محمد رکوعی

The productivity of Holstein dairy cattle herds is significantly influenced by prevailing climatic conditions. Given the potential variability in climates within a single province, this study aimed to investigate the impact of different climates across the country on the productive characteristics of these herds. The study examined average milk production, fat content, protein content, fat percentage, and protein percentage, analyzing data from 325,040 heifers belonging to 270 herds for the period between 2006 and 2021. The regions of the country were classified into five distinct climates, namely BSh, BSk, BWk, Csa, and Dsa, based on the Köppen classification system, which characterizes climates by varying temperature and humidity levels. The study found that the BWk climate, characterized by cold and dry conditions, exhibited the highest milk production levels despite the unfavorable climatic conditions. This outcome can be attributed to effective herd management practices implemented in cities such as Isfahan, which fall under this climate category. The Dsa climate, characterized by a continental climate with hot and dry summers, demonstrated the third-highest milk production levels and was found to be relatively suitable for livestock rearing, particularly during seasons other than summer. Additionally, the Dsa climate was highly conducive to the growth of fodder for livestock and exhibited the best performance in terms of both the quantity and percentage of fat and protein. Despite having the lowest number of herds among the different climates, the Dsa climate outperformed the other climates in terms of production traits. Moreover, in the period from 2007 to 2021, when increasing economic problems, such as the increase in inflation and currency rates, as well as the removal of livestock input subsidies, made it difficult for livestock farmers to cover the costs of providing animal feed, all regions except Dsa region experienced a decrease in the number of herds. From the findings of this research, it can be concluded that the climatic effect in terms of heat stress for livestock and in terms of the suitability of weather conditions for planting fodder and providing livestock feed can have a decisive effect on the productive traits of livestock.

Growth traits (such as body weights at different ages) in most of the birds have been often considered in most of the poultry breeding programs. Changes in growth pattern can be evaluated through measuring body weight traits at regular intervals and using mathematical functions (growth curve functions). For this purpose, data from 1182 wild (including 905 female and 277 male) and 674 Italian speckled (including 499 female and 175 male) quails were utilized. Accordingly, after body weight at hatch, body weights of the birds were recorded through 45 days in a 5-day interval manner. Gompertz, Logistic, Lopez, Richards, and von Bertalanffy were used to estimate growth curve parameters. To evaluate/ rank the goodness of fit for functions, the BIC, AIC, MSE, and  were used. Based on results, Richards’ function for both studied populations (wild and Italian speckled quails) and for both genders (females and males) were the best fitted model. The relatively same growth pattern and same function for describing growth pattern in these two quail strains refer to the same growth traits, therefore simultaneous production of them can be achieved under same management practices. Moreover, comparing results of the current studies with other researches, by comparing other studies with this study’s results, it can be concluded that increasing the number of records and shortening the weighing intervals can be effective in determining the appropriate function.

The longevity in dairy cow is the duration of presence of an animal the herd from the date of first calving to the date culled. In present research, the aim is 1) to estimate the genetic parameters of the longevity trait of uncensored animals using random regression model and 2) to study longevity of daughters of sires in the population using the EBV of bulls based on 20 daughters and 3) to test the random regression model (RRM) for EBV prediction of Animals with censored data. Genetic parameters of longevity and breeding value of bulls were estimated by ECHIDNA software using RRM with restricted maximum likelihood (REML) method. The file used for the genetic evaluation contained data on 18,120 daughters from 906 bulls. A number of 20 daughters that randomly selected from each sire to use for EBV prediction. In addition to the daughters used for genetic evaluation (18,120 cows), there were 285,064 daughters of the bulls in the main file. The bulls were grouped according to the Breeding value from high to low based on the area under the normal curve. Then, the mean of longevity of the daughters in each group who were not used the EBV prediction calculated. In a file 10 daughters were randomly selected of 20 daughters of each bull and their months of longevity divided by 2 and 3. These data were considered as censored in the data file. The permanent environmental effect and the additive genetic effect had the largest and smallest contribution to the total variance, respectively. The heritability of the trait was low (0.003-0.032) which is in agreement with results of other report. The difference of mean longevity between groups (LSD test) was significant (P˂0.01). Also, the increase of the mean of EBV of the groups, the mean of longevity of their daughters in the population increased. The correlation of EBV of animals with censored and uncensored data state were +0.815. In the split the low heritability of the longevity trait, using the sperm of superior bulls in terms of EBV of longevity can improve the longevity in the population. Also, it is possible to evaluate and select the bulls with a low progeny number and increase the mean of longevity in the population of Holstein dairy cows. Moreover, the EBV of longevity for young and producing animals can be predicted by RRM.

