Effect of unfavourable population structure on estimates of heritability, systematic effects and breeding values (In memory of the beloved colleague Alexandros Argyrokastritis)

Empirical estimations of heritability, systematic effects and predictions of sires’ breeding values (BVs) were obtained under various population structures for simulated populations consisted of n=400 animals in 5 herds for a trait of medium heritability (h=0.30). An infinitesimal additive genetic animal model was assumed while simulating data. Population structure was varied to allow for good and poor connectedness across herds and (non)random association between the genetic and the environmental effects. The impact of the various population structures on the parameter estimation(s) was assessed using Mean Squared Error (MSE) and Pearson’s correlations. Allowing sires to have progenies in more than one herd (good herd connectedness) and random use of sires across herds generally resulted in good parameter estimations. Poor connectedness significantly affected herd effects estimation and BV prediction but not heritability estimation as long as random usage of sires across environments was guaranteed. Selective use of the best sires in the best herds along with poor connectedness resulted in poorest estimations of all parameters examined. In the latter case, heritability was seriously underestimated (h=0.06) while highest error, lowest accuracies for the BVs and a remarkable underestimation of the genetic gain were observed. Use of reference sires on a natural mating basis to create genetic links between herds has served a good solution for both heritability and BVs estimation under unfavorable structure. Mating 0.25 of the herd ewes with reference sires resulted in a heritability estimate close to the simulated one. Significantly better estimates of systematic effects and BVs were, however, obtained when 0.5 of the herd ewes were mated by reference sires.