Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle.

In this study, we analyzed the variation of reproductive efficiency, estimated as the deviation between the optimal and real parity number of females at each stage of the cow's life, in 12,554 cows belonging to the Retinta Spanish cattle breed, using classical repeatability and random regression models. The results of the analyses using repeatability model and the random regression model suggest that reproductive efficiency is not homogeneous throughout the cow's life. The h2 estimate for this model was 0.30, while for the random regression model it increased across the parities, from 0.24 at the first calving to 0.51 at calving number 9. Additionally, we performed a preliminary genome-wide association study for this trait in a population of 252 Retinta cows genotyped using the Axiom Bovine Genotyping v3 Array. The results showed 5 SNPs significantly associated with reproductive efficiency, located in two genomic regions (BTA4 and BTA28). The functional analysis revealed the presence of 5 candidate genes located within these regions, which were previously involved in different aspects related to fertility in cattle and mice models. This new information could give us a better understanding of the genetic architecture of reproductive traits in this species, as well as allow us to accurately select more fertile cows.

Genetic analysis of the effects of heat stress before and after lambing on pre-weaning live weight in Spanish Merino lambs.

BACKGROUND: Heat stress (HS) is a major environmental effect on sheep production. Hereby, we estimated the genetic (co)variance component of HS on the pre-weaning performance of 19,022 Merino lambs by analysing the climatological index of temperature and relative humidity (recorded 30 days before lambing and after lambing) using transversal and longitudinal mixed linear models. METHODS AND RESULTS: The global impact of HS during the last 30 days of pregnancy was -17% for birthweight and ranged between -4% and -8% for live weight at 15, 30 days of age (W30), and average daily gain from birth at 30 days. The results from both statistical approaches showed very similar heritabilities (h2 ), ranging from 0.192 to 0.237 for the direct genetic (D) effects and from 0.072 to 0.082 for the maternal genetic (M) effects, but the antagonism between (D) and (M) was higher when a longitudinal model was used. A significant genotype-environmental effect was also found regardless of whether the climatological covariables were considered in the model. In addition, we employed D and M breeding values for W30 as an example to create a new subjacent index by first using a principal component analysis and employing the leading eigenvalues as a weighted factor that provides the information needed to identify those genotypes that maximise the response for both genetic effects over a wide range of climate-environment levels. CONCLUSIONS: Our study revealed that the HS indexes of the mother during the gestation period have a significant effect on the growth of the lambs during the early stages of life.

Genetic Parameters of Somatic Cell Score in Florida Goats Using Single and Multiple Traits Models.

A total of 1,031,143 records of daily dairy control test of Spanish Florida goats were used for this study. The database was edited, and only the records of the first three lactations were kept. The final database contained 340,654 daily-test somatic cell counts from 27,749 daughters of 941 males and 16,243 goats. The evolution of this count in the last 14 years was analyzed following French and American international associations' criteria for the risk of mastitis in goats, and confirmed the slight increase in SCS in the last years and the importance of this problem (50% of dairy control tests show a risk of suffering mastitis). For the genetic analysis, the SCS records were log-transformed to normalize this variable. Two strategies were used for the genetic analysis: a univariate animal model for the SCS assuming that SCS does not vary throughout the parities, and a multi-character animal model, where SCS is not considered as the same character in the different parities. The heritabilities (h2) were higher in the multiple traits models, showings an upward trend from the first to the third parity (h2 between 0.245 to 0.365). The genetic correlations of the same trait, as well as between breeding values (GVs) between different parities, were different from unity. The breeding values (EBVs) obtained for both models were subjected to a PCA: the first eigenvector (λ1) explained most of the variations (between 74% to 90%), while the second λ2 accounted for between 9% to 20% of the variance, which shows that the selection will be proportionally favorable but not equivalent in all parities and that there are some variations in the type of response.

Use of Principal Component Analysis to Combine Genetic Merit for Heat Stress and for Fat and Protein Yield in Spanish Autochthonous Dairy Goat Breeds.

