Fixed or random contemporary groups in genetic evaluation for litter size in pigs using a single trait repeatability animal model

Abstract

Summary The importance of using fixed or random contemporary groups in the genetic evaluation of litter size in pigs was analysed by using farm and simulated data. Farm data were from four Spanish pig breeding populations, two Landrace (13 084 and 13 619 records) and two Large White (2762 and 8455 records). A simulated population (200 sows and 10 boars) selected for litter size, in which litter size was simulated using a repeatability animal model with random herd–year–season (HYS), was used to obtain simulated data. With farm data, the goodness‐of‐fit and the predictive ability of a repeatability animal model were calculated under several definitions of the HYS effect. A residual maximum likelihood estimator of the HYS variance in each population was obtained as well. In this sense, HYS was considered as either fixed or random with different number of individuals per level. Results from farm data showed that HYS variance was small in relation to the total variance (ranging from 0.01 to 0.04). The treatment of HYS effect as fixed, reduced the residual variance but the size of HYS levels does not explain by itself the goodness‐of‐fit of the model. The results obtained by simulation showed that the predictive ability of the model is better for random than for fixed HYS models. However, the improvement of predictive ability does not lead to a significant increase of the genetic response. Finally, results showed that random HYS models biased the estimates of genetic response when there is an environmental trend.

Analysis of alternative models treating herd × year effects as fixed or random

“…The fraction of the phenotypic variance due to herd × year effects for this trait was small (0.06). Our results were in good agreement with those found by Estany and Sorensen (1995) and Babot et al (2003), who reported that models considering herd × year effects as random resulted in smaller MSE and higher r ŷi,yi between the excluded and predicted observations than those of the fixed models. In their case the fraction of the phenotypic variance due to herd × year effects was also small (0.01-0.04).…”

Genetic parameters for a joint genetic evaluation of production and reproduction traits in pigs

“…According to Babot et al (2003) the impact of the definition and treatment of contemporary groups in the evaluation model on the genetic response of a pig nucleus is expected to be small. This conclusion has been obtained using the contemporary group size from eight to 100 sows.…”

Comparison on models for genetic evaluation of non-return rate and success in first insemination of the Danish Holstein cows

“…In the models, contemporary group effect was decomposed to herd effect over year-seasons, year-season effect over herds, and the remaining herd-year effects for each combination of herd and year (can be understood as interaction between herd and year). Herd and year-season were treated as fixed effects to avoid bias due to possible association between genetic effect and herd effect or yearseason effect, and herd-year was treated as random effect to avoid a loss of information and a problem with extreme category (all records belong to the same category) due to few observations within herd-year (Harville and Mee, 1984;Misztal et al, 1989;Visscher and Goddard, 1993;Babot et al, 2003). Such a strategy to deal with contemporary group effects was often used for the analysis of dairy cattle data (e.g., Roxström et al, 2001;Cole et al, 2007).…”