جستجوی مقالات مرتبط با کلیدواژه « genetic diversity » در نشریات گروه « علوم دام »

DNA Mitochondria is one of the most commonly molecular markers for phylogenetic studies in animals due to its simple genome structure, which presents an ideal model to study evolution and genetic similarity. The aim of the present study was to investigate the divergence and percentage of genetic similarity along with the phylogenetic analysis of the eight species of wild and domestic goat based on the complete sequence of the mitochondrial genome and the separate sequences of 13 protein-coding genes for each genome.

In the present study, complete mitochondrial genome sequences along with separate sequences of 13 protein-coding genes per each genome from seven wild species of goat including Markhor (C. falcoeri), Capra ibex, Capra nubiana, Capra pyrenaica, Capra sibirica, Capra caucasica, Capra aegagrus, and domesticated species of goat (Capra hircus) were retrieved from NCBI database and compared to each other. Mitochondrial genomes and genes alignment were accomplished by the MegAlign module of DNASTAR software and compared by the Clustal W method. The Sequence Distances sub-section of the MegAlign module of DNASTAR also was used for the analysis of complete genome and gene sequences divergence and similarity percentage. For phylogenetic analysis, complete mitochondrial genomes and protein-coding genes’ sequences were aligned using MEGA7 software.

Based on the analysis, it was found that the highest similarity between the nucleotide sequences of the complete genome (99.50) of domestic goat (Capra hircus) and wild Capra aegagrus goat and the lowest percentage of similarity (93.79) between the nucleotide sequences of the complete genome of the breed Capra nubiana) with wild goat Capra sibirica goat. Also, based on the results of the phylogenetic tree, it was found that domestic goat breeds (Capra hircus) and wild Capra aegagrus goat are divided into one group and wild Capra ibex and Capra pyrenaica breeds are divided into another distinct cluster.

In this study, all the results obtained from complete sequences of the mitochondrial genome analysis are consistent with the results obtained from the sequence of 13 protein coding genes per each genome, which indicates the correct clustering of wild and domestic goat breeds. Therefore, mitochondrial genome sequences could be used as a suitable genetic marker for accurate phylogenetic analysis and clustering of different species of sheep.

The selection of animals by humans left detectable signatures on the genome of modern goat. The identification of these signals can help us to improve the genetic characteristics of economically important traits in goat. Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Run of homozygosity one of the most methods were used to detecting the genomic inbreeding. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. As detecting the ROH Islands, the genomic regions contain economic traits could be detectable.

In this research, the amount of genomic inbreeding and the effective size of the population were investigated using the information obtained from 879 goats of different breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. In order to determine the genotype of the samples, Illumina caprine Bead Chip 50K were used. The genomic information of goat breeds was extracted from the figshare database. Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-3. After quality control, 36,861 SNPs from Goat SNP chip 50K on 827 goats were remained for the future analysis. Inbreeding coefficient was calculated using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using the GCTA 1.0 software and run of homozygosity (FROH) using the PLINK 1.9 software. The effective population size (Ne) was calculated from linkage disequilibrium data with SNeP software (version 1.1). GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.

The lowest and highest inbreeding coefficient calculated by three methods (FGRM, FHOM, and FUNI) were related to Beetal and Barbari breed, respectively. The highest (0.159) and lowest (0.028) amount of FROH was estimated in the Barbari and Pothwari breeds, respectively. The average length of ROH ranged from 70.2 to 391.4 Mb, and the average number of ROH fragments varied between 8.19 and 48.65. Also, the highest and lowest number of ROH were observed on chromosome 2 and 29, respectively. The size of Ne in in the current generations (fifth generation) of the studied breeds was ranged from 35 to 365. The highest Ne was estimated in the Beetal breed (365 heads) and the lowest in the Barbari breed (35 heads). The average inbreeding coefficient in Beetal, Teddi, Pahari, Nachi, Barbari, Daira Deen Panah and Pothwari breeds was obtained 0.035, 0.081, 0.031, 0.052, 0.15, 0.11 and 0.02, respectively. In addition, the Ne of most of the studied populations has been decreased. The results of this study revealed that, the selection processes in different goat breeds for economic traits during several years, has led to the formation of many ROH islands in goat genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits.

our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for study goat breeds. Therefore, it is necessary to economize production and planning a suitable mating scheme to control inbreeding and genetically conserve the remaining pure animals of these breeds.

