امیر رشیدی

Artificial neural networks (ANN) have been widely used for both prediction and classification tasks in many fields of knowledge; however, few studies are available on animal science. The objective of this study was to prediction of breeding values of weaning weight in Markhoz goats based on the Mixed Model Equation (MME) and Artificial Neural Networks (ANNs). Quality control and calculation of descriptive statistics was performed using the GLM procedure of the SAS statistical package. The pedigree file included 5541 kids produced by 261 bucks and 1616 does. In the first step, genetic evaluations and Best Linear Unbiased Prediction (BLUP) of breeding values for weaning weight was computed with the mixed model equations, animal model by DMU program. Later, unique dataset was introduced to the ANN models by the R statistical program. A variety of models including, multilayer perceptron (MLP), radial basis function (RBF) and Support Vector Regression (SVR) were used to build the neural models. The artificial neural networks were trained and several networks (different hidden layers and nodes/ neurons) were evaluated. In artificial neural networks, the data were randomly divided to two parts (75% training and 25% for test/validation). Best architecture was selected according to the mean square of error and correlation. Correlation between true breeding value (BVs predicted by MME) and estimated breeding value (BVs predicted by ANNs) for MLP, RBF and SVR models were 0.72, 0.49 and 0.73, respectively. Analysis of farm data showed that the MLP and SVR models have higher performance than RBF for prediction of breeding values or ranking of individuals.

Selective signatures provide information about the stages of evolution of different species, including sheep, which lead to changes in their genome over many years. The aim of this study was to detect signatures of selection in the genome of Iranian sheep in the highlands. A total of 58 sheep from 4 breeds, two breeds scattered in the highlands and two breeds scattered in the lowlands, were genotyped using Illumina ovine SNP600K BeadChip genomic arrays. Two statistical tests of unbiased FST (Theta) and hapFLK were used to identify the selection signatures. The results of Theta revealed 22 genomic regions and the results of hapFLK revealed 15 genomic regions. Bioinformatics analysis demonstrated that many of genes had important effects on adaptation to hypoxia conditions e.g. rheumatoid arthritis (TXNDC5), hematopoiesis (FANCA), immunity and fighting infection (LEF1, NMUR1, PTMA and COPS7B), regulating blood pressure and responding to pain and inflammation (NMUR1) and suppressing cancer (CD82, GAS8, PRMT1, B3GNT7). For example, TXNDC5 and FANCA functional genes, which are located on chromosome 13 and 14, were related to reacts to hypoxic conditions and hematopoiesis. Also, genes such as LEF1, NMUR1, PTMA and COPS7B are effective in immunogenicity and fighting infection. Study of the reported QTL in these regions of the sheep genome showed that they overlapped with QTL of economically important traits such as corpuscular hemoglobin concentration, hematocrit, traits related to meat, carcass, milk, body weight, bone density, and the total number of lambs born. Due to the fact that little research has been done regarding adaptation to altitude in sheep, the results of this research may facilitate the identification of genes affecting adaptation to altitude. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

To investigate the qualitative characteristics and their effects on the economic value of the mohair of Markhoz goats in Kurdistan province, a total of 136 samples from seven flocks, two groups: yearling goats and adult female goats and seven colors: white, cream (straw colored), cream brown, light brown, red-brown, dark brown and black, were sampled in the mohair harvest season. The characteristics investigated in this research included: true fibers, modular fibers, kemp fibers, fiber diameter, staple length, and economic value of fibers. In this research, the statistical analysis was done using version 27 of Spss. Fixed effects of flocks, goat groups and fiber colors were investigated on the variables, and the GLM procedure of the software was used. The least-square means of true fibers (%), modular fibers (%), kemp fibers (%), fiber diameter (microns), staple length(cm), and the price per kilogram of mohair (Rials) were 92.36±5.14, 6.84±4.81, 0.75±1.02, 32.49±5.27, 14.46±3.27 and 1823308±452, respectively. According to the results of this research, the color significantly affected the mohair pricing (p˂0.01). The low amount of kemp and modulated fibers in the pure goats did not affect the mohair price. However, a combination of particular colors and one of the advantages of the mohair elegance or long length of the staple made the highest price to be assigned to the mohair. For this reason, red-brown and straw fibers had the highest price compared to other colors. In terms of desirability, after these two colors, different brown, white, and black colors were placed, respectively.

The principal aim of the sheep industry worldwide is to produce high-quality meat. In addition to the meat, milk, and wool production are the economic traits in sheep breeding programs. Wool production is one of the most important economic characteristics of sheep with a complex physiological and biochemical process that is influenced by genetics, environment, and nutrition. Almost all Iranian sheep breeds are double-coated and produce carpet wool. Therefore, considering the role of wool on the country's economy, it is necessary to conduct a study to identify the genetic factors affecting this trait. Identifying the genomic regions under selection is effective in understanding the processes involved in the evolution of the genome and also in identifying the genomic regions involved in the emergence of economic traits. Selective signatures in the whole genome can help us to understand the mechanisms of selection and to identify the genomic regions that have been under natural or artificial selection for many years. Since Selective signatures are usually associated with major effect genes and important economic traits, they can provide suitable information sources to improve the performance of selection programs in the future. The objective of this study was to identify the genomic regions that have been under selection in skin and wool sheep breeds.

