Sperm sexing is one of the important ways for sex preselection of offspring that with artificial insemination has the potential to considerably improve animal breeding and the efficiency of dairy and meat production. The base of this method is discrepancies between X- and Y-chromosome bearing sperms. X- and Y-bearing sperm cells can be separated by methods such as flow-cytometric measurement of sperm DNA content. In this research, to validate the accuracy of sperm sexing, we aimed to develop a simple method based on FISH technique to enable us to differentiate between X- and Y-bearing sperms. In order to do that, we attempted to make a homemade FISH probe specific for pericentromeric repetitive DNA block on the bovine Y-chromosome (locus DYZI, Yp13-q12). For this purpose, Genomic DNA was extracted from lymphocyte cells of bull. The specific DYZI primers were used for the amplification of Y pericentromeric region. The PCR products were then labeled with biotin-16-dUTP in a secondary PCR reaction. The labeled PCR product was then purified and dissolved in a hybridization buffer and used as a FISH probe. The Y specific FISH probe hybridized on the male metaphase and interphone cells fixed with methanol: acetic acid on slide show strong signals. Totally, production of the first FISH probe in Iran for detection bovine Y-chromosome was a big success and can be used for future studies about sexing. Also the made FISH probe at this study and primers can be applied to determine sex and ploidy status in bovine cells such as individual blastomeres or cell lines.

The Y chromosome simple tandem repeats (STRs), residing out of the pseudoautosomal region, pass down through the father to the male offspring, represent suitable markers for evolutionary studies and tracing human migration through male lineage as well as paternity testing and forensic genetics. In this study the common Y chromosome STRs polymorphisms were investigated among 100 unrelated male individuals that were selected randomly from Tehran population; the sample can roughly (at least in providing a general profile of existing YSTR alleles and haplotypes) be a good representative of Iran's general population due to the mixed nature of the people living in Tehran. Using a PCR based approach, the polymorphisms of nine Y chromosome specific STR markers, including DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, and DYS393, were investigated. These markers are defined as the European Minimal Haplotypes (EMH). The PCR products were run on a 1.5% agarose gel, followed by polyacrylamide gel electrophoresis for further resolution as minor differences in repeat numbers might not be resolved by conventional agarose gel electrophoresis. Gene Diversity (GD), which is a measure of allelic polymorphism, calculated for each marker. DYS385 was shown to be the most polymorphic allele and DYS391 showed the lowest polymorphism in this study. Haplotypes Diversity (HD), calculated for assessment of haplotypes distributions, found to be over 0.999. This may warrant applying some of Y-STR markers possibly in forensics, paternity testing and also in comparative studies among different ethnic groups of Iran as well as for further application in global studies due to diversity of ethnic groups residing in Iran.

Background: Recurrent pregnancy loss is a form of infertility with at least three consecutive pregnancy losses or more. Y chromosome microdeletions are a class of most likely genetic factors that occur in a special zone of Y chromosome which is named azoospermia factor region. The purpose of this study was to analyze the presence of Y chromosome complete microdeletions in male partner of couples suffering from idiopathic recurrent pregnancy loss among Iranian population. Methods: In the present study، Y chromosome microdeletions were evaluated in ninety-two male partners of couples with the experience of recurrent pregnancy loss as the patient group and also a group containing fifty fertile males as the control group. The research has done in Medical Genetic laboratory of Tehran and Islamic Azad University Science and Research Branch، Tehran، Iran within June 2013 to September 2014. The selected sequence tagged site markers (primers) including sY84، sY86، for azoospermia factor a; sY127، sY134، sY129، for azoospermia factor b and sY254، sY255، for azoospermia factor c were used to screen complete microdeletions in Y chromosome. At the first step DNA samples were extracted from all men’ s peripheral blood in both patient and control groups and then multiplex polymerase chain reaction and also agarose gel electrophoresis were performed on this DNA samples so as to detect deletions. Results: With due attention to the data resulted from multiplex polymerase chain reaction and agarose gel electrophoresis in order to recognize Y chromosome micro deletions in azoospermia factor region، in this work، all the bands related to the mentioned primers which were formed during the polymerase chain reaction، were detected on the gel obviously. It means that none of the samples neither the fifty fertile men nor the ninety-two patient men had complete micro deletions in their Y chromosome. Conclusion: This study suggests that there is no correlation between Y chromosome micro deletions and occurrence of recurrent pregnancy loss in Iranian population.