The egg production curve is defined graphically as the relationship between the number of eggs and laying time, which indicates the biological efficiency of a hen and can be effective in the selection and nutritional management of laying hens. Egg production is an essential section of the poultry industry. Appropriate mathematical models accurately represent the production phases of the hen and provide a valuable tool for biological comparisons and interpretations. Also, egg production curves help predict egg production, determine the appropriate age for poultry culling, and economic decisions. Sigmoid growth models are often used to describe size over time in plants, animals, and humans. In laying hens, the shape of the cumulative egg production curve is similar to the growth curve. Therefore, different growth models may be used to model the cumulative egg production curve. Khazak hen is one of the native birds of the Sistan region (Iran), and natural selection has adapted this bird to the conditions of Sistan over the years. The body of this chicken is small, and has low growth and is mainly kept for egg production. Since laying patterns is different in populations. Thus, the use of an appropriate model to describe the specific laying pattern of each population is necessary. Therefore, this study was conducted to investigate growth models to describe the cumulative egg production and weight of eggs and select the best model for the Khazak hen. The present study was conducted in the Research Center of Domestic Animals (RCDA), the Research institute of Zabol, Zabol (Iran). Khazak pullets are identified using foot-banded numbers before they start laying. During the experiment, all birds had access to water and feed ad libitum. The egg production was recorded daily for each hen separately. Based on daily records, the weekly egg production of each bird was calculated and then used the calculation of the cumulative egg production. A total of 365 pellet egg production records were used to analyze the production curve from the first to the fortieth week of laying. Five growth models (Gompertz, Logistics, Richards, Lopez, and Weibull) were fitted on cumulative egg production and weight records. The goodness of fit criteria, including Akaike information criterion (AIC), mean square error (MSE), Bayesian information criterion (BIC), and adjusted coefficient of determination ( ), were used to compare the growth models and to select the best model. All models were fitted on egg production records using the nlme package in R software, and the parameters of each model were estimated. After fitting the models, the cumulative production values for different ages were predicted by the models and were compared with the actual values over 40 weeks. Based on the goodness of fit criteria, the Lopez mod had the highest  value and lowest values of AIC, BIC, and MSE for cumulative egg production. While the Weibull model was the best model than other models to describe cumulative egg weight in terms of the goodness of fit criteria. The Gompertz and Logistic models overestimated initial production and underestimated the final production compared with other models. Estimates of time and production at the inflection points using Lopez and Weibull models were close to actual values of cumulative egg production and weight, respectively. Also, prediction of cumulative egg production and egg weight in different weeks using Lopez and Weibull models was accurately, respectively. In literature, various models were reported as the best model to describe the egg production curve, which indicates that the appropriate model specific to each breed should be used to evaluate its curve. The overestimation and underestimation of initial and final production using Logistic models were reported in other research that was similar to our findings. The important application of egg production models in poultry is to estimate the economic and genetic value by predicting total egg production from some records, which can be a suitable tool for biological comparisons and interpretations. The results of the present study, showed that the Lopez and Weibull models were the best models to describe the cumulative egg production and egg weight based on four good fit criteria, respectively. Therefore, these models can be used to describe the cumulative egg production and egg weight in Khazak hens. The application of these growth models can be useful to nutritional management and breeding programs to improve and change cumulative egg production and egg weight.

Fertility is one of the most important economic traits in dairy cattle breeding which, in addition to negative effects on functional traits such as milk production, reduces the profitability of the dairy cattle breeding industry. Therefore, the aim of this study was to Meta-analyze traits related to fertility in dairy cows and determine an appropriate strategy to control and improve fertility in dairy cows.

For this purpose, by searching in databases, 38 articles related to fertility in different herds of dairy cows were collected and different parameters including additive genetic and residual variance components, heritability, reproducibility, descriptive characteristics of traits including mean, minimum, maximum, coefficient variation, standard deviation as well as genetic correlations between traits that were present in at least three reports were extracted as a new variable and statistically analyzed. The studied traits included age at first service, age at first calving, calving interval, open days, number of services, conception length, the first service leading to conception and non-return rate at 56 days. Data analysis was performed with SAS software version 9.2 and Comprehensive Meta-analysis. Finally, the articles were grouped into four regions of Asia, Africa, America and Europe and different parameters including mean, heritability and reproducibility of different fertility traits were analyzed by SAS software GLM procedure and comparison of mean groups by Turkey’s test at the level 5% probability was done.

Mean of open days, age at first calving, age at first service, calving interval, conception length, first service leading to conception rate, no-conception rate in 56 days and numbers of services for each conception traits were 139.2, 888.3, ​​501.6, 411.8, 278.8 days, 62.8, 21% and 2.1, respectively. Also, the heritability of the mentioned traits was estimated to be 0.06, 0.2, 0.3, 0.06, 0.1, 0.1, 0.07 and 0.08, respectively. The reproducibility of traits were open days, calving interval, first service leading to conception, conception length and number of services per conception were 0.1, 0.1, 0.07, 0.1 and 0.06, respectively. There was a moderate and sometimes high positive and negative genetic correlation between most of the fertility-related traits. The results of comparison of estimates in the four continents of Asia, Africa, Europe and the Americas were not significant in all fertility-related traits.