Investigation of mitochondrial genome sequence of cytochrome-b region within population can be a good indicator for diversity in the studied population. A recent study was conducted to investigate the genetic diversity in Kurdish horses and phylogenetic relationship of between Kurdish horse with other horse breeds in the world using cytochrome-b region. Blood samples were collected from 30 Kurdish horses and total DNA was extracted by modified salting out method. Cytochrome-b sequences were amplified by primers pairs with 1029 bp length and then were sequenced after purifying. The sequences were trimmed to 882 bp using BioEdit software. The samples were aligned with the horse reference sequence with access number (X79547) using Clustal-W package. Haplotype and polymorphic site numbers, Haplotype and nucleotide diversity were estimated using DNASP4 software. Phylogenetic tree was constructed in MEGA7 software by neighbor joining method. 7 haplotypes with 7 polymorphic site were identified. Whole haplotypes were belonged to K haplogroup. Haplotype and nucleotide diversities were 0.784±0.001 and 0.00218±0.001, respectively. The compositional frequency of consensus sequences was including: A base, 21.27%; C base, 32.77%; G base, 13.15% and T base, 26.87%. According to the phylogenetic analysis, Kurdish horses were genetically more closely related to Japanese and Chinese breeds and one Polish and Saudi Arabian breeds which shows that Kurdish horse has genetic similarities with Asian and some European horse breeds.

In this study, genomic data of 590 cattle were used including native breeds of Sarabi, Kermani, Kurdi, Talashi, Sistani, Najdi, Mazandarani and Pars, crossbred from northwest of Iran, Holstein populations from Iran, France and Ireland. Quality control and data filtration were performed using Plink 1.9 software. After this quality control, individuals and SNPs with call rate below 0.95%, SNP makers with minor allele frequency (MAF) > 0.01%, divergence from Hardy-Weinberg Equilibrium were excluded. This procedure yielded 509 individuals with 13512 SNP marker. Then filtered data were used to genetic diversity and clustering analysis. Identification of genetic groups were performed using PCA analysis data by GenABEL software. PCA and ADMIXTURE analysis showed that studied populations are in 4 separate categories including purebred Sarabi population in the first group, crossbred from northwest of Iran in the second group, purebred Holstein populations in the third group and native breeds of Iran were in the fourth group. Further details of demographic differentiation were identified by Weir and Cockerham's fixation index. The range of differentiation in the present study varied from 0.180 between Sistani and Kurdish breeds to 0.007 to 0.004 between the Iran Holstein breed and Ireland with France Holstein breeds. The results showed that the highest difference between indigenous and Holstein breeds related to Sistani breed that had the highest difference with different Holstein breeds (0.128 to 0.138). With slight differences from other Iranian indigenous breeds, the Kurdish and Mazandaran breeds had the smallest genetic differences with the studied Holstein populations.

