gibbs sampling

In this study, genetic parameters and (co) variance components were estimated for weights at birth, 3, 6, 9 month, daily weight gain and Keliber ratio from birth to 3 month and also form 3 month to 9 month. Records of 2544 kids, the progeny of 149 sires and 851 dams were used to analysis data by MTGSAM program. Six different animal models were fitted for all traits. The most appropriate model for weight at 6, 9 and daily weight gain and Keliber ratio form 3 to 9 month was model 2. Estimated direct heritability varied from 0.01 to 0.36, which was minimum (0.01) for daily weight gain and Keliber ratio from birth to 3 month and maximum (0.36) for birth weight. The genetic and phenotypic trends for all traits were estimated near to zero and non-significant. Generally, differences between estimated genetic trends for these traits and estimated values of other studies, is due to difference in animal breeding standard followed by different program selection, difference between models and calculation method, effects of environment, interaction between genetic and environmental, nutrition and climate conditions.

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 present study was conducted to estimate the genetic and phenotypic parameters of productive and reproductive traits of Holstein cows in Mazandaran Holstein dairy cattle. To this purpose, data 39792 records of Holstein cows collected at Mahdasht Milk and Meat Company in sari during 1986 to 2015 were used. Productive traits included corrected 305 days milk records, fat and protein production, and reproductive traits were age at first calving, calving interval, dry period and days open. Genetic parameters were estimated by THRGIBBS1F90 software under single trait animal model using Bayesian statistical method based on Gibbs sampling approach. A total of 200000 cycles were implemented among which the first, 20000 cycles were considered as burn-in period. Heritabilities obtained as 0.34, 0.68, 0.65, 0.17, 0.007, 0.07 and 0.07 for milk production, fat production, protein production, age at first calving, calving interval, dry period and days open, respectively. The genetic correlation between milk production and fat production was 0.48. Genetic correlation between milk production, fat production and protein production with age at first calving was -0.003, 0.14 and 0.39, respectively, Genetic correlation between milk and protein production with calving interval was estimated to be 0.23 and 0.55, respectively. According to the results, correlations between production and reproduction traits could be considered in breeding programs.

This research was conducted with the aim of estimation of environmental factors affecting survival and estimate the genetic parameters survival from 1 to the last recording date in Zandi sheep. The survival records of 9558 Zandi sheep from 273 rams and 2328 ewes collected by Animal Breeding Center of Iran during the 25 years (1987 to 2011) were used in the analysis. The effective factors on survival and culling risk were estimated by Survival and cmprsk package. Estimation of variance components was performed by using of exponential distribution for censored dates by the fitting of model with additive genetic effect (model 1) and joint additive genetic and maternal permanent environmental of effects (model 2) under Bayesian approach and Gibbs sampling. A total of 1000000 samples with a burn-in of 100000 and a sampling interval of 75 were generated to estimate the posterior distribution of variance components. The results showed that year, month, birth weight, type birth, sex (P<0.001) and dam age (p<0.01) had significant effect on survival trait. the direct heritability of survival trait using models 1 and 2 was 0.184( 0.136-0.264) and 0.162( 0.120-0.202), respectively. the proportion of permanent variance to phenotypic variance was  0.046( 0.063- 0.031). According to the results of this study, genetic improvement of survival trait in zandi lamb is possible by genetic selection and the culling risk reduction is effective via management of environmental factors.

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.