Therefore, all the mentioned estimates, which in most cases are reliable and close to each other, indicate a low degree of heritability and repeatability of the mentioned traits, and the use of conventional breeding methods cannot determine high genetic value with good accuracy and it is recommended to improve the management of dairy cows and control environmental factors and the use of breeding programs as well as genomic evaluation of dairy cow.

The present study aimed to compare the effect of upgrade of alleles by genome editing was investigated on genomic variance, response to selection and coefficient of inbreeding. For this study, a population of dairy cattle was simulated based on over ten generations with an effective size of 100 individuals in the base population. The genomic structure was assumed consisting of 3 chromosomes with a length of 100 cM and On each chromosome were located 1000 markers 2 allelic markers with a frequency of 0.5 and fifty QTL double alleles, in random with equal frequency. Marker effects and variance components were estimated using Bayes Lasso method and additive model. Then, upgrade of alleles was performed on 5 and 10 bulls. In the first stage 1, then 20, 25 and 50 QTN was upgraded by genome editing. The BGLR package in R software was used to estimate the additive effects and variance component. In the next step, the mean inbreeding coefficient for GS+PAGE was calculated and compared with the GS by PLINK software. The effect of upgrade alleles by genome editing was increased additive variance. With 1 QTNe was upgraded and inherited by next generation, additive variance relative to genome selection increased by 0.139. The response to cumulative selection in GS+PAGE model in 5 bulls and 1, 20, 25 and 50 QTNe, increased by 0.07, 0.17, 0.29 and 0.31, respectively. With increasing the number of QTNe, the inbreeding coefficient also increased slightly, but there was no significant. Genome editting improves the genetic variance of the population without increasing inbreeding.

disadvantages of using sexed semen among dairy producers in terms of outcome and economic efficiency. A questionnaire containing 28 five-choice Likert scale questions was prepared to test the attitudes of respondents concerning the use of sexed sperm in terms of functional, economic, cognitive and infrastructural aspects. The respondents were the researchers, consultants and dairy farm employees. The findings indicated that farm employees, unlike the researchers, believed that sexed sperm was effective in reducing dystocia, and the conception rate was not deleteriously affected in differentclimates (P<0.01). Better performance of sex-sorted semen in heifers compared to multiparous cows was significantly confirmed by farm employees and consultants compared to the researchers (P<0.01). According to the researchers, the use sex- sorted semen is uncommon and hence the use of this type of sperm has a higher risk (P<0.01). The results of this study indicated that the attitude of employees in large industrial dairy farms is largely consistent with the scientific facts published in the field of sex-sorted semen, and the disagreement of this

The aim of this study was to discover QTL for body weight traits on chromosome 3 of Japanese quail in a four-generation design based on diallel crosses. For this purpose, four strains of Wild, AandM Texas, Italian and Tuxedo Japanese quail were crossed in reciprocal and diallel pattern. The first generation of hybrid birds was then used to produce the next generations, including the second, third, and fourth generations. Phenotypic data included body weight gain from hatching to 45 days with an interval of 5 days in the offspring of the selected fourth generation parents. Third and fourth generation parents and all offspring of selected fourth-generation parents (369 birds) were genotyped for three microsatellite markers on chromosome 3. Marker effects and variance components were estimated using three models for additive, dominant, and additive-dominant markers using GVCBLUP software For marker effects estimation, the point with the highest F statistic was considered as the QTL position. The results of this study indicate the presence of at least one QTL with additive effects related to body weight traits at 5, 10, 20 and 40 days at the beginning of the chromosome and for hatching traits, 15, 25, 30, 35 and 45 days at the 38cM of chromosome 3. Significant QTLs were also found in the dominance model for most traits, except for 25 and 35 days at the beginning of chromosome 3. The percentage of changes due to additive and dominance effects of markers in the phenotypic expression ranged from 1.3 to 8.7%.

The aim of this study was to investigate the genetic diversity of different camel breeds in Sistan and Baluchestan province using microsatellite markers. For this purpose, 70 camels were randomly selected from Jamazeh and Baluchi breeds. Jugular vein blood sampling was performed in the tubes containing 0.5% EDTA. The extraction of DNA was performed by salt-detergent method. Five microsatellite markers were selected from the camel genome project with specific primers and banding patterns on 5% agarose gel. Genetic and population structures were analyzed using POPGENE v1.31 software. The number of alleles in five marker positions in Jamazeh and Baluchi breeds ranged from one to six alleles. The number of alleles in five markers CVRLO6, VOLP32, LCV66, WYLLO and CMS17 in Jamazeh are equal to three, two, three, four and one alleles, respectively, and in Baluchi breed with two, four, two, five and one alleles, respectively. According to the results, the range of heterozygosity observed in the studied sites in Jamazeh and Baluchi breeds was in the range from 0.29 to 0.52. The results of FST analysis showed that the two populations were more than 96% similar and the difference between them was 3%. The results of the presentresearchindicated a low rate of polymorphism in the studied sites and in order to preserve breeds and be more adaptable to environmental conditions, it needs more attention and control of inbreeding.