 In the present study, Illumina ovine SNP600K BeadChip genomic arrays of 80 sheep from six breeds were used, three breeds were bred for their skin (Karakul, SiahKabud, and Gray Shiraz) and three breeds were bred for their wool (Sanjabi, Kermani and Baluchi). Unbiased methods of Weir and Cockerham’s FST (Theta) and hapFLK were used to detect the selection signatures. Also, to check the genes and QTLs in the selected regions, the Biomart database, OAR 3.1 version of the sheep genome, was used, and the function of the identified genes was analyzed through a wide search in different databases such as Genecards and OMIM. Finally, the list of genes related to the selected regions was reported. For this purpose, the chromosomal position of SNPs with high numerical values of theta and hapFLK, as well as the 250 kbp region around these markers, were further investigated. Then, the DAVID database online search was used to investigate the biological and functional processes of genes and to study the ontology. Finally, Cytoscape software was used to determine gene networks.Then, DAVID database online search was used to investigate the biological and functional processes of genes and to study the ontology.سپس از جستجوی آنلاین پایگاه داده DAVID برای بررسی فرآیندهای بیولوژیکی و عملکردی ژن ها و مطالعه هستی شناسی استفاده شد.Then, to investigate the biological and functional processes of genes and to study the ontology, DAVID database was used to search online. سپس برای بررسی فرآیندهای بیولوژیکی و عملکردی ژن ها و مطالعه هستی شناسی از پایگاه داده DAVID برای جستجوی آنلاین استفاده شد. Can't load full results Try again Retrying…

 The results of the Theta analysis revealed 26 genomic regions on 1, 2, 6, 19, and 24 chromosomes, and the results of hapFLK revealed seven genomic regions on 6 and 19 chromosomes. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with known genes related to pigment traits and characteristics of wool (KIT on chr 6, MITF on chr 19, IGSF10 on chr 1, PDGFRA on chr 6), muscles (MICALL2 on chr 24), vasodilation and immune response (P2RY on chr 1) and cancer (MIR339 on chr 24, ELFN1 on chr 24, MAD1L1 on chr 24, GPR87 on chr 1). The investigation of reported QTLs showed that these regions are related to QTLs of important economic traits, including traits related to meat, carcass, milk, body weight, bone density, and the total number of lambs born. Also, the analysis of Gene Ontology and Enriched pathway terms in regions under positive selection were related to the pathways involved in the differentiation of melanocytes and pigments, differentiation of stem cells, cellular processes, development of the immune system, blood system, reproductive and cellular processes. The results of the gene networks with the information obtained from Theta and hapFLK statistics showed that the genes identified were significantly active in the development and morphogenesis networks of the embryonic digestive tract, the networks related to pigment and melanocyte differentiation, and the networks related to Purine and G protein. However, to identify the exact function of the identified genes and QTLs, it is recommended to carry out more investigations.نتایج شبکه های ژنی با اطلاعات به دست آمده از آمار تتا و hapFLK نشان داد که ژن های شناسایی شده به طور معنی داری در شبکه های رشد و مورفوژنز دستگاه گوارش جنینی، شبکه های مربوط به تمایز رنگدانه و ملانوسیت و شبکه های مربوط به The results of the gene networks with the information obtained from theta and hapFLK statistics showed that the genes identified were significantly in the development and morphogenesis networks of the embryonic digestive system, the networks related to the differentiation of pigment and melanocytes and the networks related to نتایج شبکه های ژنی با اطلاعات به دست آمده از آمار تتا و hapFLK نشان داد که ژن های شناسایی شده به طور معنی داری در شبکه های رشد و مورفوژنز دستگاه گوارش جنینی، شبکه های مربوط به تمایز رنگدانه ها و ملانوسیت ها و شبکه های مربوط بهCan't load full results Try again Retrying…

 The results of the present study and the identified genomic regions can play an important role in the study of the effect of the selection on population differentiation in two sheep breeds that bred for skin and sheep production. Subsequently, this would direct us to identify the genomic regions associated with traits that differentiate these groups. However, these areas need to be confirmed in other independent studies with more samples. In general, the data of this research can be used in research related to genomic selection, design of mating systems, and additional reviews and evaluations to improve skin and wool production in sheep.

