Interaction networks and pathway analysis of genetic resistance to gastrointestinal nematodes in sheep.

Gastrointestinal nematode (GINs) infections are one of the causative agents of health and economic issues in sheep production systems worldwide. Considerable genetic variations in resistance or susceptibility in different sheep breeds are documented, but published results are conflicting. Recent advances obtained by high-throughput technologies such as commercial SNP chips, whole-genome sequencing, or whole transcriptome profiling provide new insights into breeding for host resistance or nematode control at the genetic levels. This study aimed to identify potential biomarkers associated with the resistance to ovine GINs through a network analysis approach. Comprehensive gene and protein interaction networks were reconstructed for candidate genes involved in the most related immune pathways associated with resistance to ovine GINs using data mining from literature. Generally, 30 genes including CD53, CHIA, RELN, HRH1, EPS15, LRP8, ATP2B1, IL4, IL5, IL13, IL2RA, IL23R, TNFα, IFNγ, TBX21, SH3RF1, HERC2, PTPN1, BIN1, HERC5, C3AR1, NOS2, STAT5B, STAT4, CCL1, CCL8, VIL1, CXCR1, CXCR2, and CXCR4 located on chromosomes 1, 2, 3, 4, 5, 6, 11, 13, 19, and 20 have been found as containing effective regions with the most related pathways to nematode infections. The results obtained by network analysis showed two functional modules, belonging to the interleukins family (IL4, IL5, IL13, IL23R, and IL2RA) and chemokine receptors or ligands family (CXCR1, CXCR2, CXCR4, CCL1, and CCL8). Interleukins are a group of cytokines that are expressed by white blood cells with a major role in the immune system. Chemokines are also a family of chemoattractant cytokines which play a vital role in cell migration that influence the immune system by a process known as chemotaxis. The results provide useful information for the functional annotation of candidate genes related to parasite resistance and add new information towards a consensus on quantitative trait loci (QTLs) related to the incidence of nematode infections.

Modelling growth in dairy heifers based on linear body measurements (withers height) using non-linear functions.

This research communication reports a study to model the growth curves for withers height (WH) and body weight (BW) to withers height ratio (BW:WH) using monthly records (from 1 to 24 months of age) for three breeds of dairy heifer (Holstein, Jersey and Brown Swiss). The data sets used were those reported by the Dairy Heifer Evaluation Project of Penn State Extension (USA) between 1991 and 1992. Four growth functions (monomolecular and Michaelis-Menten, both with diminishing returns behaviour, and Schumacher and López, both with asymptotic sigmoidal behaviour) were fitted using the non-linear regression procedure of the SigmaPlot software and the parameters estimated. The models were judged for goodness of fit using adjusted coefficient of determination ($R_{{\rm adj}}^2 $), root mean square error (RMSE), Akaike's information criterion (AIC) and Bayesian information criterion (BIC). Assessing the goodness of fit by $R_{{\rm adj}}^2 $ (>0.99 in all cases) reveals the generally appropriate fit of the models to the data. The non-sigmoidal functions (i.e. Michaelis-Menten and monomolecular) provided the best fits giving the lowest values of RMSE, AIC and BIC. Based on the chosen statistical criteria, the Schumacher and López equations provided acceptable fits to the WH and BW:WH growth curves, but showed points of inflexion at times before birth, indicating that these growth curves are not sigmoidal. In conclusion, evaluation of the different non-linear growth functions used in this study indicated their potential for modelling growth patterns in dairy heifers.

On the Description of Equine Somatic Growth Using Nonlinear Functions.

A better knowledge of the growth of horses can facilitate sounder intervention in their health control, nutrition and management. This study compared five growth functions with either diminishing returns (monomolecular and Michaelis-Menten) or asymptotic sigmoidal (Gompertz, Richards and Lopez) behavior for describing the growth curves of horses, based on the relationship between a given somatic growth trait (body weight, withers height, or body weight to withers height ratio) and age. Data used in this study were those available in the literature for quarter horse males and thoroughbred foals and fillies from birth to maturity. Estimates of the model parameters were obtained using nonlinear regression procedures and the Marquardt-Levenberg algorithm. Functions were compared using goodness-of-fit statistics such as adjusted coefficient of determination and root mean square error. The results obtained with the Richards, Lopez and Gompertz equations suggest that curves are not sigmoidal, and that the diminishing returns models are adequate for describing the growth curves in horses.

Investigating the Polymorphism of Bone Morphogenetic Protein Receptor-1B (BMPR1B) Gene in Markhoz Goat Breed.

