Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus

Abstract

Common full-sib families (c2) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c2 resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However, the impacts of common full-sib families on accuracy of genomic prediction for commercial traits of economic importance are not well known in many species, including aquatic animals. This research explored the impacts of common full-sib families on accuracy of genomic prediction for tagging weight in a population of striped catfish comprising 11,918 fish traced back to the base population (four generations), in which 560 individuals had genotype records of 14,154 SNPs. Our single step genomic best linear unbiased prediction (ssGLBUP) showed that the accuracy of genomic prediction for tagging weight was reduced by 96.5%–130.3% when the common full-sib families were included in statistical models. The reduction in the prediction accuracy was to a smaller extent in multivariate analysis than in univariate models. Imputation of missing genotypes somewhat reduced the upward biases in the prediction accuracy for tagging weight. It is therefore suggested that genomic evaluation models for traits recorded during the early phase of growth development should account for the common full-sib families to minimise possible biases in the accuracy of genomic prediction and hence, selection response.

Effectiveness of SNPs for Sibship Assignment in Farmed Banana Shrimp (Penaeus merguiensis)

“…Physical tagging, however, only works successfully with a high survival rate and low tag loss once animals reach a certain size or weight as tiny larvae cannot be tagged [2,3]. Physical tagging often incurs high costs and requires intensive labor to maintain animals in separate rearing facilities until they reach a suitable size for tagging, hence inducing significant full-sib family or tank effects [4,5]. The number of families in a given pedigree for breeding programs, would thus be limited by the availability of rearing facilities [6] and in the long term this may result in increased inbreeding depression if insufficient families are bred each generation.…”