This study aimed to estimate the genetic parameters of body weight traits in Markhoz goats, using B-spline random regression models. The data used in this study included 19549 records collected during 29 years (1992-2021) in Markhoz goat Breeding Research Station, located in Sanandaj, Iran. The model used to analyze data included fixed effects (year of birth, sex, type of birth and age of dam) and random effects including direct additive genetic, maternal additive genetic, permanent environmental and maternal permanent environmental assuming homogeneous and heterogeneous residual variance during the time. Akaike (BIC) and Bayesian (BIC) information criteria were used to compare the models and bspq.4.4.4.4 was selected as the best model. The direct heritability values for birth, 3-month, 6-month, 9-month and 12-month weights were estimated to be 0.14, 0.16, 0.08, 0.28 and 0.26, respectively. Genetic correlation between body weights at birth and 3-month, birth and 6-month, birth and 9-month, birth and 12-month, 3-month and 6-month, 3-month and 9-month, 3-month and 12-month, 6-months and 9-month and 9-month and 12-month were 0.22, 0.38, 0.21, 0.56, -0.26, 0.30, 0.62, 0.86 and 0.77, respectively. The highest phenotypic correlation was between the weight of 9-month and 12-month (0.82) and the lowest correlation was between birth weight and 3-month and 6-month (0.12). The results showed that the 9-month weight is a good criterion for selection in Markhoz goats.

This study aimed to compare different methods of genomic evaluation using the criteria of correlation (ρ), regression (β), mean square error (MSE), and selection effectiveness (SE). For this purpose, nine different scenarios were designed based on different levels of heritability (0.1, 0.3, and 0.5) and different numbers of QTLs (20, 200, and 1000). To simulate different scenarios, five generations with a size of 1000 animals were simulated, of which the first two generations were considered as the reference population and the next three generations as the validation population. For each animal, a genome of 500 centimorgans with a marker density of 10000 SNP consisting of five chromosomes was simulated. Genomic breeding values were predicted using three statistical methods GBLUP, Bayes A, and Bayes B. The results showed that with increasing generation interval from the reference population, the accuracy of genomic breeding values decreased for three statistical methods, although Bayesian methods performed better in terms of continuity of accuracy. Based on the criteria of correlation, regression, and selection effectiveness, with increasing the levels of heritability, improved accuracy was observed, but the criterion of mean squares error showed the opposite trend. Bayesian methods performed better in low QTLs, but differences in different genomic evaluation methods were minimized in high QTLs. The results of selection effectiveness in comparison with the accuracy of genomic breeding value showed that accuracy can’t always be a suitable criterion for determining the superior method of genomic evaluation.

The objective of the present study was to perform genetic evaluation of dystocia, using linear (observed and adjusted) and threshold models in Holstein cattle. Data and pedigree information of 8 dairy herds were obtained from Vahdat Industrial Agriculturists & Dairymen Cooperative, Isfahan, Iran. Final data included 133876 calving records during 2005 to 2018. The fixed effects of the model were included, herd, year-season of calving, calf gender and age at first calving.  The random effects of the model were included sire, maternal grandsire, permanent environment of dam and residual effects. Furthermore, 305-day milk yield was considered as a covariate in the final equation. Quality control and data validation were conducted in SAS and Microsoft Excel. Genetic evaluations and prediction of breeding values for dystocia was computed, using different statistical models by DMU program. Direct heritability for dystocia for heifers and other cows based on linear model were 0.10 and 0.07 and based on threshold model were 0.13 and 0.10, respectively. Estimated heritability was higher in threshold model compare to the linear model. The results of this study showed that beyond the environmental improvement, genetic selection might be an option for decreasing dystocia. Estimated heritability for heifers and other cows by the linear model were adjusted on the underlying scale to 0.19 and 0.14, respectively. Estimated correlations between direct and maternal genetic effects were negative and ranged from -0.56 to -0.74, indicating the genetic antagonism between direct and maternal effects. The Spearman rank correlations for breeding values predicted from the linear and threshold models were significant and different from 1, indicating that ranking of animals are not unique in linear and threshold models. Based on the Akaike Information Criterion (AIC), threshold model was better and more accurate than linear model for genetic analysis of dystocia in Holstein cows.

Genetic parameters for birth weight and survival traits were estimated using data collected from 1995 to 2009 in Jafarabad Moghani Sheep Breeding Station. Number of observation for survival and birth weight were 7202 and 6585, respectively. Genetic parameters were estimated using restricted maximum likelihood (REML) procedure under 16 different models, including animal, threshold and sire models using ASReml software. The most appropriate model for each trait was determined based on Akaike’s Information Criterion (AIC) method. The appropriate model for birth weight was included direct additive genetic, maternal additive genetic and common litter effects. Also, the animal model for lamb survival were included direct additive genetic, maternal additive genetic, maternal permanent environmental, common litter effects and covariance between direct and maternal additive genetic effects. The appropriate sire model for lamb survival was included sire direct additive genetic and common litter effects. Estimated direct heritability for birth weight was 0.09±0.02. The direct heritabilities for survival with animal model and sire model was 0.070±0.002 and 0.05±0.02, which after correction was changed to 0.22 and 0.15, respectively. Also, the estimation of heritability for lamb survival from threshold model was 0.30±0.10. Genetic, environmental and phenotypic correlation between birth weight and lamb survival were 0.61±0.24, 0.08±0.02 and 0.07±0.01, respectively. Consideration of environmental factors, including common litter effects, is essential for unbiased estimation of genetic parameters.