Reproductive traits in livestock species are genetically controlled by the action of single genes with a major effect, commonly known as fecundity genes. One of the genes involved in controlling prolificacy is BMPR1B (FecB), a dominant autosomal gene located in chromosome 6 responsible for the fecundity and twinning rate in sheep and goat species. Markhoz goat is a valuable Iranian genetic resource endangered by extinction. Increasing the genetic variability and reproductive performances of Markhoz goat could preserve and enhance its economic value. This study was carried out to detect possible polymorphisms in BMPR1B gene in a sample of 100 Markhoz goats from Iran. DNA samples were screened by PCR-RFLP to assess the presence of the previously reported FecB mutation. Finally, the amplicons from seven goats out of the 100 samples were sequenced. The results showed that all the analyzed individuals did not carry the previously reported FecB mutant allele. However, our findings revealed two novel possible mutations in exon 8 of BMPR1B gene (775A > G and 777G > A) that need further investigations.

Genetic and environmental relationships among milk yield, persistency of milk yield, somatic cell count and calving interval in Holstein cows / Relaciones genéticas y ambientales entre el rendimiento lechero, la persistencia del rendimiento lechero, el recuento de células somáticas y el intervalo de partos en vacas Holstein / Relações genéticas e ambientais entre produção de leite, persistância de produção de leite, contagem de células somáticas e intervalo de pertos em vacas Holstein

Abstract Background: Fertility and health traits, other than production traits, have a major role in the profitability of dairy cattle. Therefore, it seems necessary to include the afore mentioned traits in breeding programs. Hence, genetic parameters are needed to establish breeding plans. Objective: To estimate heritabilities as well as genetic and environmental relationships among total milk yield (TMY), persistency of milk yield (PMY), mean somatic cell count (SCC), mean loge somatic cell count (LnSCC), standard deviation of somatic cell count (stdSCC), and calving interval (CI) using two-trait and multi-trait analyses in Iranian Holstein. Methods: The dataset consisted of 25,883 first lactation records collected from 2002 to 2007 in 97 Holstein dairy herds in Iran. Four criteria of persistency of milk yield (PMY) were calculated using the Wood's gamma function. The WOMBAT1.0 software was used to estimate the (co)variance components using the Average Information Restricted Maximum Likelihood algorithm. Results: Total milk yield (TMY) resulted in the highest heritability estimate (0.29). Heritability estimates for different criteria of persistency of milk yield (PMY) ranged from 0.05 to 0.10. The unfavorable genetic correlation between TMY and calving interval (CI) was 0.71, while that of PMY with CI was 0.46. The estimated environmental correlations were lower than the genetic correlations for all traits, but the trends were generally similar. Conclusion: The results indicate that including PMY in the breeding goals could increase TMY and CI, and decrease somatic cell count (SCC).

Resumen Antecedentes: Las características de fertilidad y salud, además de las de producción, tienen un papel importante en la rentabilidad de los hatos lecheros. Por lo tanto, parece necesario incluir los rasgos mencionados en los sistemas de mejoramiento. Por ende, los parámetros genéticos son necesarios para establecer planes de cría. Objetivo: Estimar la heredabilidad, así como las relaciones genéticas y ambientales entre el rendimiento total de leche (TMY), la persistencia del rendimiento lechero (PMY), el recuento medio de células somáticas (SCC), el recuento de células somáticas de loge promedio (LnSCC), la desviación estándar del recuento de células somáticas (stdSCC) y el intervalo de partos (CI) en vacas Holstein mediante análisis de dos rasgos y análisis múltiples. Métodos: Se analizaron registros de primera lactancia de 25.883 vacas Holstein, recolectados entre 2002 y 2007 en 97 rebaños lecheros de Irán. Se calcularon cuatro criterios de persistencia del rendimiento lácteo utilizando la función gamma de Wood. El software Wombat1.0 se utilizó para estimar los componentes de (co)varianza que emplean el algoritmo de máxima verosimilitud restringida de información promedio. Resultados: El rendimiento de leche (TMY) obtuvo la mayor heredabilidad estimada (0,29). Las estimaciones de heredabilidad para diferentes criterios de persistencia del rendimiento de la leche variaron de 0,05 a 0,10. La correlación genética desfavorable entre TMY e intervalo entre partos fue 0,71, mientras que la de PMY con el CI fue de 0,46. Las correlaciones ambientales estimadas fueron inferiores a las correlaciones genéticas para todos los rasgos, pero las tendencias fueron, en general, similares. Conclusión: Incluir el PMY en la meta de cría podría aumentar el TMY y CI, además de disminuir el recuento de células somáticas (SCC).

