Genetic management of Dutch golden retriever dogs with a simulation tool

Abstract

Excessive inbreeding rates and small effective population sizes are an important problem in many populations of dogs. Proper genetic management of these populations can decrease the problem, and several measures are available. However, the effectiveness of these measures is not clear beforehand. Therefore, a simulation model was developed to test measures that aim to decrease the rate of inbreeding. The simulation program was used to evaluate inbreeding restriction measures in the Dutch golden retriever dog population. This population consisted of approximately 600 dams and 150 sires that produce 300 litters each year. The five most popular sires sire approximately 25% of the litters in a year. Simulations show that the small number of popular sires and their high contribution to the next generation are the main determinants of the inbreeding rates. Restricting breeding to animals with a low average relatedness to all other animals in the population was the most effective measure and decreased the rate of inbreeding per generation from 0.41 to 0.12%. Minimizing co-ancestry of parents was not effective in the long run, but decreased variation in inbreeding rates. Restricting the number of litters per sire generally decreased the generation interval because sires were replaced more quickly, once they met their restriction. In some instances, this lead to an increase in inbreeding rates because the next generations were more related. The simulation tool proved to be a powerful and educational tool for deciding which breeding restrictions to apply, and can be effective in different breeds and species as well.

Half of 23 Belgian dog breeds has a compromised genetic diversity, as revealed by genealogical and molecular data analysis

“…Our results are in line with other genealogical studies in various (national) dog populations. For example, for the Golden retriever breed, the inbreeding coefficient in our study was 1.6% (N e = 178), while it reached 1.27% (N e = 39) in a Dutch population (Windig & Oldenbroek ), 1.3% (N e = 219) in a French population (Leroy et al . ), 5.1% (N e = 1090) in an Australian population (Shariflou et al .…”

“…There are several strategies to maintain or increase the genetic diversity going from the introduction of more animals in breeding, the promotion of seldom used lines, a 5% limit on the number of puppies in a 5‐year period to counteract the popular sire breeding practice, to equalizing the contributions of the reproducing animals (optimal contribution selection) (Mäki ; Leroy ; Leroy & Baumung ). In practice however, optimal contributions are very difficult to realize, as the choice of the animal is made by individual breeders, and also influenced by the success and availability of matings (Windig & Oldenbroek ). Although several of these methods constrain the choice of breeders, they can be recommended for the native Belgian breeds in this study.…”

Whole genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic trait mapping

“…Although the average slope of each breed-specific N e curve ranges from 1.52 to 3.92, the breeds are each characterized by a unique N e value at any given generation point. The data was normalized relative to the breed age, as determined by the AKC date of breed recognition, and a generation interval of 3.76 years (Windig and Oldenbroek, 2015) (Fig. 1B).…”

“…, 2015) was used to calculate effective population size ( N e ) with the SNP genotypes from each breed. Predicted N e values for 13 to 995 generations prior to sample age were calculated and values were interpolated using a generation interval of 3.76 years (Windig and Oldenbroek, 2015). …”

Reducing inbreeding rates with a breeding circle: Theory and practice in Veluws Heideschaap

“…Simulations are an extension of simulations performed to determine the effect of selection for scrapie resistance in Dutch sheep breeds (Windig et al, ). Details of the simulation software can be found in Windig and Oldenbroek (). In brief, a population is set up as close as possible to the real situation.…”