The main purpose of a breeding program is to increase the genetic capacity of farm animals for important economic traits. Although the success of genetic selection to increase milk production in dairy cows is quite obvious, the fertility of herds has decreased. The heritability of lactation curve parameters has been reported to be low, indicating that the lactation curve is highly influenced by environmental factors. As a result, direct selection for these traits will not lead to effective genetic improvement, and selection based on correlated traits can be investigated. Studies on the lactation curve of Holstein cows in Iran have often been performed using three-parameter functions. The Rook function has recently been introduced as a suitable function to describe the lactation curve of Iranian Holstein cows. The purpose of this research was to estimate the correlation between the lactation curve parameters of the Rook function (initial production (a), the rate of reaching the production peak (b), maximum production (c), the curve changes after reaching the peak of production (d), the peak time (pt), amount of production at the peak (pm), and persistency (p)) with some production traits (305-d milk, fat and protein production), somatic cell score and age at first calving and also evaluating curve parameters in different phenotypic groups of the economic traits in Holstein cows. A total of 847129 test day records of milk production in the first lactation collected by the Animal Breeding Center and Promotion of Animal Products of Iran from 1983 until 2017, were used. The Rook function was fitted to the test day records and the function parameters were separately calculated for all animals. Estimation of variance components and genetic correlation between the parameters of the lactation curve with the production traits (305-d milk, fat, and protein), somatic cell score, and age at first calving was performed by bivariate analysis via the Gibbs sampling method. To investigate the relationship between economic traits and milk curve parameters, animals were divided into three phenotypic groups including high, medium, and low based on the phenotypes of economic trait, and then the value of curve parameters was evaluated between three groups. The highest genetic correlation was estimated between milk production and peak production (pm) (0.958). The genetic correlation between milk production and persistency was relatively high (0.725). Genetic correlation of somatic cell score with initial production (a), maximum production (c), and amount of production at the peak (pm) was undesirable and its correlation with parameter curve changes after maximum yield (d) was favorable. Therefore, it is expected that selection to reduce initial production and production at the peak and increase curve changes after maximum yield could decrease the somatic cell score. The correlation estimates between persistency with 305-d milk, fat, and protein production were positive, and a negative correlation was estimated between somatic cell score with age at first calving, so it can be expected that selection for persistency will increase the production traits, and udder health could be improved by reducing the number of somatic cell score and age at first calving. In most cases, the values of curve parameters among the three phenotypic groups of traits had significant differences, and in the high production group, age at first calving, the value of initial production, peak production, and persistency were higher compared to other groups; however, an inverse relation was observed for somatic cell score. The estimated correlations showed that the selection of animals for increased initial production (a) and production at the peak (pm) will improve milk production during 305 days. Increasing the somatic cell score reduces the peak time (pt), and persistency (p). A comparison of persistency between different phenotypic groups of economic traits suggested that persistency improves with increasing milk production and its components as well as decreasing somatic cell scores.

Profitability in dairy herds depend on animal survival in the herd, which is provided by reducing involuntary culling and increasing the voluntary culling in the herd. The aim of this study was to investigate the non-genetic factors affecting longevity and to estimate the genetic parameters of longevity and somatic cell score in Iranian Holstein cows. For this purpose, the data of 277715 cattle that were collected by Animal Breeding Center of Iran during 2001 to 2018, were used. Longevity was defined as length of life (LL), lifetime number of days in milk (LDIM), lifetime milk yield (LMY), lifetime fat yield (LFY), and lifetime protein yield (LPY), and the effect of environmental factors on traits and risk of culling were determined using Survival kit and cmprsk statistical packages. Variance components of longevity traits were estimated based on exponential distribution and censored data along with somatic cell score trait using two-trait analysis by Gibbs sampling method. The results showed that the effect of herd, year and season of calving and calving age of cows was significant on all longevity traits (P <0.001). Cows with a high degree of dystocia had a higher culling risk than other cows and the culling risk was higher for cows born in the spring than in other seasons (except to the LL). The range of heritability for different longevity traits varied from 0.076 to 0.186 and the heritability of the somatic cell score was estimated to be 0.31. The results showed that genetic selection for somatic cell score and some longevity traits such as LPY can be effective in improving these traits, although due to the importance of environmental factors on longevity traits, these factors should also be considered. Genetic and residual correlation between somatic cell score with longevity traits were negative and the amount of genetic correlation between traits were higher than their residual correlation. Therefore, genetic selection for somatic cell score and considering it as a selection criterion in breeding programs can indirectly improve the longevity traits in Iranian Holstein cows. Increasing and improvement of longevity is not only economically important but also improves animal welfare.

The aim of this research was to investigate the immune system responses against sheep red blood cells (SRBC) and Newcastle disease virus (NDV) in two sexes of both wild and Italian speckled quails. To compare phenotypic differences of two sexes for humoral immune responses a one-way analysis was applied, and a simple animal model using the MCMCglmm package of R software was used for genetic analysis, assuming variance components between the two sexes are different. Phenotypic comparison between males and females did not show a significant difference in any of the strains. In both strains, heritability of humoral immunity in males was higher than females. Results indicated that heritability of IgT in males (0.187), and IgY in females (0.177) were higher than other estimates in wild strain. The highest heritability was related to the NDV, which was estimated to be 0.214 and 0.268 in males and females, respectively. Therefore, genetic selection for IgN can be expected to improve the performance of the birds’ humoral immune system. Likewise, according to the higher estimates of immune responses in males, genetic selection of humoral immune responses for IgN, leads to higher genetic progression.