The aim of the present study was evaluation of genetic- economic merit for imported Holstein bull semen daughters in different climates of Iran. These progenies were categorized based on different selection indices of their sire semen exporter countries. In this study, data were milk, fat and protein yield, calving age and calving interval in the first lactation of 270566 Holstein cattle that were collected during 1993-2017 at Animal Breeding Center of Iran. The daughters breeding values were predicted under multi-trait animal model by DMU software. The genetic-economic merit of progeny was estimated using the Lifetime Net Income (LNI) index. Estimated least square means of the LNI index for daughters of imported semen under different selection indices were statistically significant in the various climates (p < 0.01). The highest estimated least square mean of LNI index in Iran was related to daughters whose sire semen came from France bulls (2001- 2011). The results obtained in this study showed that the highest estimated least square means of LNI index in cold, semi-cold, moderate and warm climates were related to daughters whose sires were imported from Germany (2008- 2013), France (2001- 2011), France (2012- 2013) and the Netherlands (2012- 2013), respectively. Thus, it could be concluded that the genetic-economic merit of daughters from imported semen in each climate depends on the selection index of bulls in the semen exporter country.

The aim of the present study was to investigate the effect of imported semen under different selection indices on phenotypic changes of production traits in Holstein cattle population in various climates of Iran. In the present research, records of first lactation on milk yield, fat and protein percentage of 269786, 216850 and 270566 Holstein cattle derived from imported semen under different selection indices in cold, semi-cold, moderate and warm climates, were used. The data were collected by the Center of Breeding and Improvement of Livestock Production during 1993 to 2017. The data were analyzed using the General Linear Model (GLM) software SAS 9.2. In cold, semi-cold, moderate and warm climates, the means of milk yield (kg) in the progenies of imported semen were estimated, 9597.92, 9654.46, 9718.34 and 8985.37, the means of fat percentage were estimated, 3.13, 3.07, 3.08 and 3.15 percent, and the means of protein percentage were estimated 3.10, 3.25, 3.14, and 3.16 percent, respectively. In the present study, the highest least square means of the phenotypic value of Holstein cattle derived from imported semen based on different selection indices in cold, semi-cold, moderate and warm climates were according to countries of France 2001-2011, Italy 1993- 2001, Netherlands 2001-2006, France 2001-2011 for milk yield, Netherlands 1999-2000, United States 1987-1988, United States 1992-1993, and Canada 1998-2000 for fat percentage and Canada 1991-1992, France 2012-2013, Sweden 2008-2012 and Germany 2002 -2007 for protein percentage, respectively.

The aim of this study was to compare three selection strategies and two properties of breeding value estimations using computer simulation. Simulated traits were weights at birth (BW1), eight weeks (BW8), twelve weeks (BW12), maturation (BWM) and also age at first laying (AFL), weight of first egg (EWM), average egg weight (EW) and egg number (EN). The first strategy was to select cockerels based on breeding value of BW12 and selection of hens based on a selection index with four traits including BW12, AFL, EW and EN. In the second strategy, cockerels and hens were selected using a selection index, as already said. But in the third strategy, cockerels were selected based on breeding value of BW12 and hens based on breeding value of EN. The individual's breeding values for three schemes were estimated by BLUP and ssGBLUP. Matings were performed based on the optimal genetic contribution. The results showed that the total economic values of the first and second programs using ssGBLUP estimations were 450, 460 and 421, and using BLUP were 434, 349 and 418, respectively. The rate of true inbreeding coefficient for ssGBLUP estimations were more than BLUP estimations (0.083, 0.287 and 0.046 vs. 0.072, 0.116 and 0.024, respectively). The results showed that the first strategy for a breeding flock of broiler production, the second strategy for a dual-purpose flock for producing egg and meat and the third strategy for a flock to achieve the highest total economic value with the lowest possible rate of true inbreeding were desirable.