Longevity records of 26991 Mehraban lambs born from 405 sires and 8114 dams which collected by the Agricultural Organization of Hamedan Province during 1981 to 2011 were used in this study. To determine the fixed effects fitted in statistical model (birth year, birth month, type of birth, age of dam, flock, lamb sex and lamb birth weight and their interactions), the GLM procedure of SAS software was used. Interaction between birth year-lamb sex and all fixed effects except for birth type, dam age and linear covariate variable of lamb birth weight was significant on longevity (P

In this research estimation of genetic parameters for milk production trait was performed by using 27065 test day records of first parity of Holstein cows in Kermanshah province.
The collected records were including 3123 cows in 22 herds that were calved from 1991 to 2013. Number of lactation days and calving age were limited to 5-305 days and 21-48 months, respectively. Test day milk records were analyzed by using a random regression model. The effects of additive genetic and permanent environment for production curve during lactation period were fitted using Legendre polynomials by GIBBS2F90 software. Results showed that the effects of herd, year and date of recording; age of calving; season and year of calving and days in milk were significant (p

This research was conducted to study genetic and phenotypic relationships between growth curve parameters in Mehraban sheep. The data set used in this study were obtained from the Agricultural Organization of Hamedan province and comprised 35414 body weight records from birth to 365 days of age during 2001to 2011. Parameters of Brody growth model were studied which included A (asymptotic mature weight or average mature weight of animal), B (proportion of asymptotic mature weight to weight gain as a percent of mature weight) and K (growth rate until reaching to mature weight). Fixed factors affecting on growth curve parameters were identified using the GLM procedure of SAS software. The model of genetic analysis included direct genetic effect, maternal genetic effect, maternal permanent environmental effect and covariance between direct genetic and maternal genetic effects. To estimate genetic relationship between growth curve parameters, Bayesian method based on Gibbs sampling was used. Direct heritabilities for growth curve parameters of A, B and K were 0.29, 0.63 and 0.27, respectively. Direct genetic correlation between A and B was positive and high (0.58), which indicates that these traits are aligned with each other while the correlations between B and K (-0.69) and between A and K (-0.54) were negative. The results indicated that improvement of growth curve parameters of Mehraban sheep is possible in selection programs. Therefore, it is worthwhile to propose an optimum selection strategy for obtaining appropriate growth curve in Mehraban sheep through changing genetically the model parameters.

The objective of this research was to estimate the genetic parameters and trend of somatic cell count in Holstein cows of Iran using test day records. The phenotypic the used data consisted of were consisting of 407167 first lactation test day records the which were collected by the center of Animal Breeding and Livestock Production Improvement center of Iran during 2009 to 2013. Somatic cell count was transformed to Somatic cell score using logarithm transformation method. The genetic parameters were estimated using random regression models with Bayesian statistical method based on Gibbs sampling. The results revealed that the observed trend for additive genetic variance and permanent environmental were similar high in early lactation compared to other days. The heritability was estimated between 0.023-0.065 for somatic cell score. Repeatability showed highest changes at the start and the end of lactation. Additive genetic correlations were estimated for days 5 and 305. The result showed high variation in genetic trend of somatic cell score in different years, without an specific trend.

The aim of this study was to estimate the genetic trend and genetic parameters of survival traits in Baluchi sheep using survival records from 27978 Baluchi sheep, which were collected by the Animal Breeding Center of Iran during1979 to 2009. Genetic parameters of lamb survival from 1 to 400 days of age and from 1 to the last recording date. Traits were estimated using animal model (with or without permanent environment of dam) for right censored data assuming an exponential distribution via Gibbs sampling. Effect of year and month of birth, sex, litter size and herd were assumed as fixed. The posterior mean of direct heritability for survival from 1 to 400 days of age and from 1 to the last recording date in first and second model ranged from 0.135- 0.158 and 0.085- 0.168, respectively. Posterior mean permanent variance ratio was 0.076 for survival from 1 to 400 days of age and 0.144 for survival from1 to last recording date. The genetic trend for these traits was −0.0005 and −0.001, respectively. Heritability for survival trait suggested that genetic selection for this trait would be effective in the breeding programs.

