This research aims to investigate the current status and estimate the extinction probability of the endangered Karakul sheep breed in Iran. To achieve this, census data and required parameters were collected from Karakul sheep flocks and available resources during project implementation. Two scenarios of past and future population dynamics assuming the continuation of the existing conditions within the Karakul sheep habitat were simulated using the Population Viability Analysis (PVA) method and VORTEX version 10.5.6. By employing the gathered biological parameters and assumptions, the simulation of past population dynamics closely replicated actual historical trends. Conversely, the simulation of future population dynamics indicated that, under current conditions, the trend of increasing inbreeding and decreasing genetic diversity within the studied population is likely to persist. The extinction probability of the Karakul sheep breed could become a reality as early as 1438, with the estimated mean time to the first extinction of this breed being 51.08 ± 4.47 years. Sensitivity testing revealed that factors such as the excessive harvest of adult ewes beyond the usual annual harvest, the frequency of feed limitations, and the use of other breeds in mating exert the most significant influence on future population viability measures, primarily due to economic considerations.

Inroduction & One of the most important economic traits in sheep is twining. Genetic studies have identified a set of genes that affect twining with major effects called fertility genes. One of them is GDF9 gene that have been identifying on sheep chromosome 5. This study conducted to investigate the GDF9 gene polymorphism and its relationship with prolificacy trait in Karakul sheep breed.
Material and Blood samples and birth data collected from 100 Karakul sheep at the Karakul breeding station of Sarakhs-Iran. After DNA extraction one pair of specific primer selected to amplify a 1503 bp fragment of the gene and Rsa I enzyme was used to digest the amplified fragment. The results showed a mutation at GDF9 locus in Karakul sheep. The relationship between genotypes and twining rate investigated using SAS 9.1 software.
The results showed a significant relationship (P Therefore, the mutation in GDF9 gene is a useful mutation and fix it will increase twining rate and will ultimately increase revenue.

Genotypes for melatonin receptor type 1A (MTNR1A) and Calpastatin (CAST) were determined by enzymatic digestion of PCR products and Calpain(CAPN) genotype detected by PCR-SSCP method in Iranian Karakul sheep. Blood samples were collected from 100 purebred Karakul sheep. The extraction of genomic DNA was based on guanidinium thiocyanate-silica gel method. PCR amplicons were digested with restriction enzymes MnlI and MspI for MTNR1A and CAST genes, respectively. The MTNR1A locus had two alleles with frequencies of 0.79 for (+) and 0.21 for (-) alleles. Allelic frequencies for CAST locus were 0.85 for M and 0.15 for N. In addition, Calpain had two alleles A and B with respective frequencies of 0.79 and 0.21. The observed heterozygosity values for MTNR1A, Calpastatin and Calpain locus were 0.42, 0.29 and 0.35, respectively. The X2 test confirmed the existence of Hardy-Weinberg equilibrium for the three loci in the population. The data showed a large variation in studied genes. The genetic polymorphism could be regarded as useful tool for selection programs based on marker- assisted selection between different genotypes of those loci.

Myostatin, also called growth and differentiation factor 8 (GDF8), acts as a negative regulator of muscle growth and development; Therefore, its role in animal growth and meat production is very important. Functional studies showed that a single nucleotide polymorphism in the 3'UTR region of this gene causes the elimination of its growth inhibitory role and finally the occurrence of double - muscled sheep. The tetra primer ARMS PCR method is an easy, fast, reliable and cost-effective method for the detection of nucleotide polymorphism. The present study was conducted with the aim of identifying single nucleotide polymorphism of myostatin gene (g+6723G>A) using tetra primer ARMS PCR technique in 86 Karakul sheep. Polymerase chain reaction was optimized using 3 control samples including 1 homozygous wild-type, 1 heterozygous and 1 homozygous mutant genotype of sharole breed sheep. All the studied Karakul sheep had the G allele, and the mutant type allele (A allele) was not observed, so the frequencies of the mutant type (A) and the wild type (G) alleles were 0 and 100%, respectively. To evaluate the accuracy of tetra primer ARMS PCR technique in this locus, all tested samples were also genotyped by PCR-RFLP method. The results indicated that two methods are the same as therefore using Tetra Primer ARMS PCR method been as economical to genotyping

