detect effect of selection on this region, used of EHH as well as investigate of bifurcation diagram of haplotype and LD. In order to evaluate the possible genes and QTLs in selected candidate regions, used of the horse SNP databases (HSDB) and the QTL of the animals. The regions on 7 and 11 chromosomes were observed as candidate positive selection while in other regions (chromosomes 5 and 15), notwithstanding allele frequency, it wasn’t affected positive selection so these alleles were the common and old alleles. In these regions, a number of genes and QTLs were identified that are active in the muscle, immune system and intracellular activity. Therefore, these genomic regions of Kurd horse, probability were targeted positive selection.

I In this study, allelic polymorphism in candidate genes of TLR4 and IL2 involved in the immune system in four Iranian indigenous chickens were examined using PCR-RFLP technique. A total of 200 birds including common, West Azerbaijan, Marandi, Mazandarani indigenous chicken breeds were selected. For detection of mutation in TLR4 (257 bp) and IL2 (600 bp) genes the PCR products were digested by Sau96I and HphI restriction enzymes, respectively. Two alleles of C (138 and 119 bp) and G (119, 99 and 39 bp) and three genotypes of CC, CG and GG were identified in TLR4 marker site. Following the enzymatic digestion of the IL2 gene, two alleles of A (465, 64, 40 and 31bp) and B (454, 64, 40, 31 and 11 bp) and three genotypes of AA, AB and BB were identified. The whole populations was in Hardy-Weinberg equilibrium for TLR4 and IL2 marker sites. The calculated Shannon information index and fixation index values for TLR4 and IL2 marker sites was estimated to be (0.56 and 0.69) and (-0.05 and -0.10), respectively. The highest observed heterozygosity value for TLR4 and IL2 loci was estimated to be (0.55 and 0.40), respectively. Regarding to the existence of polymorphism in the studied loci and reduction of heterozygosity in these populations, the occurrence of non-random crosses can be prevented. This leads to an increase in heterozygosity and thus prevents the loss of genetic diversity in the populations would be. In the populations also, by studying the immune responses associated with these two loci, these sites can be used as suitable markers in breeding programs for increase of resistance to diseases in indigenous chickens.

In order to estimate genetic parameters and genetic trends of growth traits in Lori Bakhtiari sheep using structural equation models and standard multivariate models, pedigree and phenotypic data which were collected from 1994 to 2011 in Lori Bakhtiari sheep breeding station were used. The studied growth traits included birth weight (BW), average daily gain from birth to weaning (ADG1), weaning weight (WW), average daily gain from weaning to six-month weight (ADG2) and six-month weight (6MW). Three different models including standard multivariate model (SMM), multivariate temporal recursive model (TRM) and multivariate fully recursive model (FRM) were considered. Based on DIC values, TRM had the highest plausibility. Under TRM, structural coefficients between BW-ADG1, ADG1-WW, WW-ADG2 and ADG2-6MW were estimated to be 9.343, 0.03, 10.632 and 0.14, respectively. Direct heritability estimates for mentioned traits were 0.32-0.29, 0.2-0.22, 0.17-0.18, 0.11-0.11 and 0.16-0.16, respectively. The estimated values for genetic trends under SMM and TRM were 6-23, 0.7-3, 69-129, 0.4-1.2 and 110-187 grams per year for BW, ADG1, WW, ADG2 and 6MW, respectively. The results of genetic analyses of growth traits indicated the necessity of considering causal relationships between the studied traits for developing efficient breeding program in Lori Bakhtiari sheep

Selection not only increases the frequency of new-useful mutations but also remains some signals throughout the genome. Since these areas are often control economically important traits, identifying and tracking these areas is the most important issue in the animal genetics. The aim of this study was to detecting signals of selection in the genome of Turkmen horse using 70K SNP chip. Twenty-three Turkmen horses selected from different areas of Gonbad-e kavuos, were Blood sampled. Then DNA extracted genotyped. To detect footprint of signal selection, some tests based on linkage disequilibrium (LD) such as extended haplotype homozygosity(EHH) and integrated haplotype Score (iHS) was used. First to identify regions of the genome that included the most signals of selection, iHS statistics was used and accordingly 6 genomic regions which were in the 99.99% percentile of iHS values selected for further analysis. These regions were located in 6 areas on chromosomes 4,5,7,8,9 and 10. Results of EHH test with bifurcation diagram of haplotype, confirmed signals of selection in these areas. Based on the results of the EHH test, sharp decay of LD in some regions was observed (chromosomes 7, 9 and 10) while in other regions it wasn’t so significant (chromosomes 4,5 and 8). As studied alleles on chromosomes 4,5 and 8 had long range of LD and had frequency of, respectively, %43, %52 and %37, these regions of the genome of Turkmen horse most likely has been the target of positive selection.