The purpose of this study was to evaluate traditional, genomic, gene-assisted traditional selection and gene-assisted genomic selection methods for introgression a major gene in sheep population to improve the litter size trait using computer simulation. In this regard, a trait with heritability of 0.1, including two chromosomes each with a length of 100 cM, was simulated. On chromosome 1, a single QTL as the major gene was created that accounted for 40% of the total genetic variance. This QTL was located in the position of 25.7 cM. In breed A and B, animals were selected based for favorable and unfavorable to create two breeds that has been fixed for opposite alleles. Using the gene introgression approach, the favorable allele in breed A was insert to breed B and the new population was evaluated for genetic gain, accuracy of evaluation, frequencies of favorable allele and inbreeding rate. After five backcrossing generations, genetic gain in GasGenomic and Genomic methods was 26 and 62 percent higher than GasClassic and Classic methods, respectively. The frequency of favorable allele after five generations in Classic, Genomic, GasClassic and GasClassic was 0.387, 0.778, 0.965 and 0.975, respectively. The results of this study showed that if the goal is only introgression a major gene into an indigenous breed, by using gene-assisted classic selection, the frequency of a major gene can also be increased as much as obtain by the gene-assisted genomic selection.

The objective of this study was to compare introgression and synthetic breed strategies for litter size trait improvement in sheep using computer simulation. For this purpose, a trait with heritability of 0.1, consisting of two chromosomes was simulated. On chromosome 1, a single QTL as the major gene was created that accounted for 40% of the total genetic variance. The effect of favorable and unfavorable alleles for the QTL was fixed after seven generations in both A and B breeds, respectively. The introgression and synthetic breed strategies were compared using Classical and Classical with gene-assisted selection (GasClassical) methods. The genetic gain in introgression and synthetic breed strategies using GasClassical method was 39% and 16% higher than that of Classical method, respectively. The mean of inbreeding coefficient in the fifth generation in introgression strategy was 0.049 and 0.077 using the Classical and GasClassical methods, respectively, and in synthetic breed strategy was 0.11 and 0.008, respectively. The results of this study showed that the GasClassical method in comparison with the Classical method led to an increasing frequency of favorable allele (major gene) and genetic gain in both introgression and synthetic breed strategies. However, the genetic gain for one percent increase in inbreeding in the synthetic breed strategy was greater than that of introgression strategy, and as a result, the synthetic breed strategy performs better than introgression strategy.

The aim of this study was to identify regulatory genes affecting mastitis in dairy cattle using DNA microarray data. To reach this goal, the gene expression data with the largest number of arrays pertained to GPL1221 Platform with accession number GSE24560 was extracted from the GEO database. For quality control of data, ArrayQualityMetrics package and for preprocessing of data, three step function in AffyPLM, an add-in package in R environment were used. After identifying differentially expressed genes, a Tabu search algorithm was used to determine regulatory genes using bnlearn package in R environment. The results of this study revealed the causative and regulatory role for BCL2A, CCL2, S100A12, AOX1 and MGP genes on expression of other genes in mastitis of dairy cattle. Gene anthology analysis, revealed significant differences in 7 groups of molecular function, 48 groups of biological process and 11 groups of cellular components. Also, the results of the enrichment of the gene expression data set showed that most of the differentially genes expressed in this study that were significantly (P<0.05) active in metabolic pathways (GO: 0009605, GO: 0002376 and GO: 0006954) involved in response to pathogens, immune response and response to inflammation in the mammary tissue of dairy cattle.

Faḍā’il al-Ṣaḥāba wa Manāqibuhum wa Qawl Ba’ḍihim fī Ba’ḍ (Virtues of the Sahaba and their dignities and what they have said about each other) is a book attributed to Dārquṭnī, a prominent Sunni scholar of hadiths in the 10th century, which is apparently not available to us. A few years ago, a book was published in Saudi Arabia, which was claimed by its editors to be the 11th and the only available part of Dārquṭnī’s book. The importance of this small book of hadiths lies in the fact that it only includes virtues of the first two caliphs as expressed by Imām ‘Alī and his household. In this paper, we deploy a descriptive-analytic method drawing on what is acceptable and taken granted by both sides, and then study the chains of transmitters of the books and some of its hadiths and criticize its content to show that all hadiths in this section are unreliable in terms of criteria accepted by Sunni scholars of rijal, and only two of its hadiths fair a bit better in terms of reliability, although they conflict well-established evidence from hadiths and history.

The aim of the study was to compare two strategies in Mazandaran native fowls using computer simulation.  Simulated traits included body weight at birth (BW1), at eight weeks of age (BW8), at twelve weeks of age (BW12), at maturation (BWM), age at sexual maturity (AFE), weight of first egg (EWM), mean egg weight from 28 to 32 weeks of age (EW28-32) and egg number (EN). The first strategy was to select cockerels based on breeding value of BW12 and hens based on a selection index with 4-traits including BW12, AFE, EW28-32 and EN. The second strategy was to select cockerels and hens using a selection index based on a 4-traits including BW12, AFE, EW28-32 and EN. After 10 generations, the first strategy improved BW1, BW12, BWM, EW28-32 and EWM to 1.49, 573.81, 397.58, 3.96, and 3.75 grams and AFE and EN to -3.51 days and 2.09 eggs, respectively. After 10 generations, the gain for traits in the second strategy for BW12, BWM, AFE and EN was 415.78, 218.74 grams and -9.77 days and 9.45 eggs, respectively. At the end of the tenth generation increase of inbreeding in the first and second strategies was 0.048 and 0.070, respectively.  The results showed that the first strategy was suitable for a breeder flocks with the aim of chickens suitable for broiler production and the second strategy was suitable for a dual-purpose flocks with the aim of producing egg and meat.