In order to evaluate the impact of the prediction Incomplete pedigree breeding value and genetic trends of Karakul sheep pelt, from real data collected at the Sarakhs of karakul sheep breeding station during the years 1995 to 2015 were used. Studied trait was: degree of Pelt that birth weight as auxiliary variables in the statistical model was used. For every trait, data from 21 years of selection and mating was saved in separate files. And the file of pedigree, sire’s number by 25% (from zero to one hundred percent) was removed randomly and data files for each trait in a state of complete and incomplete pedigree (removed 25, 50, 75 and 100% Number of Sires) under the animal model was used. Genetic trends of the pelt through regression of average breeding value on Birth year estimate that has to remove different percentages Numbers sire (0, 25, 50, 75 and 100 percent) from pedigree to were as follows: 0.0420 ± 0.0061, 0.0161 ± 0.0056, -0.0472 ± 0.031, 0.0161± 0.0056 and 0.0161 ± 0.0056. And heritability were, respectively: 0.74 ± 1.76, 0.72 ± 1.65, 0.71 ± 1.49, 0.73 ± 1.38 and 0.76 ± 1.25. The overall defect in pedigree by increasing percentage of elimination the number of sire, direct heritability reduced to 75% removal sire's number, then place the increase of heritability was the pelt as well as genetic trend by increasing the removal rate Sire Number fell.

Introduction Lamb production is the largest part of income in sheep industry. Therefore, the mortality rate of lambs is a key factor in profit of the sheep breeding. Mortality rate of lambs (or Lamb mortality rate) in different breeds of sheep under different climatic conditions is varying from 15% to 50% and an average of 9% to 20% has been reported. Survival rate is a combination trait that is influenced by various factors such as management, weather condition, and behavior of dam and lamb, as well as genetic effects. Quantification of non-genetic effects on mortality rate can be useful in controlling lamb survival rate and increasing profitability of sheep breeding. Therefore, identification of genetic and environmental factors affecting the productive capacity of indigenous breeds in different area is the main priority that should be considered in breeding programmes. Therefore, the objective of this study was to estimate genetic and environmental factors of growth traits and mortality in Karakul lambs. To estimate the genetic and environmental parameters of Karakul lambs before weaning growth and mortality records of 4929 lambs from 207 rams and 1856 ewes at Sarakhs Karakul sheep breeding station, from 1994 to 2009 were used.
Materials and Methods The data were used in this study included a total of 4929 record of lamb birth weight, 1 and 3 months of age, average daily gain from birth to weaning (growth traits before weaning) and mortality rate of lambs from birth to 1, 2, 4, 8 and 14 weeks (mortality rate of lambs before weaning). Data were collected during the years 1994 to 2010 in karakul breeding station in Sarakhs. The data were edited and pedigree file and data file were prepared. Uni-variate animal model was used to estimate the genetic parameters as following: where is the vector of record, b is the vector of fixed effects (year, sex, type of birth, age of dam), a is the vector of direct additive genetic effects, m the vector of maternal additive genetic effects, X, Z1 and Z2 are the matrix of coefficients (0 and 1) that relate b, a and m to records and e is the vector of residuals. Analysis of each trait was performed considering the significant factors in the model including sex, birth-type, birth-year, dam-age and ewe weight at birth. In the analysis of maternal effect model for growth traits and Cox regression for mortality traits were used. Cox Regression in SPSS software was also used to calculating the survival function. (Co) variance components were estimated by Restricted Maximum Likelihood (REML) with uni-variate animal model. The genetic, phenotypic and environmental trends were estimated as regression of average breeding values on year of birth, regression of average phenotypic values on year of birth and, difference between genetic and phenotypic trends, respectively.
Results and discussion The results showed that year of birth had a significant effect on all traits (P

Thriteen thousand, seven hundred and fifty two (13752) records on growth tarits (birth weight, 1, 3, 6, 9 and 12 month weights) as well as pelt scores, collected during 1996-2002 as Karakul Sheep Breeding Station, Sarakhs, Iran were employed in this study. Best Liner Unbiased Prediction (BLUP) of breeding values, genetic and phenotypic trends of the traits were estimated as the regression of average predicted breeding values and phenotypic values over birth year, respectively. Environmental trends were assessed as the difference between phenotypic and genetic trends. Estimates of genetic trends were found as: 0.013±0.001, 0.034±0.004, 0.119±0.010, 0.087±0.013, 0.127±0.018, 0.119±0.019 kg/year and 0.257±0.019 score/year, respectively. Phenotypic trend for the above traits were -0.151±0.005, -0.116±0.023, 0.268±0.035, 0.185±0.052, 0.443±0.065, 0.559±0.078 kg/year and -0.235±0.048 score/year, respectively. Environmental trend for the same traits were respectively estimated as -0.164±0.004, -0.151±0.019, 0.149±0.025, 0.098±0.039, 0.316±0.047, 0.440±0.059 kg/year, and -0.492±0.029 score/year.

The genotypes of the melatonin receptor 1A (MTNR1A) were determined by PCR-RFLP in the native Iranian Shall and karakul breeds of sheep. Blood samples were collected from 60 karakul and 50 Shall breeds. Genomic DNA was extracted based on the Guanidin Thiocyanate-slica gel method. After PCR reaction, PCR products were digested by the Mnl1 restriction enzyme. The MTNR1A locus had two genotypes with frequencies of 0.7 (+ +) and 0.3 (+ -) in the Karakul breed, 0.58 (+ +) and 0.42 (+ -) in the shall breed. Heterozygosis value for the MTNR1A locus in Shall and Karakul breeds were 0.42 and 0.3, respectively.This study provided evidence that sheep breeds, Shall and Karakul have variability in MTNR1A locus. Therefore, this locus can be used as a marker for the reproduction trait in selection programs.

