The effects of phenotyping and genotyping strategies, and the use of conventional or organic sires on genetic gain in an organic pig population

Optimizing organic pig breeding schemes depends on how to best allocate resources to phenotyping and genotyping. This study investigates how phenotyping and genotyping strategies affect genetic gain in a small organic pig population. We used stochastically simulated breeding schemes aimed at producing three-way crossbred finisher pigs. The simulated breeding schemes varied in the availability of phenotypes and genotypes for purebreds and crossbreds, the origin of the sire, and the genetic correlation between purebred and crossbred performance. For each simulated breeding scheme, genetic gain and rate of inbreeding were collected for up to 100 replicates. Phenotyping of crossbred individuals did not improve the genetic gain in the purebreds or the crossbreds. Genotyping purebred sows did improve genetic gain in both purebreds and crossbreds. Genetic gain and rate of inbreeding were maximized when internal sires were used, assuming strong GxE between organic and conventional production systems. Yet, breeding schemes that used internal sires had a larger variance in the genetic gain than those that used external sires. In conclusion, breeding schemes for organic pigs can be optimized by using internal sires and by genotyping the purebred parents. Yet, the rate of inbreeding and population size should be taken into careful consideration when developing an independent breeding program for a small (organic) population.