Introduction Small ruminants, especially native breed types, play an important role in livelihoods of a considerable part of human population in the tropics from socio-economic aspects. Therefore, integrated attempt in terms of management and genetic improvement to enhance production is of crucial importance. Knowledge of genetic variation and co-variation among traits is required for both the design of effective sheep breeding programs and the accurate prediction of genetic progress from these programs.
Body weight and growth traits are one of the economically important traits in sheep production, especially in Iran where lamb sale is the main source of income for sheep breeders while other products are in secondary importance. Although mutton is the most important source of protein in Iran, meat production from the sheep does not cover the increasing consumer demand. On the other hand, increase in sheep number to increase meat production has been limited by low quality and quantity of forage range. Therefore, enhancing meat production should be achieved by selecting the animals that have maximum genetic merit as next generation parents. To design an efficient improvement program and genetic evaluation system for maximization response to selection for economically important traits, accurate estimates of the genetic parameters and the genetic relationships between the traits are necessary.
Studies of various sheep breeds have shown that both direct and maternal genetic influences are of importance for lamb growth. When growth traits are included in the breeding goal, both direct and maternal genetic effects should be taken into account in order to achieve optimum genetic progress. The objective of this study was to estimate the variance components and heritability, for growth traits, by fitting six animal models in the Sangsari sheep using Gibbs sampling.
Material and Method Sangsari is a fat-tailed and relatively small sized breed of sheep, native and well adapted to Semnan province. The data set and pedigree information used in this study, recorded during 1986–2008, were obtained from the breeding station of Sangsari sheep (in Damghan, Semnan Province, Iran). The data included 9707 records for birth weight (BW), 8524 records for weaning weight (WW) and 3894 records for six months weight (6MW). Records were prepared for analysis using EXCEL 97 software. During the preparation process, abnormal data were removed. The pedigree and data files were prepared using pedigree software.
Firstly, the GLM procedure (SAS, 2002) was used for determining the fixed effects that had significant effect on the traits investigated (P

Estimation of animal breeding and management in past time is taken to measure the genetic parameters and management programs and design of programs for the future.
The object of the present study was to estimate of genetic parameters with considering the maternal effects on growth traits in Lori-Bakhtiari lambs of Khuzestan province. The present study using pedigree information and record of body weight during the years 2006 to 2011 were collected by Jahad Agriculture Khuzestan using was conducted. The studied traits were body weight at birth (BW), weaning weight (WW) and six-month weight (6MW) and 7238, 6941 and 6663 record for these traits, respectively.
The data editing is done using the software FOXPRO 16 and the estimate the effect of environmental factors of procedure GLM Software SAS 9.1. Environmental factors like birth year, sex, type of birth and age of mother on lambing time had significant effect on traits. The variances and genetic parameters were estimated by Bayesian via Gibbs, with and without maternal effects and done software MTGSAM and finally best model was determined using the Akaike information criterion for each trait.
Based on the best model, for birth weight was model has a direct genetic effect and maternal permanent environmental effect (model 2) and for weaning weight and six-month weight traits the model contains a direct genetic effect, maternal genetic and maternal permanent environmental (model 6 and 5). Estimated direct heritability BW, WW and 6 MW 0.32, 0.18 and 0.25, respectively.
Considering results of present study maternal effects gives accounted of variation in body growth Lori-Bakhtiari sheep, and lead to more accurate estimates of the variance components and heritability.

In this study, (co) variance components, genetic and phenotyping parameters for body weight traits at different ages of Zandi sheep breed were estimated. Birth weight, weaning weight, 6-month weight, 9-month weight and yearling weight were studied. The data were collected during 1991-2011 by Nakhjir breeding station in Tehran. (Co) variance components were estimated by Bayesian statistical method based on Gibbs sampling technique. Environmental factors of birth year, sex of lamb, birth type and mother's age were significant on all traits. Appropriate fitted models (based on lowest residual variance) for birth weight, weaning weight, 6-month weight, 9-month weight and yearling weight were found to be models 5, 5, 2, 1 and 1, respectively. Direct heritability was found to be 0.15±0.01, 0.26±0.003, 0.21±0.002, 0.25±0.003 and 0.26±0.001 for the traits, respectively. Maternal heritability of birth weight and weaning weight were 0.11±0.01 and 0.06 ±0.001, respectively. The results revealed that growth traits are more influenced by mother’s genetic factors in the early of age. With increasing the age of lamb and decreasing dependency to the mother, the significance of maternal effect reduced. Low to moderate heritability of the traits indicate that selection for these traits will result in a low to moderate genetic improvement.