Horse has been of great interest to humans due to its speed, strength, and endurance. Based on its role in human history and civilization, it is considered the most important domesticated animal. Iranian horse breeds are bred in the north, south, and west regions of the country. Arabian horse is one of the international breeds in the world, which is bred in more than 60 countries. Preliminary evidence shows that the Arabian horse breed was established about 3000 years ago and was bred in small populations in many countries of the Middle East, including Egypt, Iran, Saudi Arabia, and Syria. These separate populations have led to the development of different maternal strains of the Arabian horse. Genetic diversity is necessary for genetic conservation and survival of the breeds. Molecular markers are used to assess the structure and genetic diversity of different populations. Therefore, one of the suitable markers is a microsatellite. Regarding the importance of genetic diversity in the survival of the breed, and designing the genetic conservation and breeding programs, the purpose of this study was to investigate the population structure and genetic diversity of Arabian horse breeds using microsatellite markers.
In this study, hair root samples were obtained from 8673 (5602 mares and 3071 stallions) Arabian horses from Khuzestan, Yazd, Kerman, Isfahan, Lorestan, and Alborz provinces. DNA samples were extracted from hair roots using the Direct PCR Kit (Thermo Fisher Scientific, Vilnius, Lithuania). The quantity and quality of the extracted DNA were controlled by spectrophotometry and agarose gel methods. The number of 10 microsatellite markers including AHT04, AHT05, ASB02, ASB17, ASB23, HMS03, HMS06, HMS07, HTG10, and VHL20 were used based on ISAG recommendation. Then, the amplification of genomic fragments and the genotype of samples was determined by COrDIS Horse Reagent Kit (Moscow, Russia). Forward primers were labeled with fluorescent dye at 5'-end. These microsatellite loci were amplified by the multiplex PCR method. Then, the PCR products were genotyped by the Genetic Analyzer system and the capillary electrophoresis method. Obtained data were used to estimate demographic parameters. The number of effective alleles, the number of observed alleles, the observed heterozygosity, the expected heterozygosity, and the Shannon index were calculated by GenAlex 6.5 software. Genpop 4.7.5 software was used to calculate the FIS statistic or Fixation index in the population.
The results showed that the lowest and highest number of observed alleles were related to ASB17 (17 alleles), HMS06 (eight alleles), and HMS07 (eight alleles) markers, respectively. The total number of alleles observed at all loci was 113 alleles. The average number of observed alleles was estimated to be 11.3, which indicates high allelic diversity in the Persian Arabian horse. The mean number of effective alleles, Shannon index, observed and expected heterozygosity and Fixation index were 3.97, 1.58, 0.721, 0.736, and 0.021, respectively. The mean genetic diversity in the Arabian horse’s population was calculated to be 0.736. The highest and lowest genetic diversity was observed in VHL20 (0.803) and ASB02 (0.620) markers, respectively. The average number of effective alleles per locus in studies conducted in different countries on Arabian horses, including Egypt, Syria, and Western countries, with Persian Arabian horses in this research, showed that number of effective alleles is higher in Persian Arabian horses. The average Shannon's index has been reported to be slightly lower in previous studies of Persian Arabian horses, which is probably due to the small number of samples in these studies compared to the present study.  The highest and lowest observed heterozygosities in this study were related to AHT4 (0.788) and ASB02 (0.613) markers, which were consistent with the results of the research conducted on Arabian horses of Iran, Syria, and Egypt. The positive FIS value in Arabian horses made a decrease in heterozygosity in the population, an increase in homozygosity and consequently inbreeding in Arabian horse populations. In this research, all studied loci showed a significant deviation from the Hardy-Weinberg equilibrium. Except for the AHT04 marker, which deviated from the Hardy-Weinberg equilibrium at P<0.01, the others have deviated at P<0.001. Deviation from the Hardy-Weinberg equilibrium can indicate the presence of some factors disturbing Hardy-Weinberg equilibrium, such as migration and selection, which in Persian Arabian horses, the entry of stallions from outside the herd and the gene flow between different maternal strains and also the existence of a selection program among breeders are the main factors of deviation from Hari-Weinberg equilibrium.
Evaluation of the genetic structure of Arabian horses of Iran and comparison with other Arabian horses in the world, including those in the Middle East region, showed that Arabian horses of Iran have a higher genetic diversity, which is probably due to the presence of different maternal strains in Iran, high gene flow among the different strains, a large import of Arabian horses and crossbreeding with Arabian horses of Iran, as well as a high number of samples and so identification of new alleles in this research. On the other hand, the rate of inbreeding was positive according to the FIS in Iran Arabian horses, indicating a risk of genetic diversity loss and increasing inbreeding in these horses. Therefore, management of genetic diversity and prevention of mating among related animals should be considered.

The BRCA1 gene, which is called “gate keeper” It plays an important role in the process of repairing DNA damage, regulating the cell cycle, regulating the transcription process, maintaining chromosome stability, and other important pathways for the maintenance of genome stability. The current research was conducted with the aim of bioinformatic analysis and comparison the genetic diversity and phylogenetic structure of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 6 geographical regions: Western Asia, Europe, China, North Africa, South Africa and wild (Iran) using the NCBI genome databas.

The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. Also, the number of mutations, nucleotide diversity, haploid diversity, the number of positions in which similar or non-similar substitutions occurred, the percentage of gene differentiation, gene conversion were also analyzed using Dnaspv5 software.

The analyzes related to the comparison of breeds in 6 geographical regions showed 112 polymorphisms, which led to the creation of 19 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences (k) among breeds were estimated as 0.205 and 0.052, respectively. The genetic differentiation between the Chinese sheep population and the wild sheep population was the lowest. The average genetic distance between all geographical regions was calculated to be 0.29. The average nucleotide ratio (A+T):(G+C) was equal to 38:62%, which indicates the predominance of cytosine and guanine bases. The amount of conserved sequence (c) in this research was 0.313 on average, which indicates the high polymorphism of this gene and the creation of new proteins as well as new functions to adapt to different homeostasis conditions. The effective number of codons (ENC) in this research was calculated to be 56.41. The value of D in the Tajima neutrality test was 0.478, which indicates that the selection pressure is balanced.

The high genetic diversity in the wild population, the reasons for which are the presence of forest and open environments, prevention of genetic drift and reduction of inbreeding, which affects muscle strength, eating habits, aggressive behaviors, defense responses, sensory perception of confrontation with environmental conditions and stress that related to BRCA1 gene expression in these populations.

