RESUMEN
We studied the effect of including GWAS results on the accuracy of single- and multipopulation genomic predictions. Phenotypes (backfat thickness) and genotypes of animals from two sire lines (SL1, n = 1146 and SL3, n = 1264) were used in the analyses. First, GWAS were conducted for each line and for a combined data set (both lines together) to estimate the genetic variance explained by each SNP. These estimates were used to build matrices of weights (D), which was incorporated into a GBLUP method. Single population evaluated with traditional GBLUP had accuracies of 0.30 for SL1 and 0.31 for SL3. When weights were employed in GBLUP, the accuracies for both lines increased (0.32 for SL1 and 0.34 for SL3). When a multipopulation reference set was used in GBLUP, the accuracies were higher (0.36 for SL1 and 0.32 for SL3) than in single-population prediction. In addition, putting together the multipopulation reference set and the weights from the combined GWAS provided even higher accuracies (0.37 for SL1, and 0.34 for SL3). The use of multipopulation predictions and weights estimated from a combined GWAS increased the accuracy of genomic predictions.
Asunto(s)
Peso Corporal , Estudio de Asociación del Genoma Completo , Sus scrofa/genética , Tejido Adiposo , Animales , Polimorfismo de Nucleótido Simple , Sus scrofa/clasificación , Sus scrofa/fisiologíaRESUMEN
Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this study, we performed a meta-analysis of QTL on chromosome 4 in pig, using data from 25 separate experiments. First, a meta-analysis was performed for individual traits: average daily gain and backfat thickness. Second, a meta-analysis was performed for the QTL of three traits affecting loin yield: loin eye area, carcass length and loin meat weight. Third, 78 QTL were selected from 20 traits that could be assigned to one of three broad categories: carcass, fatness or growth traits. For each analysis, the number of identified meta-QTL was smaller than the number of initial QTL. The reduction in the number of QTL ranged from 71% to 86% compared to the total number before the meta-analysis. In addition, the meta-analysis reduced the QTL confidence intervals by as much as 85% compared to individual QTL estimates. The reduction in the confidence interval was greater when a large number of independent QTL was included in the meta-analysis. Meta-QTL related to growth and fatness were found in the same region as the FAT1 region. Results indicate that the meta-analysis is an efficient strategy to estimate the number and refine the positions of QTL when QTL estimates are available from multiple populations and experiments. This strategy can be used to better target further studies such as the selection of candidate genes related to trait variation.
Asunto(s)
Cromosomas de los Mamíferos/genética , Sitios de Carácter Cuantitativo , Porcinos/genética , Tejido Adiposo , Crianza de Animales Domésticos , Animales , Peso Corporal/genética , Mapeo Cromosómico , Genotipo , Carne , Repeticiones de Microsatélite , FenotipoRESUMEN
The objectives of this study were to evaluate the effect of somatic cell count (SCC) on functional longevity and to estimate the heritability of functional longevity using survival analysis in Valle del Belice dairy sheep. A total of 4,880 lactations of 2,190 ewes from 11 flocks were used. In this study, SCC was considered as an indication of subclinical mastitis. In case of clinical cases, identified by the technicians at milking time, test-day weights and milk samples of those ewes were not considered. Somatic cells were analyzed as counts, without any transformation, and were grouped in 3 classes based on the observed SCC maximum (mxSCC). The mxSCC classes, expressed as 10(3) cells/mL, were classified as 1 if mxSCC
Asunto(s)
Longevidad/genética , Mastitis/veterinaria , Leche/citología , Ovinos/fisiología , Animales , Recuento de Células , Industria Lechera , Femenino , Mastitis/fisiopatología , Modelos Biológicos , Carácter Cuantitativo Heredable , Ovinos/genética , Análisis de SupervivenciaRESUMEN
Local breeding schemes for Holstein cattle of Costa Rica were compared with the current practice based on continuous semen importation (SI) by deterministic simulation. Comparison was made on the basis of genetic response and correlation between breeding goals. A local breeding goal was defined on the basis of prevailing production circumstances and compared against a typical breeding goal for an exporting country. Differences in genetic response were <3%, and the correlation between breeding goals was 0.99. Therefore, difference between breeding objectives proved negligible. For the evaluation of genetic response, the current scheme based on SI was evaluated against a progeny testing (PT) scheme and a closed nucleus (CN) breeding scheme, both local. Selection intensities and accuracy of selection were defined according to current population size and reproduction efficiency parameters. When genotype x environment interaction (G x E) was ignored, SI was the strategy with the highest genetic response: 5.0% above the CN breeding scheme and 33.2% above PT. A correlation between breeding values in both countries lower than one was assumed to assess the effect of G x E. This resulted in permanent effects on the relative efficiencies of breeding strategies because of the reduction in the rate of genetic response when SI was used. When the genetic correlation was assumed equal to 0.75, the genetic response achieved with SI was reduced at the same level as local PT. When an initial difference in average genetic merit of the populations was assumed, this only had a temporal effect on the relative ranking of strategies, which is reverted after some years of selection because the rate of change in genetic responses remains unchanged. Given that the actual levels of genetic correlation between countries may be around 0.60, it was concluded that a local breeding scheme based on a nucleus herd could provide better results than the current strategy based on SI.