The aim of this study was to extract genes and probes hub based on Bayesian networks on probe and gene transcriptomic data over different tissues in Bovine species. Using raw probe and gene transcriptomic data in each tissue, genes and probes with the highest expression variances were extracted and fitted to Bayesian networks. The hub genes and hub probes were identified using the ratio of in-and-out degree.The size of the Markov Blanket was different in different networks. This might be indicative of existing of substructures topology of aforementioned network on different tissues. Using gene based network, in muscle (CBR1 and LOC788826); in mammary of (NID2, COL5A2, LOC616942 and FXYD3); in liver (LOC100132279; MGC127133; MBOAT2; CLDN2; ANKRD1; IGFBP1; DGAT2; CKMT1, ISG15, CKMT1), and in the ovary (LOC286871 and INHBA) were extracted as hub genes. It was shown that the hubs were different in different tissues. These results can be used for more accurate bioassays of each tissue. Using probe based network, two genes BOLA-DQB and JSP.1 would have function in liver and uterus tissues. The results of this study can reduce the gap between phonemics-and Genomics distance on investigated tissues in bovine species.

In this research, cytoplasmic inheritance of yearling mohair weight (YMW) in Markhoz kids were studied by using Bayesian statistical method. Using records which gathered through 1992-2011 in Markhoz goat breeding research station in Sanandaj. GLM procedure of SAS statistical software was used to verify statistical significant of environmental factors on YMW and Gibbs1f90 software, based on animal model and Gibbs sampling, were used to estimate genetic parameters . Environmental factors such as year of birth, maternal age and sex as fixed effects, and animal age and body weight at recording time as covariates were considered in the model. Based on the results of this research, the minimum DIC was detected in Model 12. Which includes direct additive genetic effects, maternal additive genetic, maternal permanent environment and cytoplasmic genetic effects, taking into account the covariance between direct and maternal genetic effects. The ratios of direct additive genetic variance, maternal additive genetic, maternal permanent environment, cytoplasmic genetic on phenotypic variance were respectively 19.27, 6.6, 3.03 and 1.82 percent based on the selected model (model 12). In general, the results showed that selection based on direct genetic potential and partly on maternal genetic can improve the YMW. Due to the significant of cytoplasmic effects to enter the model on one hand and the low value of its variance on the other hand, it can be concluded that the role of Cytoplasmic inheritance as a correction factor is important, but it cannot be considered as selection criteria.

Lamb survival is a complex trait that is influenced by the maternal ability, management practices, and environmental variables at the time of birth and during the rearing period.
In this study genetic and non-genetic parameters affected on lamb survival from birth to weaning were estimated for Baluchi, Iranblack and Zandi lambs.
Numbers of observation were 10793, 4826 and 6140 record of lamb survival from birth to weaning for Baluchi, Iranblack and Zandi breeds. Genetic parameters were estimated using restricted maximum likelihood (REML) procedure under 16 different models, inclusive animal, and sire and threshold models by ASReml software. In addition to an animal, sire and threshold models, using a logit link function, were used for analyses of lamb survival. The most appropriate model was determined based on Akaike’s Information Criterion (AIC) method.
Mean of survival was 89.11, 84.44 and 87.37% for Baluchi, Iranblack and Zandi lambs, respectively. The most appropriate model for survival in Baluchi sheep including direct additive genetic effects and common litter effects, for Iranblack sheep including direct additive genetic effects, maternal additive genetic effects, maternal permanent environmental effects, common litter effects and covariance between direct and maternal additive genetic effects. However, the most appropriate model for survival of Zandi sheep only including direct additive genetic effects. The most appropriate model under sire models for Baluchi sheep including direct additive genetic effects and common litter effects, for Iranblack sheep including direct additive genetic effects, maternal permanent environmental effects and common litter effects. Also for Zandi sheep including direct additive genetic effects and maternal permanent environmental effects. Estimated direct heritability for survival with animal model was 0.08±0.01, 0.07±0.02 and 0.09±0.02 which after correction were changed to 0.22, 0.20 and 0.20 for Baluchi, Iranblack and Zandi sheep, respectively. Estimated direct heritability for survival with sire model was 0.06±0.02, 0.06±0.03 and 0.05±0.02 which after correction were changed to 0.17, 0.16 and 0.13 for Baluchi, Iranblack and Zandi sheep, respectively. In addition, the estimation of heritability for lamb survival from threshold model was 0.16±0.04, 0.22±0.07 and 0.17±0.06 for Baluchi, Iranblack and Zandi sheep, respectively.
The results showed that the corrected heritability obtained from animal model and sire model did not differ from the estimated heritability from the threshold model.