Resumo Antecedentes: As características de fertilidade e saúde, além das características de produção, têmum papel importante narentabilidade das vacas leiteiras. Por isso, parece necessário incluir as características já mencionadas nos sistemas de melhoramento genético. Assim, são necessários parâmetros genéticos para estabelecer planos de melhoramento genético. Objetivo: Estimar herdabilidade, bem como as relações genéticas e ambientais entre a produção total de leite (TMY), persistância da produção de leite (PMY), contagem médiade células somáticas (SCC), contagem média de células somáticas loge (LnSCC), desviopadrao da contagem média de células somáticas (stdSCC) e intervalo de pertosem (CI) vacas Holstein por duas análises de características e traços multiplos. Métodos: O conjunto de dados consistiuem registros de 25.883 vacas Holstein de primeira lactação coletadas de 2002 a 2007 em 97 rebanhos leiteiros em Iran. Foram calculados quatrocritérios de persistência da produção de leite utilizando a função gama de Wood. O software Wombat1.0 foi usado para estimar os componentes de (co)variância que empregam o algoritmo de máxima verossimilhança com informações restritas. Resultados: A maior herdabilidade (0,29) foi estimada para produção de leite. As estimativas de herdabilidade para diferentes critérios de persisténcia da produção de leite variaram 0,05 a 0,10. A correlação genética desfavorável entre o intervalo TMY eo intervalo de parto foi de 0,71 enquanto que a de PMY com CI foi de 0,46. As correlações ambientais estimadas foram inferiores às correlações genéticas para todos os traços, mas as tendencias foram geralmente semelhantes. Conclusão: Os resultados indicaram que a inclusão de PMY na meta de reprodução poderia aumentar TMY e CI, no entanto, diminuir a contagem de células somáticas.

Genetic parameters and trends for litter size in Markhoz goats / Parámetros genéticos y tendencias para el tamaño de la camada en cabras Markhoz / Parâmetros genéticos e tendências para o tamanho da ninhada em cabras Markhoz

Abstract Background: Prolificacy has a high economic value and is one of the most important reproduction traits in small ruminants such as Markhoz goats, which is an endangered breed. Objective: To estimate genetic, environmental and phenotypic trends, and genetic parameters for litter size (LS), as a prolificacy trait of Markhoz goat does. Methods: The study was conducted using kidding records of 3,064 Markhoz does from 1992 to 2015. Genetic parameters were estimated with a logit link function using ASReml software, fitting a repeatability animal model, with birth year, kidding year, and kidding age as fixed effects, and direct additive genetic and permanent environmental effects as random effects. Genetic, phenotypic and environmental trends were estimated by using regression of breeding value, phenotypic value and environmental deviation averages on birth year, respectively. Results: Low and negligible heritability (0.002), repeatability (0.054) and coefficient of permanent environment (0.052) were estimated for LS, which indicates low possibility to achieve rapid genetic progress through phenotypic selection. A non-significant -actually, zero- genetic trend (0.00004 heads/kidding/year), and significant negative phenotypic and environmental trends (-0.01097 and -0.01100 heads/kidding/year, respectively) were estimated in this study. Conclusion: Optimizing environmental conditions and application of high-throughput technologies in selection programs could help reducing the extinction risk of Markhoz breed.

Resumen Antecedentes: La prolificidad tiene un alto valor económico y es uno de los rasgos reproductivos más importantes en pequeños rumiantes, tales como la raza caprina Markhoz. que está en peligro de extinción. Objetivo: Estimar las tendencias genéticas, ambientales y fenotípicas, y los parámetros genéticos para el tamaño de la camada (LS), como rasgo de prolificidad de las hembras de cabras Markhoz. Métodos: Se utilizaron registros de partos de 3.064 hembras Markhoz, de 1992 a 2015. Los parámetros genéticos se estimaron con una función de enlace logit utilizando el software ASReml, ajustando un modelo animal de repetibilidad, con el año de nacimiento, el año del parto y la edad al parto como efectos fijos, y genéticos aditivos directos y efectos ambientales permanentes como efectos aleatorios. Las tendencias genéticas, fenotípicas y ambientales se estimaron mediante la regresión del valor de la cría, el valor fenotípico y los promedios de desviación ambiental en el año de nacimiento, respectivamente. Resultados: Se estimó la heredabilidad -baja e insignificante- (0,002), repetibilidad (0,054) y coeficiente de ambiente permanente (0,052) para LS, lo que indica una baja posibilidad de lograr un progreso genético rápido a través de selección fenotípica. Se estimó una tendencia genética no significativa -de hecho, cero- (0,00004 cabezas/parto/año) y se estimaron tendencias fenotípicas y ambientales negativas significativas (-0,01097 y -0,01100 cabezas/parto/año, respectivamente) en el período estudiado. Conclusión: La optimización de las condiciones ambientales y la aplicación de tecnologías de alto rendimiento en los programas de selección podrían reducir el riesgo de extinción de la raza Markhoz.