We studied the effect of the Temperature Humidity Index (THI) (i.e., the average of temperature and relative humidity registered at meteorological stations) closest to the farms taken during the test day (TD), for total daily protein and fat yields (fpy) of the three main Spanish dairy goats. The data were from Florida (11,244 animals and 126,825 TD), Malagueña (12,215 animals and 141,856 TD) and Murciano Granadina (5162 animals and 62,834 TD) breeding programs and were studied by different linear models to estimate the nature of the fpy response throughout the THI and the weeks of lactation (Days in Milk, DIM) trajectories. The results showed an antagonism between THI and DIM, with a marked depression in the fpy level in animals kept in the hot zone of the THI values (THI > 25) compared with those in the cold zone (THI ≤ 16), with a negative impact equivalent to production of 13 to 30 days. We used a Reaction Norm model (RN), including THI and DIM as fixed covariates and a Test Day Model (TDM), to estimate the genetic (co)variance components. The heritability and genetic correlations estimated with RN and TDM showed a decreased pattern along the scale of THI and DIM, with slight differences between breeds, meaning that there was significant genetic variability in the animal's ability to react to different levels of THI, which is not constant throughout the DIM, showing the existence of genotype-environment interaction. The breeding values (BV) of all animals for each level of THI and DIM were subject to a principal component analysis, and the results showed that 89 to 98% of the variance between the BV was explained by the two first eigenvalues. The standardized BV were weighted with the corresponding eigenvector coefficients to construct an index that showed, in a single indicator, the most complete expression of the existing genetic variability in the animals' ability to produce fpy along the trajectories of THI and DIM. This new option will make it easier to select animals which are more productive, and with better adaptability to heat stress, as well as enabling us to exploit genetic variations in the form of the response to heat stress to be adapted to different production systems.

Genetic effect of season on the preweaning growth of beef cattle: A first approach on Retinta calves / Efecto genético de la estación climática sobre el crecimiento predestete del ganado de carne: Un primer estudio en terneros de raza Retinta / Efeito genético de estações climáticas no crescimento pré-desmame de bovinos de corte: uma primeira abordagem para os bezerros Retinta

Abstract Background: Heat stress derived from global warming is causing major economic losses in the livestock industry. Objective: To develop a novel methodological approach for determining the influence of climatic factors on the estimation of genetic parameters for growth traits in Retinta cattle breed by using reaction-norm models. Methods: Live weight records (n=7,753) from 3,162 Retinta calves born from 1,249 dams and 85 sires and raised in the Andalusian region (Spain) were analyzed. The effect of heat stress was measured using the temperature-humidity index, calculated with climatological data obtained from four weather stations. A bivariate-random-regression reaction-norm model was used to estimate the (co)variance components of weight until weaning in two different climatic seasons corresponding to warm and cold months. Results: The heritability pattern of individuals reared under diverse environments during the first 90 days of age was different. However, differences were not significant at the end of the growing period. Weaned calves reared during the cold season showed greater growth from 70 to 160 days in comparison with those reared during the warm season. Conclusions: Overall, this assessment did not show significant effects of the genotype-environment interaction. However, highly significant evidence of genotype-climatic condition interaction was found during the calf´s first three months of age.

Resumen Antecedentes: El estrés térmico derivado del calentamiento global está causando pérdidas económicas en la industria ganadera. Objetivo: Desarrollar un enfoque metodológico para estimar la influencia de algunos factores climáticos sobre la estimación de parámetros genéticos en las variables de crecimiento de la raza bovina Retinta. Métodos: Se analizaron registros de peso vivo (n=7.753) de 3.162 terneros hijos de 1.249 vacas y 85 toros, criados en la región de Andalucía (España). El efecto del estrés térmico se midió mediante un índice de temperatura-humedad obtenido a partir de los datos de cuatro estaciones meteorológicas. Se usó un modelo bivariado de regresión aleatoria de "norma-reacción" para estimar la (co)varianza del peso hasta el destete en dos diferentes épocas climáticas correspondientes a los meses cálidos y fríos. Resultados: Se encontraron diferencias en el patrón de heredabilidad de individuos criados en diferentes ambientes durante los primeros 90 días de vida. Sin embargo, tales diferencias no fueron significativas al final del periodo de crecimiento. Los terneros destetados en la época fría mostraron un mayor crecimiento entre 70 y 160 días en comparación con los criados en la temporada cálida. Conclusiones: Se encontró una evidencia altamente significativa de la interacción genotipo-condición climática durante los primeros tres meses de crecimiento del ternero.

Resumo Antecedentes: O estresse térmico devido ao aumento da temperatura média está produzindo grandes perdas econômicas na indústria pecuária. Objetivo: Realizar uma nova abordagem metodológica para estimar a importância dos fatores climáticos em parâmetros genéticos em variáveis de crescimento da população da raça Retinta. Métodos: Foram analisados registros de peso vivo (n=7.753) de 3.162 Retinta bezerros, nascidos de 1.249 vacas e 85 touros criados na região da Andaluzia (Espanha). O efeito do estresse térmico foi medido utilizando o índice de temperatura-umidade obtido com dados climatológicos de quatro estações meteorológicas. Um modelo de regressão aleatória bivariado de norma-reação foi usado para estimar os componentes da (co)variância do peso à desmama em duas estações climáticas com correspondência aos meses quentes e fríos. Resultados: Diferenças foram encontradas no padrão de herdabilidade de indivíduos criados em diferentes ambientes nos primeiros 90 dias de idade. No entanto, essas diferenças não foram significativas no final do período de crescimento. Os bezerros desmamados globalmente na estação fria apresentaram um crescimento maior dos 70 aos 160 dias em comparação com os indivíduos criados na estação quente. Conclusões: Uma evidência altamente significativa da interação genótipo-ambiente foi encontrada durante os primeiros três meses de crescimento do bezerro.