The purpose of this study was to fit different nonlinear models to describe growth curve and selection the best model to describe a growth curve forcalves of Sistani calves. Body weight records of 241 calves (118 males and 123 females) collected by the Sistani Dairy Cattle Research Station ofZahak from year 2010 to 2017 were used. Four nonlinear models (Gompertz, Logistic, Richards, and Weibull) were fitted to the body weight recordsand the best model was selected by the goodness-of-fit criteria (Mean square error, Bayesian information criterion, Akaike information criterion andcorrected coefficient of determination). According to goodness-of-fit criteria, Richards model was the most appropriate model to describe the growthcurve in male and female calves. The effect of sex on curve parameters was significant in many functions (P <0.05). Logistic and Richards models hadthe highest and the lowest initial weight parameter, respectively. Male calves reached to the inflection point in a higher age and weight compared tofemale calves. According to the results of this study, a proper model can be used to study the growth pattern of this breed in order to better nutritionalmanagement and selection for rapid growth with high accuracy.

The aim of this study was to qtl mapping of body weight traits from hatch to 45 days on chromosome one in Japanese quail. For this purpose, a crossbred population from a four-generation crossbreeding pattern was used. The four strains A and M Texas, Wild, Italian Speckled and Tuxedo Japanese quail were crossed in diallel-cross, creating the first generation. Then, from the crossbreed of first generation, a mapping population including second, third and fourth generations was created. Blood samples were collected for DNA extraction and amplification of microsatellite markers on the chromosome 1 of the subcutaneous veins in tubes containing 0.5% EDTA. Observations included body weight traits from birth to 45 days with an interval of 5 days. The effects of markers and components of variance were performed with three models of additive, dominance and additive-dominance with AI-REML procedure of GVCBLUP software. Based on the estimated effects of markers, the point with the highest value of F statistic was reported as the QTL location. The results of QTL analysis in the additive model for hatch weight traits, 5 and 30 days indicate the presence of QTLs affecting body weight traits at the end, QTLs of 10, 15, 20, 25, 40 and 45 day body weight traits in the middle and for body weight trait 35 days, they were at the beginning of chromosome one. In the dominance model, QTLs affecting body weight traits including hatch, 5, 10, 15, 35, 40 and 45 in the middle and for body weight traits 20, 25 and 30 at the end of chromosome one were identified. The percentage of additive and dominance genetic variance due to markers in different models ranged from 0.17 to 9.4% and 3.3 to 23.3% of the total phenotypic variance, respectively. Therefore, the results of this study confirm the existence of at least two distinct gene loci with additive effects and dominance affecting body weight traits on chromosome one in Japanese quail.

The aim of this study was to analyze survival and its relationship with body weight and average daily gain traits in Japanese quail. For this purpose, Data base with 1854 Japanese quail survival records were used which collected during 4 generations from 1396 to 1398, by Khorasan Razavi Agricultural and Natural Resources Research and Education Center. The Survival and cmprsk statistical packages were employed to determine the non-genetic effects on survival and culling risk at different times, and variance components estimates of survival trait was performed by MCMCglmm package. Genetic parameters of traits were estimated using single and two-trait analyses via Gibbs sampling. The mean mortality of breeding period (0.206) and the average survival rate (0.793) were calculated. The estimated average heritabilities for survival in single and two-trait analyses were 0.216 and 0.153, respectively. The range of heritability of body weight in single trait analysis was estimated between 0.135 to 0.307) with a mean of 0.219 by two- trait analysis. In two-trait analysis, heritability of body weight trait ranged from 0.155 to 0.014. The highest genetic correlation was -0.3113 (between body weight and average daily gain) and the lowest genetic correlation was -0.0277 (between survival trait and average daily gain). The results showed that optimal management of environmental factors is effective in reducing the culling risk and genetic selection for survival trait can improve the genetic potential of survival.

The experiment was carried out to investigate the effect of tryptophan, melatonin and dimethylglycine on the growth performance and meat quality of Japanese quails fed diets contaminated with aflatoxin B1 toxin. In this experiment, 680 Japanese quail from 7 to 35 d of age was allotted to 17 treatments and 4 replicates with 10 Japanese quail in each were performed using a central composite design. The performance of birds was calculated on a weekly basis and at the end of the experiment; the amount of Malondialdehyde in meat was examined. the results showed that tryptophan increase weight gain (p < 0.05) and melatonin had an increased effect on feed intake (p < 0.05). The effect of tryptophan and as well as the interaction of tryptophan and dimethylglycine reduced the amount of malondialdehyde in meat (p < 0.05). The results obtained from this research states that dietary supplementation with Tryptophan and methyl group donors have good antioxidant capacity to reduce aflatoxin B1 poisoning on growth performance and Malondialdehyde content of meat, and the use of these supplements in the diet of Japanese quail seems desirable.