Resumo Antecedentes: A prolificidade tem um elevado valor económico e é uma das mais importantes características de reprodução nos pequenos ruminantes, como a raça de caprinos Markhoz, que está em perigo de extinção. Objetivo: Estimar tendências genéticas, ambientais e fenotípicas, e parâmetros genéticos para o tamanho da serapilheira (LS), como um traço de proliferação de cabras Markhoz. Métodos: Este estudo foi realizado usando registros de parto de 3.064 Markhoz entre 1992 e 2015. Os parâmetros genéticos foram estimados com uma função logit link utilizando o software ASReml, ajustando um modelo animal de repetibilidade, com o ano de nascimento, o ano de parto ea idade de caçoar como efeitos fixos e efeitos ambientais diretos e genéticos diretos como efeitos aleatórios. As tendências genéticas, fenotípicas e ambientais foram estimadas pela regressão do valor de criação, valor fenotípico e médias de desvio ambiental no ano de nascimento, respectivamente. Resultados: Herdabilidade baixa e negligenciável (0,002), repetibilidade (0,054) e coeficiente de ambiente permanente (0,052) foram estimadas para LS, o que indica baixa possibilidade de alcançar um progresso genético rápido através da seleção fenotípica. Foi estimada uma tendência genética não-significativa e realmente zero (0,00004 cabeças/parto/ano) e tendências fenotípicas e ambientais negativas significativas (-0,01097 e -0,01100 cabeças/parto/ano, respectivamente) no período estudado. Conclusão: Parece que a otimização das condições ambientais ea aplicação de tecnologias de alto rendimento em programas de seleção poderiam reduzir o risco de extinção para a raça Markhoz.

Genetic evaluation of dystocia and its relationship with productive and reproductive traits in Holstein cows¤ / Evaluación genética de distocia y su relación con las características productivas y reproductivas en vacas Holstein / Avaliação genética de distocia e sua relação com características produtivas e reprodutivas em vacas da raça Holandesa

Abstract: Background: dystocia is one of the most economically significant secondary traits in dairy cows and has adverse effects on the subsequent survival, health, and performance of mothers and offspring. Objective: the aim of this study was to estimate direct and maternal genetic parameters for calving ease (CE) and its relationship with productive and reproductive traits in Iranian Holstein cows. Methods: data from 1991 through 2011 were collected from the Animal Breeding Center of Iran, and contained 132,831 records of CE, 183,203 records of productive traits including 305-d adjusted milk yield (MY305), 305-d adjusted fat yield (FY305) and 305-d adjusted protein yield (PY305), and 129,199 records of reproductive traits including days open (DO), days to first service (DFS) and calving interval (CI). Univariate and bivariate linear animal models were used for the analysis of traits in two different models on which direct genetic effect (model 1) and direct + maternal genetic effects (model 2) using AI-REML algorithm were included. Results: estimated heritabilities for CE in model 1 were 0.02 in univariate and 0.02-0.03 in bivariate analyses. Direct and maternal heritabilities in model 2 were 0.02 and 0.002 for univariate, and 0.03 and 0.0004-0.006 in bivariate analyses, respectively. Genetic correlations between direct effects of CE with MY305, FY305, and PY305 were -0.99, 0.02 and-0.07 in model 1, and -0.2, -0.02 and -0.13 in model 2, respectively. Conclusion: this study suggested that a selection index that includes both direct and maternal effects should be included in CE breeding programs.

Resumen Antecedentes: la distocia es uno de los rasgos secundarios económicamente más significativos en las vacas lecheras y tiene efectos adversos sobre la posterior supervivencia, salud y el rendimiento de las madres e hijos. Objetivo: estimar parámetros genéticos directos y maternos para facilidad de parto (CE) y su relación con las características productivas y reproductivas en vacas Holstein iraníes. Métodos: se recogieron datos desde 1991 hasta 2011 en el Centro de Reproducción Animal de Irán, que contenían 132.831 registros de la CE, 183.203 registros de características productivas, incluyendo 305-d ajustado la producción de leche (MY305), 305-d de rendimiento graso ajustado (FY305) y 305-d de producción de proteína ajustada (PY305), y 129.199 registros de características reproductivas, incluyendo días abiertos (DO), días al primer servicio (DFS) y el intervalo entre partos (CI). Se utilizaron modelos animales lineales univariantes y bivariantes para el análisis de rasgos en dos modelos diferentes en los que se incluyeron el efecto genético directo (modelo 1) y los efectos genéticos maternos directos + (modelo 2) usando el algoritmo AI-REML. Resultados: las heredabilidades estimadas para la CE en el modelo 1 fueron 0,02 en uni y 0,02-0,03 en los análisis bivariados. Las heredabilidades directas y maternas en el modelo 2 fueron 0,02 y 0,002 para univariado, y 0,03 y 0,0004 a 0,006 en el análisis bivariado, respectivamente. Las correlaciones genéticas entre los efectos directos de la CE con MY305, FY305 y PY305 fueron -0,99, 0,02 y -0,07 en el modelo 1 y -0,2, -0,02 y -0,13 en el modelo 2, respectivamente. Conclusión: este estudio sugiere que un índice de selección que incluye tanto los efectos directos y maternos se debe incluir en los programas de mejoramiento de la CE.