Introduction: Among domesticated animals, the horse can be considered as one of the most influential animals in the process of human life modernization. Based on archaeological evidence, the presence of horses in Iran goes back to 3000 BC. Today, over 300 horses are recognized worldwide and a great number that is indigenous to Iran. The statistics provided by FAOSTAT indicate that there are about 140, 000 horses. Due to climate diversity in Iran, there are various horse breeds in different parts of the country, such as Turkmen, Kordi, Drehshuri, Arab, Sistani, Northwest native and Caspian horses. Study of variations in Y chromosome and mtDNA make it possible to the characterization of genetic diversity in the maternal and paternal lines, respectively. Despite the high diversity in the genome of mitochondria in horses, but variation in Y chromosome is in low level. Low variation in Y chromosome of horses can be due to small male effective population size and loss of variations due to bottleneck during domestication. Several studies on Chinese indigenous and European modern horses revealed that native horses have more Y chromosomal variation in compared with modern breeds. So, the aim of present study was an assessment of genetic diversity in paternal line of Iranian horses using Y chromosome. Identified the genetic structure is important for appropriate breeding programs. Material and Methods: Blood samples were collected from Jugular vein using 4 ml tubes containing EDTA (1 mg/ml) of 81 horse belonging to six different populations including Ardebil’ s stables horses (24 samples), Northwest horses (17 samples), Kordi horses (15 samples), Arab horses (10 samples), Darehshuri horses (10 samples) and Qarebagh horses (5 samples). Total genomic DNA was extracted from whole blood. A total of the 264-bp fragment (locus: Y-50869) of Y chromosome was amplified using a pair of 20-nucleotide primer (Genbank accession number: JX646950). Polymerase Chain Reaction (PCR) was carried out and then, products of PCR sequenced using Sanger sequencing method. Alignment of sequences was performed by MEGA 6. 0 software. Also, MEGA 6. 0 used for segregating sites identification and also phylogeny tree construction based on identified haplotypes. DnaSP5 was used to the estimation of haplotype diversity (Hd), nucleotide diversity (π ), genetic distance (Dxy) and an average number of differences (k). Finally, the median-joining network was generated using the Network 5 program to present the possible relationships among haplotypes. Results and Discussion: Alignment of sequences led to the identification of six segregating sites and consequently nine haplotypes based on Y chromosome sequences. Three haplotypes (H_1, H_2, and H_6) are widely distributed among under study samples, so that, 65 of 81 (more than 80 %) individuals have placed in three haplotypes. Among haplotypes with more than one individual, there is no special haplotype for any of breeds. Haplotype diversity values ranged from 0. 6 for Arab breed to 0. 86 for Kordi breed. The nucleotide diversity values ranged from 0. 00288 for Arab breed to 0. 01442 for the Qarebaghg breed. Average values for nucleotide diversity and haplotype diversity were 0. 0067 and 0. 81 respectively. Comparison of present results with the previous study on mtDNA diversity of Iranian horses revealed that maternal line of Iranian horses is more divers from paternal line. Among Iranian breeds, Dareshuri breed has the lowest nucleotide diversity 0. 00481 and haplotype diversity 0. 00481 and 0. 8 respectively. Assessment of genetic distance among breeds revealed that Ardebil and Qarebagh horses have the highest distance (0. 00822), while Arab and Dareshuri horses showed the lowest genetic distance (0. 00327). Obtained results indicated that, unlike Arab breed, Qarebagh horses had low influence in Iranian horses. Phylogeny tree based on haplotypes of Iranian horses showed that divided into two branches. Generally, 73 individual (90. 12% of all horses) and 8 individuals (9. 88% of all samples belongs to each of the two branches. Conclusion: The number of haplotypes which was found for Iranian native horses was placed among three haplogroups, which indicate moderate genetic variety and numerous maternal lines in native horses of Iran. It seems that the presence of the accurate pedigree information along genetic studies can help us to better categorize Iranian horses. In fact, to designing effective breeding strategies, we need to identify the precise genetic structure of Iranian horses. What we learned from this study was that Iranian horses in compared with European pure breeds are more diverse. Obtained results from this study showed that Stalions of Arab breed had high impact in Iranian horses.