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.

The estimate variance components with a satisfying accuracy of important economic traits such as reproductive traits is a prerequisite for designing breeding strategies. Genetic grouping was suggested in order to predict breeding values of phenotypic records in different years with high accuracy. As there is unknown information in the pedigree of Holstein dairy cows in Iran, genetic group animal models with unknown parents seem necessary. Therefore, the present study was conducted to estimate the genetic parameters, genetic trend and accuracy of estimated breeding values of some reproductive traits (i.e. calving to first service (CTFS), first service to conception (FSTC) and calving interval (CI)) in dairy cows with considering genetic grouping for animals with unknown parents.

Information on calving and insemination dates of the first three calving periods from 3361 herds of the Iranian Holstein, collected by the Animal Breeding Center of Iran during 1981 to 2013 was used. Animals with unknown parents were grouped based on the year of birth and sex and the traits were analyzed using two models, with (model 2) or without genetic grouping (model 1). The model with the lowest Bayesian information criterion (BIC) and the Akaic information criterion (AIC) is considered the best model. Spearman's rank correlation coefficient was used to change in animal rank by considering the genetic grouping. The accuracy of estimated breeding values and genetic trend of the traits was estimated using two models and was compared. Preparation of data for statistical and genetic analysis were carried out using R-software and ASReml software, respectively.

The amount of variance and the standard error of additive variance in model 2 was lower than model 1 and for the residual variance was conversely, but there was no significant difference between the values of the two models. Model 2 was selected the best model for all studied traits based on the goodness of fit criteria. Heritability of CI and CTFS using model 2 was estimated lower (non-significant) than model 1. The heritability value for all reproductive traits was estimated less than 0.05 by two models. The rank of males and females changed duo to genetic grouping. The accuracy of estimated breeding values (EBVs) for all studied traits in model 2 was significantly higher than model 1 (P <0.001). The genetic trend of all traits (exception of the FSTC in the first and third calving period) was positive by model 1 and 2, and the estimated values between the two models were different.

The results of the current study showed that using genetic grouping for reproductive traits analysis of Iranian Holstein cows and accurate prediction of genetic merit of animals seems necessary.

The aim of this study was to estimate the genetic parameters of lactation curve traits (milk yield at beginning of lactation, the rate to reach peak yield, a parameter related to maximum milk yield, the changes in curve shape after reaching maximum yield, peak time, peak milk, persistency) was fitted by Rook function and the inbreeding effect on these parameters for Holstein cows in Iran. For this purpose, the test-day milk yield records of the first three lactations that were collected by the Animal Breeding Center of Iran from 1983 to 2017, were used. The Rook function parameters were calculated for all animals and the peak time, peak milk and persistency were estimated from the curve parameters. The estimation of variance components and genetic parameters of traits were performed by single and two- trait analysis via Gibbs sampling method using of Gibbs3f90 software. The effect of inbreeding was negative on the most of the traits; especially those had a higher heritability and also decreased milk production persistency. The heritability range of the aforementioned traits varied from 0.0003 to 0.086 and the highest heritability was related to persistency trait (0.086) in second lactation and peak milk (0.067) in third lactation. In general, the parameters of the lactation curve had a low heritability, so genetic selection would not show favorable results and changes in environmental and management conditions could be more effective for improving these traits.

The lack of sufficient information in the pedigree of the animals prevents the correct estimation of the breeding values. Henderson proposed a genetic grouping for a more realistic estimation of breeding values for phenotypic records in different years. For these groups, the birth year, the year that the first daughter of the male had recorded, or the year that the male animal was used for insemination were used for grouping. In fact, this grouping was considered for calculating the genetic trend over the years. The incomplete recording of the animals in the population will result in the elimination of true genetic relationships between animals. Although, these animals are considered as the base animal in the analysis, but not born at the same time, and can affect the accuracy of estimated breeding values. The available pedigree information in Iran does not have a good quality index. So that the average of pedigree completeness criterion for Iranian Holstein cows has been reported less than 0.7. Genetic evaluation of Iranian Holstein cows with unknown parents may cause a bias in estimating genetic parameters and breeding values. The use of genetic groups in genetic analysis can partly correct the problem of animals with unknown parents. In this regard, the purpose of this study was to estimate the genetic parameters and breeding values of the production traits (milk, fat, protein) of Iranian Holstein cows with and without genetic grouping in model.