Resumo Antecedentes: distocia é uma das características secundárias economicamente mais significativas em vacas leiteiras e tem efeitos adversos sobre a subsequente sobrevivência, saúde e desempenho de mães e filhos. Objetivo: o objetivo deste estudo foi estimar parâmetros genéticos direto e maternos para facilidade de parto (CE) e sua relação com características produtivas e reprodutivas em vacas da raça Holandesa iranianos. Métodos: dados de 1991 a 2011 foram coletados a partir do Centro de Melhoramento Animal do Irã, estes continham 132.831 registros da CE, 183.203 registros de características produtivas, incluindo 305-d rendimento ajustado leite (P305), 305-d produção de gordura ajustada (FY305) e 305-d rendimento ajustado proteína (PY305), e 129.199 registros de características reprodutivas, incluindo jornadas de portas abertas (DO), dias para o primeiro serviço (DFS) e intervalo entre partos (CI). Modelos animais lineares univariados e bivariados foram utilizados para a análise de características em dois modelos diferentes em que foram incluídos efeito genético direto (modelo 1) e efeitos genéticos maternos diretos + (modelo 2) usando o algorítmo AI-REML. Resultados: a herdabilidade estimada para CE no modelo 1 foi 0,02 na análise univariada e 0,02-0,03 na análise bivariada. A herdabilidade direta e materna no modelo 2 foi 0,02 e 0,002 para univariada, e 0,03 e 0,0004-0,006 na bivariada, respectivamente. As correlações genéticas entre os efeitos diretos da CE com P305, FY305 e PY305 foram -0,99, 0,02 e -0,07 no modelo 1 e -0,2, -0,02 e -0,13 no modelo 2, respectivamente. Conclusão: este estudo sugere que um índice de seleção que inclua efeitos diretos e maternos deve ser incluído em programas de melhoramento para CE.

Modelling lactation curve for milk fat to protein ratio in Iranian buffaloes (Bubalus bubalis) using non-linear mixed models.

The aim of this study was to compare seven non-linear mathematical models (Brody, Wood, Dhanoa, Sikka, Nelder, Rook and Dijkstra) to examine their efficiency in describing the lactation curves for milk fat to protein ratio (FPR) in Iranian buffaloes. Data were 43 818 test-day records for FPR from the first three lactations of Iranian buffaloes which were collected on 523 dairy herds in the period from 1996 to 2012 by the Animal Breeding Center of Iran. Each model was fitted to monthly FPR records of buffaloes using the non-linear mixed model procedure (PROC NLMIXED) in SAS and the parameters were estimated. The models were tested for goodness of fit using Akaike's information criterion (AIC), Bayesian information criterion (BIC) and log maximum likelihood (-2 Log L). The Nelder and Sikka mixed models provided the best fit of lactation curve for FPR in the first and second lactations of Iranian buffaloes, respectively. However, Wood, Dhanoa and Sikka mixed models provided the best fit of lactation curve for FPR in the third parity buffaloes. Evaluation of first, second and third lactation features showed that all models, except for Dijkstra model in the third lactation, under-predicted test time at which daily FPR was minimum. On the other hand, minimum FPR was over-predicted by all equations. Evaluation of the different models used in this study indicated that non-linear mixed models were sufficient for fitting test-day FPR records of Iranian buffaloes.