The Melanocortin-1 Receptor MC1R is encoded by the extension locus, playing a fundamental role in the determination of coat color in a number of mammalian species. However, so far there has been no report regarding the Single Nucleotide Polymorphisms (SNPs) of the MC1R promoter region and the potential association of its SNPs with coat color in sheep (Ovis aries). Throughout the present study, the promoter region of the MC1R gene was screened using Single Strand Conformation Polymorphism SSCP and DNA sequencing in the Karakul breed of sheep. A total of 4 distinct SSCP patterns were observed which revealed 3 novel SNPs and an insertion/deletion of 26 nucleotides upon sequence analysis in the analyzed population. In silico analysis of the MC1R promoter sequence predicted no consensus TATA-box motif at an appropriate position but detected multiple putative transcription factor binding sites for Ets, AML-1a, NF-E2, MZF1, USF, Oct-1 and GATA-1. The analysis of identified polymorphic sites also showed that the polymorphism at nucleotide position -89 relative to the start codon abolishes the USF transcription factor binding site. The SNP identified at the -100 position is located within a putative AML-1a transcription factor binding site. The insertion of 26 nucleotides at position -126 made a putative binding site for the MOK2 transcription factor. The possible functional activity of the identified genetic variations could be confirmed using gene expression analysis.

Inbreeding is the increase in homozygosity of offspring resulted from mating between related animals or animals that have common ancestors. The main effect of inbreeding is decline in performance of inbred animals known as inbreeding depression. The magnitude of inbreeding depression is not the same across the various traits and population. Recent studies revealed that inbreeding depression also shows variation among founders within a population. Variability of inbreeding depression arises when distribution of deleterious recessive alleles among founders are not equal. Furthermore, the detrimental effects of inbreeding can be reduced if deleterious recessive alleles were removed (purged) by selection against homozygotes in earlier generations. Estimating the partial and ancestral inbreeding coefficients makes it possible to assess the balance of distribution of recessive alleles among founders and incidence of purging of deleterious alleles in population. The objective of this study was to estimate wright inbreeding, partial inbreeding, Ballou ancestral inbreeding and Kalinowski ancestral inbreeding coefficients in the breeding flock of Karakul sheep. In this study the pedigree file of the breeding flock of Karakul sheep containing 7477 pedigree records collected during 1989-2014 was used to estimate wright inbreeding, partial inbreeding and ancestral inbreeding coefficients of animals. Pedigree completeness index was calculated to evaluate the quality of pedigree. Animals that born in the last 4 years of the pedigree with pedigree completeness index of greater than 0.6 was considered as a reference population to decomposition of the inbreeding to partial inbreeding arises from founders. Ballou ancestral inbreeding of all animals was estimated. Also, inbreeding coefficients of animals were decomposed to the New and Kalinowski ancestral inbreeding. The mean of wright inbreeding coefficients of animals in all population and reference population were 0.85 and 1.36, respectively. A total of 108 of 280 founder animals (38%) have a positive contribution to the inbreeding of the reference population. Mean and standard deviation of the partial inbreeding coefficients of these 108 animals were 5.19 and 7.37%, respectively. The 10 and 25 founders contributing the most to inbreeding explained a large part of the inbreeding of the reference population (i.e., 42 and 66%, respectively). Mean Ballou ancestral inbreeding of the whole and reference population were 1.17 and 2.12, respectively. Most of the animals in the population have positive Ballou ancestral inbreeding. Kalinowski ancestral inbreeding of animals was low and its mean was 0.07% in the population. Ancestral inbreeding in this population was in accordance with Ballou definition of ancestral inbreeding. Correlation of wright inbreeding coefficient with Ballou ancestral inbreeding, Kalinowski ancestral inbreeding and New inbreeding coefficients was 0.1, 0.37 and 0.99, respectively. Based on the results of this study, Ballou ancestral inbreeding coefficients of animals in this flock has increasing trend which can lead to purging of deleterious alleles in this population. Therefore, for assessing the incidence of purging of deleterious alleles in this population, estimating of the effects of ancestral inbreeding on reproductive and production traits are suggested. Also, the estimated partial inbreeding coefficients of animals can be used to determine the contribution of each founder to observed inbreeding depression. On the other hand, estimated partial inbreeding coefficients can help to detect founders that carry the deleterious alleles. Then, these information could be used in mating programs so that new born lambs have a less partial inbreeding arises from carrier animals or those animals which have greater contribution to inbreeding depression.