In this study, the pedigree of 1555702 heads of the Iranian Holstein cattle from 14623 sires and 697940 dams that collected by Animal breeding center of Iran till 2013, were used. Production traits, including milk, fat and protein corrected for 305 days and twice milking from first to third lactation periods were used to estimate variance components and breeding values. Herds under 100 heads were not considered for analysis and for all production traits; pedigree related to animals with the record was extracted from the general pedigree using CFC software and used. For animals with unknown parents, genetic grouping was performed based on the sex and the birth year. Traits at different lactation periods analyzed with (model 2) and without (model 1) genetic grouping in the model and genetic trend was calculated. Then the accuracy of breeding values and genetic trend of traits obtained from different models were compared with each other. The Spearman rank correlation was used to investigate the change in animal ranking in a result of considering the genetic grouping.

The additive genetic variance and their standard error were lower for milk, fat and protein production traits in model with genetic grouping (model 21) than the model without genetic grouping (model 1). The estimated heritability range for milk, fat and protein production in three lactation periods with model 1 was 0.094-0.162, 0.069-0.114, and 0.079-0.123, respectively, that these values were higher than model 21 in terms of magnitude. Spearman rank correlation between the estimated breeding values with model 1 and 21 was significantly different from 1, indicating a change in animal rank with consideration of genetic grouping in the model. The spearman rank correlation was lower for males than females, suggesting a higher change in male animal's rank than females. The average accuracy estimated breeding values with model 21 was higher than model 1 and the average accuracy difference was significant between two models. The genetic trend in the first, second and third lactation periods with the model 21 was estimated 63.06, 59.60 and 44.64 for milk production, 1.346, 1.095 and 0.943 for fat and 1.542, 1. 514 and 1.035 kg per year for protein, which were higher than the estimates of model 1.

The results showed that consideration of genetic grouping in the model reduced the additive genetic variances of traits and the heritability estimated were higher without consideration of genetic grouping. The significance of the Spearman rank correlation indicates that the rank of males and females changed by inserting genetic groups into the model and change in the animal's rank for males was higher than females. The high accuracy of estimated breeding values and the genetic trends of traits in the model with genetic grouping suggests that genetic grouping for animals with unknown parents has been done and entered into the model in order to more accurately estimate the breeding values and to better reflect the performance of the breeding programs.

Animal breeds are often recognized through their specific characteristics, nevertheless, the breeds' anatomical and biochemical characteristics have not considered yet in many of the researches done on one-humped camels. There are some particular differences in camel breeds due to different climate conditions and rearing necessity.

The aim of the current study was to compare differences in anatomical and plasma biochem- ical parameters of two Iranian one-humped camels, the Jammaz (racing) and Balouchi (dual-purpose) breeds.

Anatomical parameters were body length (BL), neck length (NL), chest girth (CG), barrel girth (BG), hump circumference (HC), fore limb length (FLL), hind limb length (HLL), height at hump (HH), fore limbs interval (FLI), hind limbs interval (HLI), fore hoof circumference (FHC), hind hoof circumference (HHC), abdominal circumference (AC), shank circumference (SC) and leg circumference (LC). Moreover, concentra- tions of Glucose, blood urea nitrogen (BUN), creatinine, cholesterol, total bilirubin (Bili-T), direct bilirubin (Bi- li-D), calcium (Ca), phosphorus (P), magnesium (Mg), aspartate aminotransferase (AST), creatine kinase (CK), lactate dehydrogenase (LDH), total protein (TP), albumin (Alb), triiodothyronine (T3) and thyroxine (T4) were measured as plasma biochemical parameters. Data analysis was conducted through t-test statistics.

Results revealed significant differences between body type traits of breeds, especially in organs related to running ability, while the Jammaz breed has more height and longer limbs than the Balouchi breed. Some blood parameters (glucose, LDH, BUN, cortisol and T4) are considerably higher in Jammaz breed, too.

Results of the current study suggest some anatomical (especially fore and hind limb lengths, neck length and body height at hump) and physiological characteristics (lactate dehydrogenase, blood urea nitrogen, cortisol, glucose and T4) of Iranian racing and dual purpose camels as breed markers.

The aim of this study was to estimate genetic parameters of humoral immune responses (antibody titers against sheep red blood cells (SRBC) and Newcastle Disease Virus (NDV)) and residual feed intake from 20 to 45 days of age in Japanese quail. For this purpose, a total of 2492 records of residual feed intake traits and 5238 records of immune traits were used. The analyses of Genetic parameters of traits were estimated through single and bivariate animal models via Gibbs sampling method. Heritability estimates of total antibody titer (AbT), titer of immunoglobulin Y (IgY), titer of immunoglobulin M (IgM) and titer of immunoglobulin F (IgF) against SRBC were 0.08, 0.14, 0.02 and 0.24, respectively, however, heritability of antibody titer against NDV was lower than estimated of SRBC antigen (h2= 0.05). heritability of RFI in different ages were in ranges of 0.04 to 0.07. genetic correlations estimate between total antibody and IgY were positive and high and was 0.92. The negative genetic correlations were related to IgM with RFI and genetic correlations estimates between RFI and other immunoglobulins (IgY, AbT, IgF) and NDV were positive. As a conclusion, selection for IgF due to its heritability (0.24) and negative genetic correlation (-0.23) with RFI, cause improve in RFI and reduce costs, related mainly to feeding and selecting of animals with phenotyping. On the other hand, due to moderate to high positive genetic correlations (0.34-0.80) were found between IgF and other immunoglobulins, selection of it didn’t lead to decline of humoral immune responses in quail.