Introduction The mating of related individuals produces an inbred offspring and leads to an increased homozygosity in the progeny, genetic variance decrease within families and increase between families. The ration of homozygosity for individuals was calculated by inbreeding coefficient. Inbred individuals may carry two alleles at a locus that are replicated from one gene in the previous generations, called identical by descent. The inbreeding coefficient should be monitored in a breeding program, since it plays an important role at decreasing of homeostasis, performance, reproduction and viability. The trend of inbreeding is an indicator for determining of inbreeding level in the herd. Inbreeding affects both phenotypic means of traits and genetic variances within population, thus it is an important factor for delimitations of genetic progress in a population. Reports showed an inbreeding increase led to decrease of phenotypic value in some of the productive and reproductive traits.
Materials and Methods In the current study, the pedigree data of 14030 and 6215 records of Baluchi and Iranblack lambs that collected from 1984 to 2011 at the Abbasabad Sheep Breeding Station in Mashhad, Iran, 3588 records of Makoei lambs that collected from 1994 to 2011 at the Makoei sheep breeding station and 6140, records of Zandi lambs that collected from 1991 to 2011 at the Khejir Sheep Breeding Station in Tehran, Iran were used to estimating the inbreeding coefficient and its effects on lamb survival in these breeds. Lamb survival trait was scored as 1 and 0 for lamb surviving and not surviving at weaning weight, respectively. Inbreeding coefficient was estimated by relationship matrix algorithm (A=TDT') methodology using the CFC software program. Effects of inbreeding coefficient on lamb survival were estimated by restricted maximum likelihood (REML) method under 12 different animal models using ASReml 3.0 computer programme. Coefficient of inbreeding for each lamb added to models as a covariate. The most appropriate model for this trait was determined by Akaike’s Information Criterion (AIC) test.
Results and Discussion The number of survival records for Baluchi, Iranblack, Makoei and Zandi sheep breeds were 10793, 4826, 3588 and 6140, respectively. The inbred individuals were 17.63, 58.25, 4.88 and 36.32 per cent for Baluchi, Iranblack, Makoei and Zandi sheep, respectively, (2473, 3620, 175 and 2230 head respectively). The mean of inbreeding coefficient for whole and inbred populations for Baluchi lambs were 0.66 and 3.73 per cent, respectively, for Iranblack lambs were 4.59 and 7.90 per cent, respectively, for Makoei lambs were 0.25 and 4.86 per cent, respectively and for Zandi lambs were 1.22 and 3.61 per cent, respectively. Maximum of inbreeding coefficient for Baluchi, Iranblack, Makoei and Zandi lambs was 31.25, 34.70, 25.00 and 31.35 per cent, respectively. The mean of lamb survival in Whole and inbred population for Baluchi lambs were 89.11 and 88.30 per cent, respectively, for Iranblack lambs were 84.44 and 83.84 per cent, respectively, for Makoei lambs were 90.40 and 86.95 per cent, respectively and for Zandi lambs were 87.37 and 86.90 per cent, respectively. The average of inbreeding coefficient for 4 breeds was increased. The estimation of positive inbreeding coefficient trend for Baluchi, Iranblack, Makoei and Zandi were 0.035±0.012, 0.31±0.03, 0.010±0.012 and 0.020±0.012 per cent on each year, respectively. The most suitable model for survival in Baluchi, Iranblack, Makoei and Zandi breeds was 7, 12, 2 and 1, respectively. The regression coefficient of inbreeding on lamb survival were -0.26±0.11, -0.35±0.11, -0.25±1.83 and -0.04±0.20 per cent for Baluchi, Iranblack, Makoei and Zandi sheep, respectively.
Conclusion The levels of inbreeding below 5% in whole population, or annual rates of inbreeding under 1% unlikely result in substantial reduction of performance and economic income in sheep production and serious genetic variation in the population. Inbreeding depression was observed for survival trait although the levels of inbreeding coefficient were acceptable in all of the breeds investigated in this study. Therefore, the general policy in the flocks should be continued to avoid mating between close relative parents and use of enough sires and dams selected per annum. Estimated inbreeding coefficients for Baluchi and Iranblack breeds showed high degree of close mating in these herd and due to the significant effect of inbreeding on survival, it is suggested that this breeding stations should use a breeding plan to avoid mating of close relative animals.