Comparison of non-linear models to describe growth of Iranian Guilan sheep / Comparación de modelos no lineales para describir el crecimiento de ovejas iraní Guilan / Comparação de modelos não lineares para descrever o crescimento de ovinos iraniano Guilan

Summary Background: non-linear mathematical models, empirically developed by plotting body weight against age, are used to describe the growth curve in different animals. Objective: to describe the growth pattern in Guilan sheep using non-linear models. Methods: six non-linear mathematical equations (Brody, Negative exponential, Logistic, Gompertz, von Bertalanffy and Richards) were used to describe the growth curves in Guilan sheep. The Agricultural Organization of Guilan province (Rasht, Iran) provided the dataset used in this study. The dataset included 42,257 weight records of lambs from birth to 240 days of age during years 1994 to 2014. Each model was separately fitted to body weight records of all lambs, males and females, using the NLIN and MODEL procedures of SAS. The models were tested for goodness of fit using adjusted coefficient of determination, root means square error (RMSE), Durbin-Watson statistic, akaike's information criterion (AIC) and bayesian information criterion (BIC). Results: the Richards model provided the best fit to the growth curve in females and all lambs, with the lowest RMSE, AIC, and BIC values compared to the other models. The Brody model provided the best fit of growth in male lambs due to the lower values of AIC and BIC compared to the other models. The negative exponential model provided the worst fit of growth for males, females and all lambs. Conclusion: the evaluation of the growth equations used in this study indicates the potential of non-linear functions for fitting body weight records of Guilan sheep.

Resumen Antecedentes: los modelos matemáticos no lineales desarrollados empíricamente mediante la comparación del peso corporal contra la edad se han usado para describir la curva de crecimiento en diferentes animales. Objetivo: describir el patrón de crecimiento en ovejas Guilan usando modelos no lineales. Métodos: seis ecuaciones matemáticas no lineales (Brody, Exponencial negativo, Logístico, Gompertz, von Bertalanffy y Richards) se utilizaron para describir las curvas de crecimiento en ovejas Guilan. El conjunto de datos utilizados en este estudio se obtuvo de la Organización para la Agricultura de la provincia Guilan (Rasht, Irán), y comprendió 42,257 registros de peso de corderos, recogidos desde el nacimiento hasta los 240 días de edad durante los años 1994 a 2014. Cada modelo fue ajustado por separado a los registros de peso corporal de todos los corderos, machos y hembras, utilizando los procedimientos NLIN y MODEL de SAS. Los modelos fueron probados para la bondad del ajuste mediante el coeficiente de determinación ajustado, la raíz cuadrada del error cuadrático medio (RMSE), el estadístico de Durbin-Watson, el criterio de información de akaike (AIC) y el criterio de información bayesiano (BIC). Resultados: el modelo de Richards proporcionó el mejor ajuste de la curva de crecimiento en las hembras y todos los corderos debido a los valores más bajos de RMSE, AIC y BIC con respecto a los otros modelos. El modelo Brody proporcionó el mejor ajuste de la curva de crecimiento de los corderos machos debido a los valores más bajos de AIC y BIC con respecto a los otros modelos. El modelo Exponencial negativo porporcionó el peor ajuste de la curva de crecimiento para machos, hembras y todos los corderos. Conclusión: la evaluación de diferentes ecuaciones de crecimiento utilizadas en este estudio indica el potencial de las funciones no lineales para el ajuste de los registros de peso corporal en ovejas de raza Guilan.

Resumo Antecedentes: os modelos matemáticos não lineares desenvolvidos empiricamente através da representação gráfica do peso corporal com a idade têm sido adequados para descrever a curva de crescimento em diferentes animais. Objetivo: o objetivo deste estudo foi descrever o padrão de crescimento em ovinos Guilan usando modelos não lineares. Métodos: seis equações matemáticas não lineares (Brody, Negativo exponencial, Logístico, Gompertz, von Bertalanffy e Richards) foram utilizadas para descrever as curvas de crescimento em ovelhas Guilan. O conjunto de dados utilizado neste estudo foi obtido a partir da Organização Agrícola da província de Guilan (Rasht, Irã) e composta 42.257 registros de peso de cordeiros que foram recolhidos desde o nascimento até 240 dias de idade, durante 1994 a 2014. Cada modelo foi ajustado separadamente para os registros de peso corporal de todos os cordeiros, machos e fêmeas, utilizando os procedimentos NLIN e modelo em SAS. Os modelos foram testados para a qualidade do ajuste por meio do coeficiente de determinação ajustado, a raiz quadrada de erro quadrático médio (RMSE), o estatístico Durbin-Watson estatística, o critério de informação de Akaike (AIC) e critério de informação Bayesiano (BIC). Resultados: o modelo de Richards providencia o melhor ajuste da curva de crescimento nas fêmeas e todos os cordeiros, devido aos menores valores de RMSE, AIC e BIC do que outros modelos. O modelo Brody da o melhor ajuste da curva de crescimento em cordeiros devido aos menores valores de AIC e BIC do que outros modelos. O modelo exponencial negativo oferece o pior ajuste de curva de crescimento para machos, fêmeas e todos os cordeiros. Conclusão: avaliação diferentes equações de crescimento utilizados neste estudo indicaram o potencial das funções não lineares para a montagem de registos de peso corporal de Guilan.