Camels play a major role in the life of people in parts of Africa and Asia, especially in the desert areas. Today, camels are important for sustainable livestock production species in many arid regions of the world. Camels are economically important in terms of meat, milk and wool production in the desert. Due to climate change, camel as a desirable animal for arid areas, requires more extensive scientific view. According to FAO statistics, about 95% of 35 million humped camels worldwide are single-humped camels. The cytochrome b sequence is part of the mitochondrial DNA, passing from mother to offspring’s, can be used to elucidate genetic diversity and evolutionary history within and between different species. The aim of this study was to compare the genetic diversity using cytochrome b sequence in Turkmen camel and its genetic relationship with one and two-humped camels. In addition, the genetic relationship of within and between different species of camels has been objected. After preparing a blood sample from the abdominal vein of Turkmen camel, DNA extraction was performed using salting out method. Turkmen camel sequencing was performed using Illumina HighSeq 2000. Sequencing creates 150 bp reads of the genome sequence. The reads were assembled by Denovo method using CLC software and the contig of containing the cytochrome b gene was isolated based on the reference gene, NC_009849. Relevant data were obtained to compare the CYTB reference gene in new (Lamini) and old (Camelini) world species of camels. To study the genetic diversity of the camel species, a total of 42 one-humped camels, 31 wild tow-humped camels, 121 domestic tow-humped camels, and wild lamas including 31 guanicoe (Lama guanico) And 6 vicogna-vicogna (vicogna vicogna) and domestic llamas including 6 lama glama and 5 alpaca (Lama pacos) were compared. The alignment of CYTB gene sequence samples of different species was performed using CLC Genomics Workbench 12 software. Then the number of gaps, the number of differences and identities were obtained. A phylogenetic tree was drawn to investigate the genetic relationships between and within species. Sequences of Turkmen camels and other Iranian and Arabian one-humped camels along with other species were analyzed for alignment using CLC software. Phylogenetic tree of DNA and proteins sequences of the gene was performed using Neighbor Joining method with Jukes-Cantor protein distance size with 1000 bootstrap replications. DNA extraction based on spectrophotometry was 304 ng/μl and was suitable for sequencing. After sequencing, 589,326,158 readings of 150 base-pairs containing more than 88 billion bases were obtained. Assembling of the obtained reads produced 235978 contigs from which the contig of containing cytochrome b gene was selected based on the reference gene. The sequence of other camel species was extracted from the database and used based on the fact that the data contained the entire cytochrome b gene, which corresponds to 1140 bp of the reference gene. There is the biggest difference between new world of wild and domestic camels. There was a minimal difference between Arabian and Turkmen camels with 100% similarity, followed by Lama Glama and Lama Guanico, as well as between wild and domestic two-humped camels. The Turkmen camel was completely similar to the Arabian camel and had the greatest difference with wild two-humped camels. In the study of Di Rocco et al. (2010) it was shown that the difference of cytochrome b sequence between wild camels (VV and L Cuanicoe) was 6.4%, which in this study was 6.3% which could be due to the larger number of samples in this study. The phylogenetic tree of cytochrome b protein sequence showed that the llamas and one and two-humped camels are located in different branches of the tree. According to the results of DNA phylogenetic tree, llamas were on one side and two-humped camels were on the other side of the tree and one-humped camels were located between them. There was a great diversity within the population of llamas. Some domestic one and two-humped camels are associated with wild two-humped camels. The results indicate that wild two-humped female camels were mated with domestic one and two-humped males that resulted one and two-humped domestic camels phenotype. The same is true of llamas, with domesticated Lama Glama and Lama Pacos locating among the wild species of Lama Guanicoe and Vicogna vicogna phylogenetic branch. Ming et al. (2016) demonstrated that domestic and wild two-humped camel species are genetically distinct from each other. In this study, it was shown that the domestic and wild two-humped camels is phylogenetically close to each other and distanced from one-humped camels. Based on the cytochrome b sequence, Cui et al. (2007) were concluded that one and two-humped camels separated before migrating to Eurasia. Similarly, in this study, it has been shown that one-humped camels are separated from two-humped camels, then wild and domestic two-humped camels are separated from each other. As a result, there is a greater phylogenetic distance between llamas and humped camels. Iranian one-humped camels can be classified into four genetic groups, two of which are originated from wild and domestic two-humped camels and the other two groups are among the one-humped camels. Iranian domestic two-humped camels were also phylogenetically divided into four genetic groups.

