Full sib pens of pigs are not suitable to identify variance component of associative effect: a simulation study using Gibbs Sampling

Jiqiu Cheng, Steven Janssens, Nadine Buys
2009 BMC Genetics  
Accounting for and quantifying the associative effect of each animal could improve both welfare of animals and response to selection. Because of the limitation of REML, Gibbs Sampling could be an alternative technique to estimate the variance component of the associative effect. The objective of this study was to investigate the estimation accuracy of the variance component of associative effect by using simulation via Gibbs Sampling. The simulated data comprised five generations of pigs. The
more » ... eeding animals of each generation were selected randomly. In the simulation, variations were introduced for the methods of assigning pens (random, mixed sib and full sib), the number of pigs per pen (5 or 10), the number of breeding animals per generation (162 or 324) and the correlation between genetic direct effect and genetic associative effect (-0.5, 0.1 or +0.5). Each set of simulation was run for 30 replications. Results: Random assignment or mixed sib assignment resulted in bias of estimated variance components in only 3 of 24 combinations. Furthermore, these 3 cases occurred with 162 breeding animals. With full sib assignment, 9 out of 12 groups of estimates significantly deviated from the true parameter value. The Root Mean Square Errors obtained with the full sib assignment were higher than with the other two methods of pen assignment in most of the cases. The Root Mean Square Errors obtained with datasets with 324 breeding animals were notably smaller than the datasets from 162 breeding animals. Within each method of pen assignment, the relative bias of the associative effect was significantly smaller with group size 10 than with group size 5. Conclusion: Full sib assignment caused difficulties to estimate variance components in most of the cases, due to a lack of identifiability. With random and mixed assignment, most data structures yielded unbiased results but increasing the number of breeding animals or group size improves the estimation. Thus to get identifiable and unbiased estimates of the genetic associative effect, it is recommended to avoid close genetic relationship between animals within one pen and to use sufficient numbers of breeding animals and sufficient group sizes.
doi:10.1186/1471-2156-10-9 pmid:19250536 pmcid:PMC2678166 fatcat:tz475h7kcnazzpblpggpyxtzqa