This study was carried out for identification of deletions, insertions (INDELs) and assessment of their related functional groups in two Iranian dromedary camels (Yazdi camel and Trodi camel) using whole genome sequencing data. In this study, two powerful variant callers (GATK and SAMtools) were used to increase precision and accuracy of detected INDELs. Finally, common identified variants between two programs, after quality filtration, were considered as final INDELs. The present study led to identification of 351429 INDELs for Yazdi camel and 341479 INDELs for Trodi camel. Annotated INDELs that classified as high impact INDELs, were used for further analysis. The numbers of high impact INDELs were 3424 and 3506 for Yazdi and Trodi camels, respectively. To compare Iranian camels with non-Iranian camels, we used whole genome sequencing data of one African origin camel. Comparison of high impact INDELs between three samples showed that 1595 INDELs were common between them. Assessment of gene ontology’s results showed that many of significant terms are related to the ability of camels to withstand serve desert conditions.

In this study, allelic polymorphism in candidate genes of Mx and SLC11A1 involved in the immune system in some Iranian Common, West Azarbaijani, Marandi, Mazandarani indigenous and commercial chicken strains examined using PCR-RFLP technique. A total of 300 birds were selected and for detection of mutation in Mx and SLC11A1 genes the PCR products were digested by Hyp81 and SacI restriction enzymes, respectively. For the Mx gene, one fragment with length of 299 bp and two fragments with the length of 200 and 99 bp were identified for the A and G alleles respectively. One fragment with the length of 801 bp for T allele and two fragments with the length of 722 and 79 bp for C allele were identified in SLC11A1 gene. Between different groups of chickens, in the Mx and SLC11A1 genes, the most frequency of susceptible to disease alleles (G and C) were in the indigenous chicken strains and meat commercial chicken strain. In the Mx loci, Shannon's information index was in different groups of chicken from 0.1347 to 0.6641 and in the SLC11A1 loci was from 0.3669 to 0.6769. In the Mx loci, fixation index was positive for indigenous chickens group and in the SLC11A1 loci was negative for different groups of chickens. The results of this study indicate that these genes loci can be used as marker for genetic breeding to reduce the diseases of indigenous and commercial chicken strains.

The aim of the present study was to investigate allelic diversity in upstream regulatory region of calpastatin and calpain genes, bioinformatics analysis of studied genes and association of allelic variants with body weight and fat-tail traits in Lori-Bakhtiari sheep.
One hundred and fifty blood samples were collected randomly and DNA was extracted by modified salting out method. The specific primer pairs were designed using Oligo 7 software for amplification of fragments with lengths of 245 and 225 bp from upstream regulatory region of calpastatin and calpain genes, respectively. After PCR, the amplified products of calpastatin and calpain marker sites were subjected to endonuclease digestion with PstI and HaeIII enzymes, respectively. Due to the monomorphic of RFLP results, the SSCP technique was used for more accurate assessment of amplified fragments. After genotyping, one sample from each banding patterns of calpain gene was sequenced. The obtained sequences were investigated for identification of motifs involved in gene regulation and also mutations in different banding patterns by DNASIS MAX and BioEdit softwares. Association between observed banding patterns and body weight traits at birth, 3, 6 and 12 months of age and weight, upper bound, lower bound and the height of fat-tail was investigated by Glimmix procedure of SAS (version 9.1) software.
Three banding patterns of A, B, and C with frequencies of 66, 9, and 25% were observed in Lori-Bakhtiari samples, respectively. The upstream region of calpastatine gene was monomorph in present study. Statistical analysis showed significant association between banding patterns of calpain marker site and body weight at birth in Lori-Bakhtiari sheep (P According to the polymorphic pattern in upstream regulatory region of calpain locus and its significant association with birth weight, this marker site may be used in breeding programs to improve meat quality in sheep.