Factors affecting secondary sex ratio in Iranian Holsteins.

The objective of this study was to evaluate the factors affecting secondary sex ratio (SSR) in Iranian Holsteins. Data of 942,941 Holstein calving events from the Animal Breeding Center of Iran, recorded between January 1996 and December 2007, were used in the analysis. A multivariable logistic regression model was used to model the logit of the probability of a male calf being born. Male births accounted for 49.6% of the total observations. The ratio of males to females varied from 52.5:47.5 in calving year 1996-1999 (odds ratio (OR)=1.18; P<0.0001), to 48.5:51.5 in calving year 2004-2007. The greatest occurrence of male births was observed in spring (OR=1.02; P<0.0001), and the lowest incidence of male births was for summer or fall calvings. Also, the frequency of male births decreased from parity 1 to parity 4 and beyond (P<0.0001; OR=1.11). The greatest number of sires had the SSR equal to 0.5 with a minimum SSR of 32% while the maximum was 97%. Among cows that had a male birth, the chance of delivering a male calf again was 25.5% when cows had delivered a male once (OR=1.14; P<0.0001), and 12.7% if a male calf was delivered twice by a cow. This indicated that characteristics peculiar to the dam influence the sex of her offspring and suggests some degree of repeatability of calf sex within cows.

Lamb survival analysis from birth to weaning in Iranian Kermani sheep.

Survival records from 1,763 Kermani lambs born between 1996 and 2004 from 294 ewes and 81 rams were used to determine genetic and non-genetic factors affecting lamb survival. Traits included were lamb survival across five periods from birth to 7, 14, 56, 70, and 90 days of age. Traits were analyzed under Weibull proportional hazard sire models. Several binary analyses were also conducted using animal models. Statistical models included the fixed class effects of sex of lamb, month and year of birth, a covariate effect of birth weight, and random genetic effects of both sire (in survival analyses) and animal (in binary analyses). The average survival to 90 days of age was 94.8%. Hazard rates ranged from 1.00 (birth to 90 days of age) to 1.73 (birth to 7 days of age) between the two sexes indicating that male lambs were at higher risk of mortality than females (P < 0.01). This study also revealed a curvilinear relationship between lamb survival and lamb birth weight, suggesting that viability and birth weight could be considered simultaneously in the selection programs to obtain optimal birth weight in Kermani lambs. Estimates of heritabilities from survival analyses were medium and ranged from 0.23 to 0.29. In addition, heritability estimates obtained from binary analyses were low and varied from 0.04 to 0.09. The results of this study suggest that progress in survival traits could be possible through managerial strategies and genetic selection.

Evaluation of the potential effects of abortion on the productive performance of Iranian Holstein dairy cows.

Calving records from the Animal Breeding Center of Iran collected from January 1983 to December 2007 and comprising 1,163,594 Holstein calving events from 2552 herds were used to evaluate the potential effect of abortion occurrence on 305-day milk yield, milk fat yield, fat percentage of milk and milk protein yield in Iranian Holsteins. Statistical analyses of production traits were performed using a linear mixed model procedure. Normal-calved cows had greater 305-day milk production, fat yield and protein yield of milk than abortive-calved cows (P < 0.05). However, abortive-calved cows had the greater milk fat percentage than normal calved cows (P < 0.05). The linear and quadratic effects of age of dam were significant on all of the studied traits (P < 0.05). The results of regression analysis showed that increase in the quadratic effect of age can cause an increase in the fat percentage of milk for all calvings including normal and abortive calvings. Because abortion is one of the most important conditions that limit a cow's ability to produce, maintaining the general health of cattle is important in minimizing the risk of abortion problems.

Bayesian estimates of genetic parameters for metritis, retained placenta, milk fever, and clinical mastitis in Holstein dairy cows via Gibbs sampling.

The objective of this study was to estimate heritability and genetic correlations between the liabilities of clinical mastitis (CM), milk fever (MF), metritis (MET), and retained placenta (RP) within the first three lactations of Holstein dairy cows. The records of 57,301 dairy cows from 20 large dairy herds in Iran between January 2005 and June 2009 were analysed with univariate and bivariate threshold animal models, using Gibbs sampling methodology. The final model included the fixed class effects of herd-year, season of calving, parity of dam, the linear covariate effect of age at calving, and the random direct genetic effect of animal. Posterior means of heritability for liabilities in first, second, and third lactations were 0.06, 0.08, and 0.09, respectively, for CM; 0.10, 0.12, and 0.11, respectively, for MF; 0.09, 0.07, and 0.10, respectively, for MET, and 0.07, 0.08, and 0.08, respectively, for RP. Posterior means of genetic correlations between disease liabilities were low or moderate (from -0.01 to 0.26). The results of this study indicated the importance of health traits for considering in the selection index of Iranian Holstein dairy cows.