Asunto(s)
Cruzamiento/métodos , Bovinos/genética , Semen , Animales , Cruzamiento/economía , Costa Rica , Femenino , Masculino , Carácter Cuantitativo Heredable , Reproducción , Selección GenéticaRESUMEN
Nine mathematical models were compared for their ability to predict daily milk yields (n = 294,986) in standard 305-d and extended lactations of dairy cows of Costa Rica. Lactations were classified by parity (first and later), lactation length (9 to 10, 11 to 12, 13 to 14, 15 to 16, and 16 to 17 mo), and calving to conception interval (1 to 2, 3 to 4, 5 to 6, 7 to 8, and 9 to 10 mo). Of the nine models, the diphasic model and lactation persistency model resulted in the best goodness of fit as measured by adjusted coefficient of determination, residual standard deviation, and Durbin-Watson coefficient. All other models showed less accuracy and positively correlated residuals. In extended lactations, models were also fitted using only test-day records before 305 d, which resulted in a different ranking. The diphasic model showed the best prediction of milk yield in standard and extended lactations. We concluded that the diphasic model provided accurate estimates of milk yield for standard and extended lactations. Interpretation of parameters deserves further attention because of the large variation observed. As expected, the calving to conception interval was found to have a negative effect on milk yield for cows with a standard lactation length. In extended lactations, these negative effects of pregnancy on milk yield were not observed.
Asunto(s)
Bovinos/fisiología , Lactancia/fisiología , Modelos Biológicos , Animales , Costa Rica , Femenino , Leche/química , Leche/metabolismo , Estadística como AsuntoRESUMEN
Dynamic programming was used to determine optimal replacement and insemination policies for Holstein-Friesian cattle in the southeastern region of Brazil. Optimal insemination and replacement decisions were determined for two disposal alternatives: selling all cows exclusively for slaughter (A) or selling the cows either for slaughter or to other farmers for production (B). Disposal alternative B reflects the common practice among dairy farmers to sell some of their cows to other farmers at a higher price than the carcass price. In the model, cows were described in terms of lactation number, stage of lactation, calving interval, and milk produced during present and previous lactation. For disposal alternative A, the optimal average herd life was 54.9 mo, corresponding to annual replacement and voluntary culling rates of 21.8 and 4.1%, respectively. For disposal alternative B, the optimal average herd life was 44.0 mo, which corresponded to annual replacement and voluntary culling rates of 27.3 and 10.0%, respectively. In this case, from the total of voluntarily culled cows, 70% were sold to other farmers for production. Sensitivity analyses showed that changes in the disposal value of cows and replacement heifer prices strongly influenced the optimal insemination and replacement policy.
Asunto(s)
Industria Lechera/normas , Inseminación Artificial/veterinaria , Mataderos , Crianza de Animales Domésticos/normas , Animales , Brasil , Bovinos , Femenino , Industria de Alimentos/normas , Inseminación Artificial/normas , Lactancia , Masculino , Carne , Leche/química , Leche/metabolismoRESUMEN
Estimates of variance components for test day records in an animal model that considered multiple traits over multiple lactations were calculated using REML methodology. Test day records were classified into 11 periods within first and later lactations. Missing ancestors in the relationship matrix were classified in genetic groups. Data were collected from Costa Rican dairy farms. Estimates of components for total and additive genetic variance were clearly heterogeneous during the lactation. Heritabilities for traits in later parities were slightly higher than those for traits in first parity. Heritabilities were highest for records of midlactation. Phenotypic and genetic correlations for adjacent test days were close to 1. Phenotypic correlations were lower than genetic correlations. Heterogeneity of variances during the lactation suggests the adequacy of the multiple-trait test day model to describe milk yield during the lactation. When missing ancestors were allocated to a single base population instead of genetic groups, the estimates of residual variance were lower, and the estimates of genetic variance and genetic correlations were higher. When standardized records were used instead of actual test day records, the estimates of residual and total variance were lower, and the estimates of genetic variance were higher. Consequently, estimates of heritability and genetic correlations were also higher. Use of standardized data obtained by interpolation procedures is not advised for estimation of genetic variance components in a test day model.