Humped species of camel have been used as a source of meat, milk and wool since their domestication around 3000 6000 years ago and they also can be breed and used to transportation in the tropical and cold desert areas. The mitochondrial circular genome with double-stranded DNA passes from mother to offspring and has a low recombination and high evolution rate, the sequence of which is commonly used for elucidate rate of genetic diversity and evolutionary history. According to the effect of ATP6 gene on ATP synthesis and energy metabolism, it can be affect economical traits. Therefore, the aim of this study was to investigate inter and intra species consideration of the ATP6 gene in camels and compare them with Turkmen camels. For this reason, sequence of ATP6 gene with 681 nucleotide in length were prepared for 123, 26 and 32 one-humped, domestic and wild two-humped camels, respectively. Sequence alignment and phylogenetic tree of gene and protein for inter and intra species of the camels were constructed using CLC Genomics Workbench 21 software. Then, genetic diversity and phylogenetic tree within and between camel species were constructed. Results showed that the one-humped and wild two-humped camels had the highest and the lowest diversity also, some of one-humped camels was closely related to the two humped wild camels. This study showed that the genetic diversity of ATP6 gene in one-humped camel species is much higher than other species.

Whereas high levels of inbreeding in domestic animals reduce genetic diversity and increase the probability of animals being homozygous for deleterious alleles. Therefore, the longevity of inbred animals is decreased due to reduced genetic merit. Therefore, in designing breeding programs, preknowledge about the level of inbreeding is essential to control the increase in inbreeding and thus control the inbreeding depression in animals. In this regard, genomic data can be used to estimate inbreeding coefficients. The aim of this study was to investigate the rate of inbreeding using SNP marker data available throughout the genome from the Illumina OvineSNP600K array in Iranian native sheep.

In this study, the genomic inbreeding of 154 samples including 11 Iranian sheep breeds (Kermani, Baluchi, Afshari, Karakul, Sanjabi, SiahKabud, LoriBakhtiari, Shal, Ghezel, Chios, GrayShiraz) was studied. For this purpose, five different methods were used by using Plink software: molecular indices of inbreeding coefficient based on observed and expected heterozygosity (FIS), inbreeding coefficient based on “runs of homozygosity” (FROH), inbreeding coefficient based on genomic relationship matrix (FGRM), inbreeding coefficient Based on the number of observed and expected homozygous genotypes (FHOM) and the correlation between uniting gametes (FUNI).

The average minor allele frequency in Iranian native sheep was 0.268. Also, the mean of observed heterozygosity and expected heterozygosity was 0.341 and 0.360, respectively. The lowest rate of inbreeding according to FIS was related to Baluchi breed and the highest was related to Shal breed.  The highest amount of FROH (0.129) was observed in Kermani breed and the lowest amount (0.019) was observed in Baluchi breed. Also, the highest amount of FGRM, FHOM and FUNI indices was observed in Kermani breed and lowest amount was related to Baluchi breed. The highest ROH coverage was observed on chromosome 26 (20.23%), while the lowest was on chromosome 2 (6.62%).

The genetic diversity of Iranian native sheep was moderate and ranged from 0.315 to 0.354. ROH was found in all breeds, so that the average length of ROH was between 48 to 318 Mb, while the average number of ROH was between 8 to 53. The mean of genomic inbreeding coefficients for the whole population of native sheep were similar (0.05). The results of this study indicate that there is no high level of genomic inbreeding in most of the native sheep populations of Iran.

The aim of the current project was study of population structure using pedigree analysis and also inbreeding depression of growth traits in Iran-Black sheep. Pedigree information related to 5481 animals and records of body weights at birth, weaning, six-month, nine-month and yearling, collected from 1982 to 2011 at Abbasabad Sheep Breeding Station in Mashhad, were used. Calculation of inbreeding coefficients was done by CFC, and Endog (v4.8) to compute other pedigree analyses, and WOMBAT software was used for estimating the inbreeding depression of growth traits. The total number of founders, the effective number of founders, the effective number of ancestors, the effective number of founder genomes, and the effective number of non-founder genomes, were 167, 22, 17, 11, 22 heads, respectively. The estimated average for coancestry, relationship and inbreeding coefficients was 4.71, 9.42 and 4.80 percent, respectively. The generation interval and the effective population size based on individual increase in inbreeding were 4.85 years and 26 heads, respectively. The average generation interval in the sire-progeny pathway was greater than the dam-progeny pathway. Also, half of the genetic diversity of the study population originated from 6 ancestors. The inbreeding depression for body weight traits at birth, weaning, six, nine and 12 months of age were 10.3, 130.6, 491.8, 525.5 and 414.7 g, respectively. The results showed a decrease in genetic diversity of the study population compared to the founder animals and observed inbreeding depression in the studied traits could also confirms it.