Evaluation of the genetic trend of milk yield in the multiple ovulation and embryo transfer populations of dairy cows, using stochastic simulation.

Stochastic modeling of dairy cattle populations using multiple ovulation and embryo transfer (MOET) was used to compare 15-year genetic responses with an artificial insemination (AI) program. MOET and AI techniques were simulated in four populations, two with 100 breeding females each and two with 400 breeding females. The selection goal was to maximize genetic progress in milk yield. The reduction in genetic variation due to inbreeding and linkage disequilibrium was accounted for in the simulation process. All four MOET breeding schemes studied achieved larger genetic responses than the realized and theoretical genetic gains from the current AI progeny testing populations. Strict restriction against inbred matings slowed genetic progress significantly in the small population but would not be consequential in the larger population. However, allowing inbred matings in the smaller population caused a rapid accumulation of inbreeding. Linkage disequilibrium was as important as inbreeding in reducing genetic variation. Genetic drift variance was much smaller in the larger population.

Bio-economic evaluation of the use of sexed semen at different conception rates and herd sizes in Holstein populations.

A stochastic bio-economic model was used to determine the effects of applying artificial insemination (AI) with conventional or sexed semen at different conception rates and herd sizes on the genetic progress of productive trait and net profit over a 15-year period. The genetic means of the cattle population was predicted to increase over the years and the rate of genetic progress in the population program using sexed semen was significantly greater than the rate of progress in the population using conventional semen. The theoretical genetic gain was greater than the realized genetic gain for milk yield for all the AI scenarios. In addition, the genetic means for milk yield in the expanding herds were greater than in the fixed sized herds. The trend in net profit generated by using AI strategies with conventional semen over the time horizon was greater when herds were expanding(P < 0.01). The trend in net profit for fixed sized herds was generally negative, however,expanding herds experienced positive net profits over the years. Also, the net profit of using AI strategies with sexed semen was greater when dairy herds were expanding. On the other hand, the net profit of using AI with sexed semen was greater than that of AI with conventional semen at the end of the time horizon. The results of sensitivity analyses indicated that a 20% increase or decrease in milk sales income and feed costs have significantly modified the net profit of AI strategies using either sexed or conventional semen.

Heterogeneity of variance for milk traits at climitical regions in Holstein dairy cattle in Iran and the best method(s) for data transformation.

In this research, heterogeneity of variance components in cattle populations at climatical regions in the first three lactations was studied. The data set included the following: 161328 records of first, 123369 records of second and 81013 records of third lactations, which was collected by Animal Breeding Center of Iran from 1983 to 2004. Records of three lactations were divided in the base of Domarten method. Bartlett test for heterogeneity of variance components was significant among all subgroups. In order to decrease the heterogeneity of variance components, we used several data transformation methods including Logarithmic, Square root and Arc sin transformations. Logarithmic transformation decreased the heterogeneity of variance components in the three lactations and other methods had not effect for removing the heterogeneity in any group. Genetic parameters and heritability were estimated for three lactations by MATVEC program, using animal model. Results showed that the heritability estimates of milk yield were decreased from the first lactation to the third; also the heritability estimates of transformed data were slightly higher than the original data. Comparison between estimated parameters in single trait and two traits analysis, before and after data transformation, showed that there were not significant differences between derived results.

Effect of the threshold nature of traits on heritability estimates obtained by linear model.

In this research we used stochastic method to simulate litter size data under assumption that the phenotype of the trait of interest is categorically distributed with a liability of normally distributed background effect. For the phenotypic categorical measurements, normal distribution of liability was assumed. Analysis was conducted by DFREML for phenotypic categorical data set. In the simulation process, we applied different true background heritabilities in combination with different threshold points. The points with the lowest heritability had the lowest variation in estimated heritability and those with the highest heritability had the highest variation. Results clearly show that by moving threshold points from the population mean towards the two tails of the distribution and also by increasing the true heritability, the differences between estimated heritability and true heritability increases. The linear model has always underestimated true heritabilities. It is possible to use our estimates to obtain a confidence range for true heritability when we have information about approximate location of threshold and estimates of heritability obtained by linear model.