Random regression models to account for the effect of genotype by environment interaction due to heat stress on the milk yield of Holstein cows under tropical conditions.

The present study had the following objectives: to compare random regression models (RRM) considering the time-dependent (days in milk, DIM) and/or temperature × humidity-dependent (THI) covariate for genetic evaluation; to identify the effect of genotype by environment interaction (G×E) due to heat stress on milk yield; and to quantify the loss of milk yield due to heat stress across lactation of cows under tropical conditions. A total of 937,771 test-day records from 3603 first lactations of Brazilian Holstein cows obtained between 2007 and 2013 were analyzed. An important reduction in milk yield due to heat stress was observed for THI values above 66 (-0.23 kg/day/THI). Three phases of milk yield loss were identified during lactation, the most damaging one at the end of lactation (-0.27 kg/day/THI). Using the most complex RRM, the additive genetic variance could be altered simultaneously as a function of both DIM and THI values. This model could be recommended for the genetic evaluation taking into account the effect of G×E. The response to selection in the comfort zone (THI ≤ 66) is expected to be higher than that obtained in the heat stress zone (THI > 66) of the animals. The genetic correlations between milk yield in the comfort and heat stress zones were less than unity at opposite extremes of the environmental gradient. Thus, the best animals for milk yield in the comfort zone are not necessarily the best in the zone of heat stress and, therefore, G×E due to heat stress should not be neglected in the genetic evaluation.

Multi-trait linear reaction norm model to describe the pattern of phenotypic expression of some economic traits in beef cattle across a range of environments.

The multi-trait reaction norm (MTRN) model was extended to beef cattle reared under tropical conditions with the following objectives: to compare multi-trait (MT) and MTRN models regarding the genetic parameters obtained; and to characterize G × E, the pattern of phenotypic expression, and the environmental sensitivity of animals for postweaning weight gain (PWG), scrotal circumference (SC), and annual average productivity of the cow (PRODAM). There was divergence in the estimates between the MT and MTRN models when the posterior probability intervals of additive genetic variances and heritability coefficients of PWG and PRODAM were analyzed. The MTRN model indicated an increase in heritability for PWG and PRODAM with improvement of the environmental conditions. For SC, heritability was practically the same, irrespective of the environmental conditions. The genetic correlations between the traits studied were low but varied over environments by the MTRN model. Considering genetic correlations obtained by the MTRN model for the same trait, lower estimates were obtained between extreme favorable and unfavorable environments. This finding suggest re-ranking of breeding values in different environments mainly for PWG and PRODAM. Thus, G × E is more important for PWG and PRODAM than for SC and should be included in the genetic evaluation of these traits. The traits PWG and PRODAM can be considered plastic traits, whereas SC is poorly plastic. The genetic trends in individual animal slopes indicate that the population is moving towards greater plasticity. This could be a matter of concern for breeders since greater plasticity seems to limit heritability and, consequently, the responses to selection.

Effect of alphas1-casein ( CSN1S1) genotype on milk CSN1S1 content in Malagueña and Murciano-Granadina goats.

There is substantial evidence showing that the polymorphism of the goat alphas1-casein (CSN1S1) gene has a major effect on milk protein, casein and fat content as well as on cheese yield. However, its influence on the synthesis rate of CSN1S1 has been less studied, with measurements only available in French breeds. In this article, we have measured milk CSN1S1 content in 89 Malagueña and 138 Murciano-Granadina goats with 305 and 460 phenotypic registers, respectively. In the Malagueña breed, average values of CSN1S1 content estimated for BB, BF, EE and FF genotypes were 6.94+/-0.38, 5.36+/-0.22, 4.58+/-0.13 and 3.98+/-0.27 g/l, respectively, being all significantly different (P<0.05). Conversely, in the Murciano-Granadina breed only the BB genotype (8.50+/-0.60 g/l) was significantly associated with increased levels of CSN1S1 (P<0.05), whereas BF (6.56+/-0.82 g/l), EE (6.39+/-0.60 g/l) and EF (6.91+/-0.76 g/l) genotypes displayed non-significant differences when compared with each other. Our results highlight the existence of breed-specific genetic and/or environmental factors modulating the impact of the CSN1S1 gene polymorphism on the synthesis rate of the corresponding protein.