The objective of this study was to evaluate some environmental factors (sex, season and year of birth, birth type and dam age) on fleece weight, estimate of phenotypic and genetic parameters and trends of this trait on Cashmere goat of the southern Khorasan. GLM procedure of SAS software version 1.9 was used to assess the significant environmental effects on this trait. Records of 1455 kids, the progeny of 127 sires and 562 dams, collected between 1996 and 2012, were used to estimate phenotypic and genetic parameters. Results showed that Cashmere weight was significantly higher in males than females. Genetic analyses was carried out by MTGSAM program. The results of this study indicated that the effects of year of birth and sex at 5% and remaining effects at 1% were significant. To detecting of maternal additive genetic effect and maternal permanent environmental effect, six different animal models were fitted for fleece weight. The most appropriate model according to Akaikes information criterion was model 3with direct additive genetic and permanent environmental maternal effects. Direct and maternal heritability for first fleece weight were 0.49 and 0.09. The results indicated that fleece weight was influenced by maternal genetic effects. The genetic and phenotypic trends for this trait were estimated near to zero and insignificant. It seems, developing of selection index and removing of the environmental obstacles are major steps in the development of genetic and increase profitability in this Cashmere goat population.

Prolificacy trait of Iran black was compared with Baluchi and Arman sheep breeds and the environmental factors affecting the trait were studied. Furthermore, estimation of genetic parameters and evaluation of the genetic trend of the Iran black breed for the prolificacy and average birth weight of the lambs per lambing (as a trait for the ewes) were carried out using bivariate (linear-threshold) repeatability model. Total recorded animals was 2,701 (offspring of 110 sire and 840 dam) and the data were collected during 1980-2009 by Abbas Abad breeding station that located in Mashhad, Iran. Lambing rate was significantly higher in Iran black and Arman breeds than in Baluchi breed (P<0.01). Lambing rate decreased with aging of the ewes, such that, ewes older than 8 years old showed the lowest prolificacy. Ewes with age between 2 to 6 years did not differ to each other significantly. Heritability of average birth weight of the lambs and prolificacy were 0.148 and 0.266, respectively. Repeatability estimates of the traits were 0.674 and 0.381, respectively. Phenotypic, environmental and genetic correlations among the traits were highly negative and were -0.484, -0.369 and -0.968, respectively. The genetic trend for the prolificacy trait was ascending until year 1996 (0.016 lamb/year) and descended afterwards (-0.012 lamb/year). Genetic trend for average birth weight of the lambs were opposite in direction with genetic trend of prolificacy in both periods. It seems that lack of a sustainable breeding strategy for genetic improvement of Iran Black breed for prolificacy and other economically important traits has resulted in a non-constant genetic progress during the past years.

In this study, genetic parameters and (co)variance components were estimated for weights at birth, 3, 6, 9, 12, 24 months, daily weight gain from birth to 3 months and daily weight gain from 3 month to 12 month, Keliber ratio from birth to 3 months and Keliber ratio from 3 to 12 month, and production of fleece for South Khorasan goats at Sarbisheh station over a period of 16 years (1996–2012). Records of 2544 kids, the progeny of 149 sires and 851 dams were used in the study. Analyses were carried out by MTGSAM program. Six different animal models were fitted for all traits. The most appropriate model was model 2 with only permanent environmental maternal effects. Estimates of direct heritability varied from 0.01 for weight at 12 months to 0.49 for production of fleece. Maternal effects are important sources of variation on growth traits significantly and ignoring maternal effects in the model would cause inaccurate genetic evaluation of kids. Bivariate analysis was also used to estimate correlations between traits. Direct genetic correlations among studied traits ranged from 0.01 for daily weight gain and Keliber ratio from birth to 3 months and 3 to 12 month-almost traits to 0.88 for weight at 3 months- Keliber ratio from birth to 3 months. Phenotypic and environmental correlations were generally lower than those of genetic correlations