The major histocompatibility complex (MHC) genes are very important in horse breeding according to relationship with immunity response and resistance or susceptibility to disease. The aim of this research is study of polymorphism possible in exon gene region and population genetics. To do this, 120 horses were selected randomly from Thoroughbred, Oldenburg, Caspian pony and Arab breeds. Genomic DNA was extracted via blood samples and polymerase chain reaction was done for a 309 bp MHC gene region. The PCR products were digested by RsaI restriction endonuclease for genotyping determination. Results show that there were three allele of A, B and C and six types of genotype of AA, AB, AC, BB, BC and CC with 0.3208, 0.3208 and 0.3584 allele frequency and 0.05, 0.25, 0.2917, 0.1333, 0.125 and 0.15 genotype frequency in all studied samples respectively. The most and least allele frequency in Thoroughbred, Oldenburg, Caspian pony and Arab are related to B, A, A, C and A, B, B, A alleles respectively. The Hardy-Weinberg equilibrium study by X2 and G2 tests shows the equilibrium situation in Oldenburg and Caspian pony breeds and non-equilibrium situation in Thoroughbred and Arab breeds. The overall results shows that the genetic diversity in studied samples can be used as a resource for horse breeding programs.

The aim of this study was to investigate the genetic structure of Iranian native horse breeds to compare genetic diversity and understanding the relationships between the populations using 11 ISAG microsatellite markers. For this reason, 565 samples of the Iranian Equestrian database from different ages including the Iranian Arab Asil, Caspian, Darehshouri, Kurdish and Turkmen and 113 samples were used for each breed. The number of observed alleles for each locus was 7 to 19 alleles with an average of 10.81 alleles, and it was 19 for ASB17 and 7 for HTG4 locus with the highest and lowest observed alleles ranking respectively. The average observed heterozygosity from the largest to the lowest rank was, Turkmen (0.68±0.11), Caspian (0.67±0.07), Kurdish (0.66±0.06) Darehshouri (0.65±0.07), and Arab Asil (0.62±0.08). Population structure analysis with UPGMA method showed that Caspian and Kurdish populations were grouped as a unit cluster while the other populations grouped as a separate cluster. These results confirmed this hypothesis that the Caspian and Kurdish populations are close to the Nisa horses. In general, the results of this study indicate that the Iranian native horses have got a high genetic diversity, despite of populations have genetic similarity and the other hand genetic clustering of the populations is consistent with their geographic distances. The result of this study shows that the ISAG microsatellite markers are polymorphic and have more efficiency for assignment genetic diversity and genetic structure analysis of Iranian native horse breeds.

Mutations during gene sequencing lead to nucleotide changes, resulting in new function in gene. The aim of the present study was to evaluate the genetic diversity and analysis the reasons for the differential expression of immune-related genes between the two populations of purebred and crossbreed Sistani and Montebeliarde cows. In this study, the results of the analysis of differential expression among the population of purebred and crossbreed Sistani and Montebeliarde cows using RNA-Seq data were used for genetic analysis and phylogenetic tree mapping. Clustal W nucleotide sequences were aligned using the MegaAlign software, and the phylogenetic tree and matrix of differences and similarities of the sequences were plotted. Based on the results of this study, the mean difference between nucleotides (nucleotide divergence) and the total number of mutations for the studied genes among purebred and crossbreed Sistani and Montebeliarde populations were in the range (2598-1869) and (3898-74) . Also, conserved regions make up a small part of the sequence of genes studied, indicating a high polymorphism of these genes and their susceptibility to nucleotide changes and mutations. The results of the phylogenetic tree for the nucleotide sequence of the studied genes showed that there is genetic diversity and divergence in the studied genes among purebred and crossbreed Sistani and Montebilliard and Indicus populations. The numerical value of the dN/dS ratio for the studied genes indicated the positive selection for these genes.

Microsatellites are repetitive regions in DNA including homogeneous array of mono, di, tri, tetra, penta and hexa nucleotides with length of less than 1 Kbp which are non-randomly distributed in genome. The number and density of microsatellites is vary within species even in very close spices such as humans and chimpanzees. The frequency of microsatellite motifs and their mutation rate is reported differently in various organisms. In mammalian genomes di-nucleotide microsatellites are the more abundant type following by mono and tetra microsatellite motifs as next. Tri microsatellites are more frequent in plants. However, the effect of variety in microsatellite motifs on genetic diversity or population structural parameters is a topic that has received less attention.

In the present study with using the 36 VCf file of microsatellite markers extracted from whole genome of Iranian sheep “Ovis aries and Ovis orientalis” by NGS, the total number of 163973 microsatellite markers were detected. The distribution of Ovis aries samples is from north-west part of Iran and ovis orientalis samples are belongs to central part and north-west of Iran. After rearrangement and filtration on data file using Samtools and VCFtools softwares, we classified the whole markers on four different motif types including di- tri- and tetra-nucleotide microsatellites and a file includes all three microsatellite types. Several subsets including 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400 and 500 markers were generated from each microsatellite motif types using a R script. Six common genetic diversity parameters including observed and expected heterozygosity, Nei diversity index, Shanon index, Allelic richness and FIS were calculated for each different subset of number and motif type of microsatellites in MSA (V.4.05) software. 10 replications were considered for each parameter. The mean and variance were calculated among 10 replications and results were represented by boxplots using R (v.3.3.3). The statistical investigation of parameter estimation differences using different microsatellite number and motif types were analyzed using ANOVA for testing the hypothesis of equality of means in R (v.3.3.3).