The availability of thousands of polymorphic single nucleotides (SNPs) spread across the genomes made it possible to use genome-wide marker information to predict total breeding value in the implementation of genomic selection. The interaction between several gene loci contributes to the phenotypic changes associated with the expression of complex polygenic traits. The present study aimed to compare the performance of different models with additive and non-additive genetic effects, especially epistasis effects in predicting variance components and genomic breeding values as well as QTN in a dairy cow population based on Bayes Lasso model.

A population of dairy cattle was simulated based on a choice of four pathways to maximize the rate of genetic progress over ten generations with an effective size of 100 individuals in the base population. The genomic structure was assumed consisting of 3 chromosomes with a length of 100 cM and On each chromosome were located 1000 markers 2 allelic markers with a frequency of 0.5. 50 QTL double alleles with equal frequency were randomly assigned to each chromosome. For QTL allelic effects, a gamma distribution with a parameter slope of 0.4 was used in QMSim software and sampling was performed. Phenotypic and genotypic data of the last 10 generations were used for analysis. Marker effects, variance components and genetic parameters were estimated using the Bayes Lasso method in the form of 6 statistical models, that model 1 includes only the marker additive effects, model 2 includes the polygenic effects of animal, model 3 includes the combined effects of additive marker effects and polygenic effects of animal, model 4 includes the dominance effect of markers and polygenic effects of animal, model 5 includes the dominance and additive effects of markers in addition to the polygenic effects of animal, and finally, model 6 includes the additive, dominance and epistatic effects of markers in addition to the polygenic effects of animal. To control the type I error in estimating marker effects, Bonferroni test was used at 1% probability level.

The results of this study showed that the additive model or the polygenic model alone could not show the missing or hidden variance, in such a way that adding non-additive genetic effects including dominance and epistatic effects reduced the residual variance effects. Also in the complete model including additive and non-additive effects, the total genetic variance increased. With the addition of non-additive effects in the statistical model the Hertability in the broad sense was increased and the Hertabilitity in the narrow sense of trait decreased. The accuracy of breeding value estimation in model 1 was the lowest and in models 3 to 6 was the same. Model 5 with the lowest false positive QTN and the highest true positive proportion was the appropriate model for genetic evaluation of the studied traits. By including polygenic and non-additive effects in the model, the number of false positive errors was reduced.

The results of this study showed that the components of additive and dominance variance markers had a small share in the genetic diversity of the studied trait, but the polygenic effects of animal and epistatic had the largest share in the exploring of genetic diversity of trait. The results also showed that the major contribution of gene loci in the exploring of traits is related to additive genes with an additive effect that have a normal distribution. Ignoring non-incremental effects causes inflammation in the additive variance of the trait.

The aim of the current study was to estimate the genetic parameters of growth traits at the late ages (25-45 days of old) as well as humoral immune responses in Japanese quail. Therefore, the studied traits were growth traits (body weights (BW) at 25, 30, 35, 40 and 45 days of age, average daily gain (ADG) in 5 day periods as well as the immune system responses against SRBC (IgT) and Newcastle vaccine (IgN)). To estimate genetic parameters, a multivariate analysis was utilized using Gibbs sampling through Gibbsf90 software. The heritability for BW and ADG were varied between 0.303-0.437 and 0.053-0.338, respectively. Moreover, heritability estimates for IgT and IgN were 0.252 and 0.015, respectively. Genetic correlation between growth traits with immune responses were negative and ranged from low to moderate (−0.218 to −0.483). According to the results, genetic selection based on BWs might to result in higher genetic response than ADG and immune system performances. Among body weight traits, the BW30 based on its higher genetic correlation with BW45 (0.809), moderate heritability (0.406) and negative and relatively low genetic correlation with IgT (−0.226) and IgN (−0.235) would be consider as an appropriate criterion introduce applicable breeding program to improve growth traits with lower decreasing in the immune system performance.

The aim of the present study was to investigate the codon usage pattern and their relationship with gene expression for genes with different expression between pure and crossbreed Sistani and Montbeliared breed. In this study, the results of differential gene expression analysis using RNA-Seq technology between pure and crossbreed Sistani and Montbeliared breed (two pure and two its crossbreed) were used. For this purpose, after determining the ORF regions for these genes, CodonW software was used to estimate codon usage pattern indices including CAI, ENC, GC and GC3s. Results showed that there was a significant correlation between total GC and GC3s (0.74). There was also a significant correlation between ENC and GC and GC3s (0.65, 0.77), indicating the role of mutation in codon formation. Based on the results of this study, the factors such as nucleotide composition (GC content), mutation, and gene expression level played important roles in codon formation in the genes studied in this study. This study is the first comparison between pure and crossbreed Sistani and Monti-billiard samples, which helps to better understand the evolutionary mechanisms of codon usage pattern formation and its association with gene expression.