A combination of walk-back and optimum contribution selection in fish: a simulation study

The aim of this paper was to study the performance of a novel fish breeding scheme, which is a combination of walk-back and optimum contribution selection using stochastic simulation. In this walk-back selection scheme, batches of different sizes (50, 100, 1000, 5000 and 10 000) with the phenotypically superior fish from one tank with mixed families were genotyped to set up the pedigree. BLUP estimated breeding values were calculated. The optimum contribution selection method was used with the rate of inbreeding (ΔF) constrained to 0.005 or 0.01 per generation. If the constraint on ΔF could not be held, a second batch of fish was genotyped etc. Compared with the genotyping of all selection candidates (1000, 5000 or 10 000), the use of batches saves genotyping costs. The results show that two batches of 50 fish were often necessary. With a batch size of 100, genetic level was 76–92% of the genetic level achieved for schemes with all fish being genotyped and thus candidates for the optimum contribution selection step. More parents were selected for schemes with larger batches, resulting in a higher genetic gain, especially when all selection candidates were genotyped. There was little extra genetic gain in genotyping of 1000 fish instead of 100 for the larger schemes of 5000 and 10 000 candidates. The accuracy of breeding values was similar for all batch sizes (~0.30), but higher (~0.5) when all candidates were included. Since only the phenotypically most superior fish were genotyped, BLUP-EBV were biased. Compared with genotyping of all selection candidates, the use of batches saves genotyping costs, while simultaneously maintaining high genetic gains.