m. razmkabir

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.

The profitability of dairy cattle herds mainly depends on the reproductive performance of cows. Because reproductive performance is effective on the amount of daily milk and calf production per cow, increasing the number of inseminations per conception, lengthening the calving interval in the herd, and causing the voluntary (due to the age of the animal) and involuntary (due to illness or fertility disorders) elimination. For evaluating fertility traits, we sometimes come across domains whose records were incomplete at the time, out of range, or delayed. These records are called censored records. The typical way to deal with such records is to delete them from the data set. However, this reduces the information available for genetic evaluation and may affect trait variance by masking actual genetic differences between animals. Another way is to use appropriate statistical methods to place censored records in genetic evaluations. The use of censored records in genetic evaluations yields more reliable genetic parameters, and it can increase the estimation accuracy of breeding values giving the support that the breeding value estimation is close to the true breeding value. The present study aimed to investigate the role of censored records in the estimation of genetic parameters of the number of inseminations per conception in Iranian dairy cows.
The dataset included 29621 records collected from 2005 to 2019 by the Vahdat Cooperative of Isfahan in Iran. FoxPro software (version 9.0) was used to edit and prepare data, remove incorrect records and create contemporary groups. Five animal models, including Threshold Model (TM), Penalty Model (PM), Modified Penalty Model (MPM), Threshold-Threshold Model (TTM), and Modified Threshold-Threshold Model (MTTM), were used for the genetic evaluation of this trait. The predictive ability of the models was assessed using cross-validation. Also, a simulation study was performed to determine the appropriate model.
The estimated heritability using different models was 0.3 (0.013), 0.07 (0.013), 0.07 (0.013), 0.3 (0.13), and 0.4 (0.012) for TM, PM, TTM, MPM, and MTTM, respectively. The highest correlation of breeding values for all animals was between MPM and TM (0.98). The same result was obtained for the best sire (sire with at least 20 daughters). The high correlation shows that these models work similarly in selecting the best sires. The low correlation between models indicates that the models rank sires differently. Therefore, the choice of model can affect the ranking of males. The top 10 sires showed less correlation between models than the active sires. When the number of males decreases, the selection becomes more strict. The prediction accuracy in models with censored records is higher than in models without censored records because the use of models that include censored records is due to the increased information about the trait, and the absence of bias due to deleting records improves the accuracy of estimating breeding values. Consequently, if the censoring status is not taken into account, animals with superior breeding values may be biased. The low ratio of common superior animals in different percentages between models showed that these two models rank the animals differently. Still, the high proportion of common superior animals indicates the similarity of the two models in choosing the best animals. So, model selection can be effective in ranking superior animals because when the censored record is used, the information is increased and the situation would be closer to reality. The cross-validation showed that the accuracy of the breeding value prediction by different models was higher in models with censored records than in models without censored records. The results of the simulation study showed that the models with censored records provided better genetic parameter estimates. TTM has been able to estimate expected heritability better than other models. The percentage of top animals in common between the top 10 and the top one percent of simulated animals with different models showed that the ability of the TTM model to select real top animals is more than other models, which shows that this model has identified top animals better.
The results of the present study showed that the censored records are important for estimating the genetic parameters of the number of inseminations per conception in Iranian dairy cows and ignoring those led to a biased estimation of the parameters. Data simulations also showed that using censored records provided more realistic genetic parameter estimates.

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 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.

In the present study the potential consideration of calf birth weight (BW) and gestation length (GL) as correlated traits for improving genetic evaluation of calving difficulty (CD) in Iranian Holsteins at first calving was studied applying data collected from 2002 to 2013 in 131 herds by Animal Breeding and Production Improvement center of Iran. The influences of direct and maternal additive genetic effects on each trait were tested and the most appropriate model for each trait determined. Considering the most appropriate model for each trait, predictive abilities of four genetic evaluation models of CD including univariate model of CD, bivariate model of CD and BW, bivariate model of CD and GL and trivariate model of CD, BW and GL were compared applying mean of squares and correlation between observed and predicted values. The obtained results revealed that the model included direct additive genetic and maternal additive genetic effects as random effects, without considering covariance between them, was the most appropriate model for estimating variance components of the considered calving traits. Comparisons of the models revealed that model included CD and BW had better predictive ability than univariate model included CD and the bivariate included CD and GL in terms of lower mean square of error and higher Pearson correlation between observed and predicted values of CD. There was no difference between bivariate model (CD- BW) and multivariate model (CD-BW-GL) in terms of predictive ability. Therefore, BW can be considered as a suitable correlated trait for genetic evaluation of CD at first calving in Iranian Holsteins.