Background & Aims: Infertility means that a couple does not become fertile after one year of sexual intercourse, which is faced by 10-15% of young couples, and in 50% of cases it is related to male defects. The spermatogenesis genes involved in male fertility are located in the proximal region of the long arm of the Y chromosome (Yq11) in the azoospermia factor region, which includes the AZFa, AZFb, and AZFc subunits. Microdeletion in AZF regions causes changes in testicular histology from Sertoli Cell Only Syndrome to hypospermatogenesis. Yq microdeletions are the most common molecular cause of male infertility and include three regions: AZFα, , AZFb and AZFc. These regions contain different genes involved in spermatogenesis. Yq microdeletions have been reported in 5-10% of infertile men and 6-16% of azoospermic men. In some other studies, the prevalence of these microdeletions has been reported in 20 to 30% of patients with non-obstructive azoospermia and in 3 to 7% of patients with severe idiopathic oligospermia. So far, ethnic patterns in the distribution of these microdeletions in the Iranian infertile male population have not been extensively studied. Accordingly, considering that Iran is a geographically vast country and has a high population / ethnic diversity, the present study aims to investigate the overall prevalence of these microdeletions in the population of Iranian infertile men and compare its frequency distribution in it was designed and implemented between different ethnicities. Methods: In this study 1887 infertile men with severe oligospermia or azoospermia were referred to the Royan Institute beween 1391 to 1392 were evaluated for the presence of Yq microdeletions. At first, DNA was extracted from the peripheral blood by salting out method and multiplex PCR was performed based on the determination of six different STS markers. To identify Yq microdeletions in three regions of AZFa, AZFb and AZFc, six STS markers were used inside two separate mixes. Two STS markers were considered for each AZF region and sY14 marker was used to examine the SRY gene and the ZFX / ZFY marker were used as internal controls. Information about semen analysis (Spermogram) and the results of patients' hormonal tests for the three hormones LH, FSH and testosterone were also extracted from their files. The ethnic segregation and classification of the Iranian male population was based on latest version of the Encyclopaedia Britannica (2010) book from the Statistics Center of Iran. Accordingly, the men studied in this study were classified into the ethnicities mentioned in the Table 1. For the appointment of ethnicity in each of the men under this study, the place of birth and dialect of three consecutive generations of clients were determined and then were placed in one of the seven ethnic groups including Fars, Azeri (Turkish), Kurdish, Lor, Gilak/ Mazeni (northern), Arabic And non-Iranians (Afghans and Iraqis). Results: Among the 1887 studied infertile men, 100 were diagnosed with microdeletions (5. 29%), 69 patients (68. 3%) had azoospermia and 31 patients (30. 6%) had severe oligospermia. Among men with microdeletions, 70% had deletion in AZFc, 25. 4% had deletion in AZFb and 4. 6% had deletion in AZFa. Combined deletions of AZFbc were observed in 18 patients and AZFabc in three patients. All men with AZFa, AZFb, AZFc, AZFbc, and AZFabc regions had non-obstructive azoospermia, and only men with AZFc and AZFb microdeletions showed evidence of sperm production. Among the patients with microdeletions, 47 patients (46. 5%) had normal hormone levels, 22 patients (21. 7%) had higher than normal levels of FSH, two patients had high levels of LH and 14 patients (13. 8%) had high levels of both LH and FSH. The results of hormonal tests were not available in 16 of them. Ethnic distribution in 100 patients showed that 38% were Azeri, 30% Persian, 11% Kurdish, 8% Lor, 6% Gilak/ Mazani, 2% Arab and 5% Iraqi and Afghan nationals. The results of chi-square test showed that the distribution of different Y chromosome microdeletions is not uniform among Iranian ethnicities (p <0. 001). Conclusion: Ethnic and racial differences can also be influential factors in the prevalence of these microdeletions, which we examined in the present study. Such a complete study of Iranian ethnicities has not been done before, and in other parts of the world, studies have not usually been aimed at comparing ethnicities. The overall frequency and distribution pattern of Yq microdeletions in the population of Iranian infertile men is similar to other populations in the world. The pattern of distribution of different microdeletions among different Iranian ethnicities seems to be similar. This means that in all ethnicities that accounted for a significant number of deletion patients (Turks, Fars, and Kurds), Yq microdeletions were most common in the AZFc region. After that, AZFb and AZFa were more frequent, respectively. In fact, ethnicity did not have a significant effect on the distribution of these microdeletions and no significant results were observed in this regard. Regarding the frequency of different microdeletions (frequency of distribution) in various Iranian ethnicities, considering that the number of samples of some microdeletions in some ethnicities was less than the amount required for statistical analysis, the number of people studied in each ethnicity has been adjusted. Statistical analysis of these results using chi-square test showed that the frequency of microdeletions in ethnicities is not uniform (p <0. 001), therefore, the ethnicity of the Iranian infertile man is influential in the frequency of distribution of these microdeletions. However, due to the insufficient number of people with microdeletions in some ethnicities, it is not possible to determine with sufficient statistical accuracy which microdeletions occurs more frequently in which ethnicity. In this regard, it seems that the referral of Royan Infertility Treatment Center and the existence of infertility treatment centers in the centers of some provinces have affected the ethnic composition of the client. Therefore, it is suggested that in future and supplementary studies, in order to create an appropriate ethnic distribution in the referring population, while increasing the sample size (especially for some ethnicities) if possible with the cooperation of infertility treatment centers in other provinces, comprehensive studies in this regard be used to achieve a more definite result in this regard.