Estimating breeding values with molecular relatedness and reconstructed pedigrees in natural mating populations of common sole, Solea solea.

Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using DNA marker data. With missing parents and natural mating groups, commonly used pedigree reconstruction methods are not accurate and lead to loss of data. Relatedness estimators, however, infer relationships between all animals sampled. In this study, we compared a pedigree relatedness method and a relatedness estimator ("molecular relatedness") method using accuracy of estimated breeding values. A commercial data set of common sole, Solea solea, with 51 parents and 1953 offspring ("full data set") was used. Due to missing parents, for 1338 offspring, a pedigree could be reconstructed with 10 microsatellite markers ("reduced data set").