The aim of this study was to estimate (co)variance components and genetic parameters for body weights at different ages of Najdi cow using Gibbs sampling of Bayesian approach. For estimating (co variance components and genetic parameters, the records collected over 21 years (1990-2010) in Najdi cattle breeding station (Shushtar city) was used. The traits were body weights in different age (birth weight, weaning weight, weight at age six months (W6), yearling weight and weight at age 18 months (W18). Environmental factors such as birth year, birth season, sex and age of mother had significant effects on birth and weaning weights (P<0.05). W6, yearling, W18 were significantly influenced by birth year, birth season and sex (P<0.05). The best model obtained for birth weight, weaning weight, and W6 was model 2 in which direct additive genetic effect of animal and maternal permanent environmental effects were taken into account. The best model for yearling and W18 was model 1 in which only direct additive genetic effect of animal was included. Direct heritability for birth weight, weaning weight, W6, yearling weight W18 were 0.45, 0.17, 0.10, 0.18 and 0.13, respectively. Low heritability detected in this study (except the birth weight) is due tohigh environmental variance. Therefore, the possibility of improving these traits through phenotypic selection is low by and the genetic progress achieved will not be high. In conclusion, good management beside improved environment quality can change the performance of the traits.

For this study, a total of 6,326 records of wool weight obtained from 273 rams and 1,927 ewes of Lori-Bakhtiari sheep were used. The data were collected in Shahrekord sheep breeding station (Sholi) during 1990-2011. SAS statistical software was utilised to determine the effect of environmental factors, and MTGSAM software via Gibbs sampling was applied to estimate genetic parameters. Environmental factors such as birth year, sex, type of birth, and age of mother had significant effect on the trait. The interaction between age of mother and sex of lamb, and interaction between type of birth and sex of lamb were significant. Animal’s age at shearing and birth weight were taken into account as covariates in the models. Using the best model, direct and maternal heritabilities for wool weight were 0.31±0.02 and 0.06±0.01, respectively. Direct and maternal genetic trends were 3.23±0.24 and 0.3±0.04 gr per year,respectively and statistically significant. Phenotypic and environmental trends were found to be 0.003 and -0.001, respectively but non-significant. Genetic progress was considerable at different years which could be due to breeding programs targeted at these stations.

The object of this study was to estimate (co)variance components and genetic and environmental parameters for body weights at different ages in Lori-Bakhtiari sheep using a Bayesian approach.In this study, pedigree information and birth weight, one month weight, weaning weight, 6 month weight, 9 months weight and 12 months weight, of 7697 lambs from the 291 rams and 2097 ewes were used. The data was collected in Shahrekord sheep breeding station (sholi) during 1989- 2011. The SAS statistical software was used to determine the effect of environmental factors, and MTGSAM software via Gibbs sampling was applied to estimate genetic parameters. Environmental factors like birth year, sex, type of birth and age of mother on lambing timehad significant effect on traits, which included in the model as fix effects. Animal’s age at weighting day was introduced to the model as covariate. Using best chosen model, the direct heritability for birth weight, one-month, weaning weight, 6 months weight, 9 months weight and 12 months weight were respectively obtained as follows: 0.33±0.03, 0.11±0.02, 0.15±0.02, 0.23±0.02, 0.29±0.03 and 0.38±0.03. Gibbs sampling in Bayesian statistical analysis could provide reasonable range expected estimations for parameters. The results showed that growth traits more are influenced by mother’s genetic factors in the early of age. With increasing age, due to decreases dependence to her mother, the significance of this effect is reduced. The lower to moderate estimates of direct heritabilityfor growth at different ages, obtained in this survey indicate that selection for these traits will be lead to lower to moderate genetic improvement.