Estimation of all six parameters revealed various results using different number of loci as well as motif types. Additionally, the results revealed higher values for parameters estimated with di microsatellite motifs compared to others. In addition, the highest and lowest value for most parameters were obtained by 40-di and 10-tri/tetra microsatellites respectively. The statistical significance on findings of parameter values using different number/motif of microsatellite markers were analyzed using ANOVA in R (v.3.3.3). In the case with significant results, Tukey Honestly Significant Difference test was used to test pairwise contrasts between different subsets.

Our result proposes a better application of di microsatellites for genetic diversity studies in sheep populations. Moreover, results showed that for stable estimation of population parameters in genetic diversity studies a minimum of 50 microsatellite loci are needed.

Today, genes in the mitochondrial genome are widely used as a strong genetic marker.The purpose of this study was to determine sequence of ND6 gene of the mitochondrial genome of Khazak chicken and investigate the phylogenetic relationship of this region of the genome with other chicken breeds and some fowls of around the world. 20 blood samples of wing vein were collected from Khazak chicken of Research Center of specific livestock of Sistan and Baluchestan province. DNA was extracted from whole blood. Then, the ND6 gene along with a portion of upstream and downstream tRNA (854 bp) was amplified from mitochondrial genome by specific primers in Polymerase Chain Reaction. Samples were sequenced after purification and genetic diversity was investigated within the population. After Download similar sequences of the other mitochondrial genome from the chicken breeds and some fowls of the NCBI, phylogenetic analysis was carried out. The results showed that there was no nucleotide difference between ND6 sequences of native Khazak chicken. The results of the phylogenetic tree from native Khazak chicken with other breeds showed that the highest genetic similarity was observed from this region of the mitochondrial genome of native Khazak chicken with HuangLang, Zhuxiang, Fiji, Philippines, Hengshan Yellow, Jinhu Wufeng and Red jungle fowl breeds which indicates that there are a high genetic relationship between the native Khazak chicken with the Japanese and Chinese (southeastern Asia) chicken breeds. The least genetic similarity of ND6 sequence from native Khazak chicken was observed with the Grus japonesis.

Horses (Equus ferus caballus) have always been alongside humans and played an important role in the formation of human civilization. Horses are vertebrates that belong to the Mammalia class, the Equidae family, and the Equus genus. There are free and wild horses in Africa, Asia, Australia, Europe, North and South America, and some oceanic islands. Because of the long-standing relationship with human civilization, horses are considered as companions, a symbol of power and predilection, human assistant, and rival of other animals. The origins of domesticated horses have always been interesting to humans, and studying them is very important. Archaeological evidence and analysis of the horse's body color indicate that the first horses were found in the Eurasian steppes between 5th and 4th millennia BC. Among the genetic studies, simple repeat sequencing can be implied. Random repetitive sequences are scattered throughout the genome and show high polymorphisms that are harbored consecutively and repeat almost every 3-5 Kbp of genome. These sequences comprise a total of 20% of the mammalian genome sequence.

Blood samples were obtained from Arabian horses and their DNAs extracted using salting out method. Extracted DNAs was run in an agarose gel and concentration and quality of DNAs were measured by Nano-drop. Four microsatellite markers were used that all have been recommended by International Society for Animal Genetics (ISAG) for testing the parentship. These markers included ASB17, LEX3, HMS1 and CA425. These loci were amplified by multiplex polymerase chain reaction (PCR) with fluorescent dye-labeled primers. PCR was performed using total volume of 25 ml for each sample and PCR products were separated and analyzed with capillary electrophoresis and the products were evaluated using GenMapper software.