Meat quality and carcass composition are the most important economic traits in sheep. Body fat and fat-tail are key factors affecting carcass quality and meat production in each breed, and mutations in sequences of the genes that control these traits can affect the animal performance and therefore the breeding value. The aim of this study was to investigate the polymorphism in some regions of SAR1B, SEC24A and VDAC1 genes in candidate genomic regions for fat traits on ovine chromosome 5. Blood samples were collected randomly from 300 Lori-Bakhtiari and 100 Mazandaran sheep and DNA was extracted using modified salting out method. Polymerase chain reaction (PCR) was performed for amplification of 478, 579 and 348 bp fragments of studied genes using specific primer pairs and genotyping of samples was done by SSCP technique. The obtained results showed three banding patterns of A, B and C for SAR1B marker site in Lori-Bakhtiari sheep but it was monomorph in Zel sheep. For SEC24 gene, three banding patterns of A, B and C were observed in both sheep breeds, but VDAC1 was monomorph in both sheep breed. The effect of banding patterns of SAR1B gene on fat-tail characteristics were significant (P

This study was carried out to identify polymorphisms of BMP15, GDF9 and BMPRIB genes in cross- bred of Romanov×shal sheep. For this reason 79 blood samples were collected from a flock in Gonbad kavous city in Golestan province. DNA was extracted using modified salting out method. Polymerase chain reaction was done by specific primers for amplification of two fragments with 141and 153 bp from exon 2 of BMP15, one fragment with 190 bp from BMPR-IB gene and two fragment with 462 bp, 139bp from exon 1and 2 of GDF9 genes, respectively. The results obtained from digested PCR products did not confirm the existence of mutation in BMp15, BMPR-1B and in exon 2 of GDF9 marker site. While, polymorphism was observed in exon 1 of GDF9 marker site and the heterozygotes were estimated as 0.11 in this population.

Introduction The accumulation of improperly folded forms of host-encoded cellular prion protein (PrPc) in the central nervous system (CNS) lead to a fatal neurodegenerative disease in sheep and goats, namely Scrapie. The application of genetic breeding programs to eradicate transmissible spongiform encephalopathies in goats is an important aim for reasons of animal welfare as well as human food safety and food security. Scrapie and scrapie-like diseases are associated with polymorphisms and mutations of the gene coding for PrP, a host neuronal membrane glycoprotein which is found in an aggregated form (scrapie-associated fibrils) in extracts of brain tissues from all mammals affected by these diseases. The different allelic forms of PrP gene have been shown to make animals variably susceptible to this disease. It has been established that presence of abnormal forms of the prion protein (PrP) is associated with scrapie. Several amino acid polymorphisms caprine PrP encoding genes have been reported to be associated with scrapie susceptibility. Sheep exposed to Scrapie have been shown to gain highest scrapie resistance in the presence of Q171R polymorphism and maximum scrapie susceptibility in the presence of A136V polymorphism. Based on A136V, R154H and Q171R/H polymorphisms and their five alleles (ARQ, VRQ, AHQ, ARR and ARH) sheep and goats can be classified into five groups (R1-R5). The most resistant genotype (R1) is ARR/ARR and the most susceptible genotypes (R5) are VRQ/VRQ, VRQ/ARQ, VRQ/ARH and VRQ/AHQ. Additionally, other caprine PrP polymorphisms I142M, H143R, N146S/D, R154H, R211Q and Q222K have been shown to be associated with low scrapie risk. Although scrapie is an animal health issue, its presence has not been investigated in Iranian goat breeds, where sheep and goats are major livestock species. Based on the positive impact of PrP genetics on sheep scrapie in Europe in the past decade, we have established caprine PrP gene variation in 120 Naeinian goats from the Isfahan, Iran to evaluation of genetic variation in this important region of PrP gene.
Material and Methods The DNA was extracted from 120 blood samples of Naeinian goats from Isfahan province using modified salting out method. After amplification of the desired fragment by polymerase chain reaction (PCR), genotyping of samples was carried out by PCR-SSCP Analysis (Single-Strand conformation Polymorphism). In the following, direct sequencing method was used to confirm the genotyping results. Obtained sequences were analyzed by Chromas Pro and BioEdit. In order to evaluate the amino acid polymorphisms caprine PrP encoding gene was used from Expasy server site. In addition, to evaluate the Hardy-Weinberg equilibrium, we used the chi square test in SAS 9.1 software. All statistical tests were considered significant with a level of P≤0.05.
Results and Discussion The results of the present study showed that nine binding patterns were observed at PrP locus in studied goat population. The results of direct sequencing were confirmed the PCR-SSCP analysis results. Genetic analysis on protein sequences revealed an amino acid polymorphism in codon 186 (T- M or K) and two silent polymorphisms in codons 138 and 143. Based on codons 136, 154 and 171, all goats showed ARQ haplotype and there is no variation in these three codons. Additionally, the results of Hardy-Weinberg test confirmed that this population was not compatible with the HWE (P Material and The DNA was extracted from 120 blood samples of Naeinian goats from Esfahan province using modified salting out method. After amplification of the desired fragment by polymerase chain reaction (PCR), genotyping of samples was carried out by PCR-SSCP Analysis. In the following, direct sequencing method was used to confirm the genotyping results. Then, obtained sequences were analyzed by bioinformatics softwars, for example, Chromas Pro, BioEdit. In order to evaluation of amino acid polymorphisms caprine PrP encoding gene was used from Expasy server site.
The results of the present study showed that nine binding patterns were observed at PrP locus in studied goat population. The results of direct sequencing was confirmed the PCR-SSCP analysis results. Genetic analysis revealed an amino acid polymorphism in codon 186 (T- M or K) and two silent polymorphism in codons 138 and 143.
it is noticed that all of polymorphisms in exon 3 of PrP gene are important and can be used to improve the breeding programs. According to three codon system (codons 136, 154 and 171), all of the studied goats had shown ARQ haplotype which offer Naeinian goats were classified in low resistance group (R3).