The Markhoz goat is one of the most important breeds In Iran. These animals had an important cultural role in Kurdistan because the mohair obtained from these animals is used for making national clothes. The mating of related individuals produces an inbred offspring and leads to an increased homozygosity in the progeny, genetic variance decrease within families and increase between families. The ratio of homozygosity for individuals was calculated by inbreeding coefficient. The trend of inbreeding is an indicator for determination of inbreeding level in the herd. Result of researches showed increasing of inbreeding resulted to decrease of phenotypic value in some of production and reproduction traits. So the aims of this study were estimation of inbreeding coefficients and its effects on birth weight (BW), weaning weight (WW), average daily gain to weaning (ADG), 6 month weight (6MW), 9 month weight (9MW) and yearling weight (YW) of Markhoz goats.
In this study, pedigree data of 4186 Markhoz goats which were collected from 1992-2012 by Markhoz Goat breeding center located in Sanandaj, were used. Inbreeding coefficient was estimated by the CFC software program. Inbreeding depressions in growth traits were estimated by restricted maximum likelihood (REML) method under 12 animal models that animal and dam’s inbreeding coefficients added to models as a covariate. The most appropriate model for each trait was determined by Akaike’s information criterion (AIC).
The 58.07% of animal were inbred. The mean inbreeding coefficient for the herd and inbred population was 3.03 and 5.21% respectively. Maximum inbreeding coefficient was 31.25%. The 47.04% of animal was inbreeding coefficient between 0 to 10 percent. 553 head of dams were inbred and inbreeding coefficient for the whole and inbred dams was 2.05 and 4.91% respectively. Inbreeding coefficient was increased 0.24±0.04 percent in each year (P Estimated inbreeding coefficients for this breed showed high degree of close mating in this flock and due to significant effect of inbreeding on some growth traits it is suggested that this breeding station should use a breeding plan to avoid mating of close relative animals.

In this research, 6517 records, collected by Khojir sheep Breeding Station (Tehran, Iran), during 1991 to 2011 were used to estimate genetic parameters of lamb survival in Zandi sheep. Genetic parameters were estimated using 16 different models of animal model, sire and threshold models using REML procedures. The AIC criterion was used to evaluate the models. The effects in the most suitable animal model were included direct additive genetic, maternal additive genetic and permanent environmental effects. The effects in the most suitable sire model were included sire additive genetic effects and maternal common litter effects. The effects in the most suitable threshold model were included only sire additive genetic effect. The estimated heritability of lamb survival based on animal, sire, and threshold models were 0.09 ± 0.001 and 0.13 ± 0.02, and 0.19 ± 0.06, respectively.

The aims of this study were estimation of inbreeding coefficients and its effects on birth weight (BW), weaning weight (WW), 6 month weight (6MW), 9 month weight (9MW) and yearling weight (YW) of Zandi sheep. The pedigree data and records were of 6140 Zandi sheep, which were collected during 1991-2011 by Zandi sheep Breeding Center located in Tehran. 36.32 % of the animals were inbred. Mean inbreeding coefficient for the herd and inbred population was 1.22 and 3.61 percent, respectively. Inbreeding coefficient was increased by 0.02±0.01 percent per year (P<0.05). Effects of inbreeding on traits were estimated by restricted maximum likelihood method using 12 animal models. The most appropriate model for each trait was determined based on Akaike’s Information Criterion. The regression coefficients of inbreeding on BW, WW, 6MW, 9MW and YW were -3.49±4.87 (P>0.05), -42.20±20.18 (P<0.05), -60.35±25.12 (P<0.05), -40.70±24.80 (P>0.05) and -76.55±29.24 gr (P<0.01), respectively.

In order to evaluation of genotype by environment interactions in Holstein cows, Iran was divided into cold, middle cold, temperate and hot climate regions. For this purpose used from 39570, 35813 and 18955 records for milk, fat and protein yields, respectively, to progeny test for 35 sires that have 50 daughters in each climate. The data were collected by the Centre of Breeding and Improvement of Livestock Production from 775 herds, during 1991 to 2009 years. Breeding values for milk, fat and protein yield for each animal were predicted from multiple traits with animal model (BLUP). Average of breeding value estimated for sires in cold, middle cold, temperate and hot climate was 75.53, 377.74, 167.08 and 81.49 kg for milk yield, -0.18, 5.42, 1.85 and 1.63 kg for fat yield and 0.96, 8.05, 3.93 and 1.94 for protein yield respectively. Spearman correlation for milk yield for cold-middle cold, cold-temperate, cold-hot, middle cold-temperate, middle cold-hot and temperate-hot also was 0.63, 0.61, 0.45, 0.87, 0.54 and 0.48 respectively, for fat yield was 0.63, 0.69, 0.52, 0.91, 0.49 and 0.40 respectively, and for protein yield was 0.61, 0.62, 0.39, 0.81, 0.48 and 0.41, therefore spearman correlation estimated show that ranking of sires was difference at different climates and existent genotype by environment interaction at difference regions of Iran.