Pedigree relatedness and pseudo-phenotypes as a first approach to assess and maintain genetic diversity of the Walloon Piétrain pig population

Abstract

The breeding of pure Piétrain animals is currently performed in two different contexts: industrial lines and individual breeders. As one of the four main pig breeds worldwide, the Piétrain breed might not be considered to be endangered. However, in Wallonia (southern Belgium), even though the Belgian Piétrain programme aims to preserve the Walloon Piétrain population through cryopreservation of semen of relevant boars, only 10 pure Piétrain breeders remain and produce traditional breeding stock. Current breeders are retiring and no new breeders are replacing them. Moreover, the genetic diversity of the pigs from these individual breeders may highly contribute to the global gene pool of the breed, therefore it is important to assess this diversity. This was done on a local level by using pedigree relatedness but also differences in phenotypes. Pedigree parameters such as effective population size (Ne), genetic diversity and inbreeding coefficients were estimated for 219 boars from which offspring performances were recorded at the Walloon test station. A multi-dimensional scaling (MDS) was performed based on genetic distances. Considering the current owners of the boars, a principal component analysis (PCA) was made on deregressed breeding values (pseudo-phenotypes) based on the performances of their crossbred offspring at the test station. The Ne was 223, the genetic diversity parameter was 97.96%, while the mean inbreeding coefficient was 2.74%. The MDS identified four main clusters of boars. Two principal components indicated two major directions of selection: growth or meat traits. Genetically close boars did not necessarily show similar performances in their offspring. Different performances for genetically linked animals should reflect the breeding objectives of their owner, a practice that was confirmed by most owners during interviews. Pedigree, phenotypes and genotypes provide complementary information and therefore should be used simultaneously in the implementation of conservation programmes. These first results also showed that the genetic diversity of the Walloon Piétrain population is so far well preserved. However, recommendations need to be developed in order to maintain it. For example, boars provided to the progeny-testing scheme should come from equally contributing breeders, allowing the Belgian Piétrain programme to sample boars from a larger variety of animals taking into account genetic and phenotypic diversity. Finally, in-situ preservation of Piétrain diversity will require the development of new tools and mating schemes.