Scrapie or transmissible spongiform encephalopathy (TSE), is an infectious fatal disease of sheep and goats which affects the central nervous system. In the present study, 300 blood samples were collected from three breeds of Iranian indigenous Ghezel, Harki and Makoei sheep breeds. A DNA fragment with the length of 173 bp from exon 3 of PrP gene was amplified with specific primer pairs. The banding pattern of each sample in the study population was identified by means of PCR-SSCP. Then, after sequencing, comparison and analysis of the observed polymorphism between different breeds were performed at codons: 136, 154 and 171. In the present study, tow haplotypes of ARR and ARQ were identified and the wild type scrapie-susceptible ARQ was the most frequent haplotype. In this study more than 98% of animals were with the genotype ARQ/ARQ which was classified as low resistance to this disease.
Three novel alleles (L178, E147and L173) were observed for the first time in this study. The comparison of genotype frequency between Makoei-Ghezel and Makoei-Harki sheep breeds were statistically signi ficant (P

In comparison to traditional breeding methods, using genomic information causes considerable increase in response for selecting young animals which have no phenotypic records. Genomic selection refers to selection based on estimated breeding value (BV). The purpose of this study was to survey the effects of heritability of trait and the numbers of QTL on accuracy of estimating genomic BVs. For this reason, genome design and required population was done by computer simulation. The results of the effects of trait heritability on the accuracy of genomic BV estimation showed that the accuracy of genomic BV estimation of reference group via three strategies of trait heritability 0.05, 0.1 and 0.25 were 0.790, 0.827 and 0.876, respectively. Therefore, increasing the level of trait heritability increased the accuracy of estimated BV. In strategies for numbers of 4, 10, 20 and 40 simulated QTLs (in each chromosome) through the genome, the calculated accuracy in reference group was 0.813, 0.833, 0.826 and 0.798, respectively. Totally, with increasing the simulated QTL, the range of alterations of the accuracy was not significant. Also, the alterations of accuracy along the consecutive generations from 51 to 57 generation had a decreasing trend in all four strategies.

Avian influenza is a contagious viral disease affecting the respiratory, digestive and nervous system of birds belong to orthomyxovirus family. In the chicken Mx gene, type of amino acid at position 631 determines the antiviral activity against influenza and vesicular stomatitis virus. A single nucleotide polymorphism (SNP) at position 2032, responsible for the variation of amino acid at position 631 (Ser to Asn) of the Mx protein, has been demonstrated to be responsible for positive or negative antiviral activity of Mx proteins., The allele A and G at position 2032 corresponds to the positive and negative antiviral activity, respectively. In order to identify gene polymorphism at Mx locus, 250 blood samples randomly were collected from Sari, Shiraz, Mashhad native fowls breeding station, commercial broiler and layer flocks. DNA was extracted and a fragment with the length of 299 bp from the exon 13 of Mx locus was amplified by a specific primer pairs. PCR-RFLP method was used to identify of polymorphism in coding sequence of the Mx gene using Hpy8I restriction enzyme. The frequency of alleles were estimated A (0.692) and G (0.308) in Sari, A (0.577) and G (0.423) in Shiraz, A (0.604) and G (0.396) in Mashhad, A (0.46) and G (0.54) in commercial broiler and A (0.86) and G (0.14) in layer strain, repectively. According to the observed polymorphism at position 631 of Mx protein and its important role in susceptibility to influenza disease it may be possible to use this marker gene in breeding programs.