According to the results obtained, the smallest allele was found is 88 bp at the position of ASB17 locus, as expected. Moreover, the largest allele observed in this population was 110 bp. The most frequent allele observed in the population was also 110 bp, with an allele frequency of 0.46%. For LEX3, the smallest allele observed is 144 bp, which was expected. The largest allele observed in this population was 166 bp, which was more than expected range. The most frequent allele observed in the population was 160 bp, with an allele frequency of 0.32%. However, the smallest allele observed in the population at position HMS1 was 172 bp, which was expected to be within the normal allele frequency range. The largest allele observed in the population was 182 bp, which was expected to be in the allele range. The most abundant allele observed in the population was the 174 bp allele, with a frequency of 0.41%, which has a high prevalence in other races. For CA425, the smallest size of the allele observed for this site was in the population of 242 bp, which was smaller than the expected allele size and had a significant frequency of 0.11%. The largest allele size observed in this site was 248 bp, which was expected to be above the expected allele range. The largest allele observed in the population was 182 bp, which was expected to be in the allele range. The most abundant allele observed in the population was the 174 bp allele, with a frequency of 0.41%, which has a high prevalence in other races. For CA425, the smallest size of the allele observed for this site was in the population of 242 bp, which was smaller than the expected allele size and has a significant frequency of 0.11%. The largest allele size observed in this site was 248 bp, which was expected to be higher than the expected allele range.

According to the results obtained from the observed alleles in the studied population of Arabian horses, there is a relatively high genetic variation among this population. It can also be said that for some alleles, there is a high prevalence in the Arabian horse population, while they were not seen in other breeds of horses. In general, several alleles in the Arabian horse population of Iran have been observed with different frequencies that were not present in rest of the races, which implies to the differentiation of this race from horses of other races.

 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.

 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.

 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.

 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.

Due to having historical value and climatic diverse, Iran has unique horse breeds. Unfortunately, due to the lack of attention and control of the import of foreign breeds into this rich
genetic source, huge damage has been created. Therefore, many horse breeds in the country got crossbred and their racial purity reduced. Knowing the genetic structure of native breeds will play an important role in their safeguarding and ensuring of their survival. Indigenous breeds, due to their unique characteristics, are considered as part of the genetic resources of the country, and their genetic structure will help them to protect and develop eugenic programs.

 This study was conducted on 136 horses including Taleshi (25 samples), Caspian (49 samples) and Arabic (62 samples) breeds from their breeding areas. Taleshi horse samples was captured from local stock in the Guilan province, Caspian samples was captured from horse riding clubs around Tehran and Guilan provinces, and Arabian samples was captured from horse riding clubs around the provinces of Tehran, Khuzestan and Alborz. They were unrelated and selected randomly. The race recognition of horses was based on books published by the Federation of Equestrian and their phenotypic characteristics. After determining of the concentration and uniformity of the concentration of extracted DNA, all individuals under study were conducted for 12 microsatellite markers recommended by the Animal Genetic Association (ISAG) to determine the genotype in order to estimate the parameters such as heterozygosity, inbreeding, Hardy and Weinberg equilibrium, and so on and find an appropriate strategy to maintain these valuable breeds. The number of observed alleles (na), and effective (ne), observed heterozygosity (Ho) and the Expectation case (He), Shannon index (I), inbreeding coefficient (ISF), genetic distance, genetic similarity, Hardy-Weinberg equilibrium, and phylogeny tree between races were calculated using POPGENE 1.31 software.

 All of the used markers were multi-shaped and the ASB17 markers with 12 alleles and HMS6 produced the highest and lowest number of alleles with 6 alleles, respectively.
The highest and lowest expected heterozygosity were calculated in VHL20 (0.78) and ASB23 (0.62) markers, and the average Shannon index for all sites was 1.72. Hardy Weinberg balance
analysis by Chi square test showed that except ASB2 and HMS3 markers in Taleshi breed, ASB17 and HTG4 markers in the Caspian breed and ASB17 markers in the Arabic breed, all markers had a significant deviation from Hardy and Weinberg equilibrium (P <0.05). The highest observed heterozygosity was related to AHT5 marker (0.81) and the lowest observed heterozygote was related to ASB17 and HTG4 markers (0.68). The Shannon index, like the observed heterozygosity, shows the amount of genetic diversity, and because the maximum value is equal to Ln (n), it is useful to express the genetic diversity of multi-formed sites. The highest and lowest values of Shannon index were 1.96 and 1.46, respectively, for VHL20 and HTG4 markers. Given the fact that the VHL20 marker showed the highest and the HTG4 marker showed the least effective allele, so the calculated values for the Shannon index are justified. Phylogeny diagram showed that Caspian and Taleshi horses were placed in one branch and Arab horses in separate branch.

Breeds with fewer populations are more at risk for genetic changes and extinction. Reducing of the genetic diversity of indigenous populations will result in the loss of many useful
genes, especially those that are compatible with different environments and resistant to regional diseases. Undoubtedly, it is very important to pay attention to the genetic diversity of small-sized
population of breeds such as Taleshi and Caspian. The results of this study showed that due to the low number of Caspian and Taleshi horses, genetic diversity is still at a high level, so it would be hoped that by adopting the principled measures, we would prevent their extinction in the long duration.