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Pre-selection against a lethal recessive allele in breeding schemes with optimum-contribution selection or truncation selection
Genetics Selection Evolution  (IF5.1),  Pub Date : 2021-09-22, DOI: 10.1186/s12711-021-00669-4
Hjortø, Line, Henryon, Mark, Liu, Huiming, Berg, Peer, Thomasen, Jørn Rind, Sørensen, Anders Christian

We tested the hypothesis that breeding schemes with a pre-selection step, in which carriers of a lethal recessive allele (LRA) were culled, and with optimum-contribution selection (OCS) reduce the frequency of a LRA, control rate of inbreeding, and realise as much genetic gain as breeding schemes without a pre-selection step. We used stochastic simulation to estimate true genetic gain realised at a 0.01 rate of true inbreeding (ΔFtrue) by breeding schemes that combined one of four pre-selection strategies with one of three selection strategies. The four pre-selection strategies were: (1) no carriers culled, (2) male carriers culled, (3) female carriers culled, and (4) all carriers culled. Carrier-status was known prior to selection. The three selection strategies were: (1) OCS in which $$\Delta {\text{F}}_{{{\text{true}}}}$$ was predicted and controlled using pedigree relationships (POCS), (2) OCS in which $$\Delta {\text{F}}_{{{\text{true}}}}$$ was predicted and controlled using genomic relationships (GOCS), and (3) truncation selection of parents. All combinations of pre-selection strategies and selection strategies were tested for three starting frequencies of the LRA (0.05, 0.10, and 0.15) and two linkage statuses with the locus that has the LRA being on a chromosome with or without loci affecting the breeding goal trait. The breeding schemes were simulated for 10 discrete generations (t = 1, …, 10). In all breeding schemes, ΔFtrue was calibrated to be 0.01 per generation in generations t = 4, …, 10. Each breeding scheme was replicated 100 times. We found no significant difference in true genetic gain from generations t = 4, …, 10 between breeding schemes with or without pre-selection within selection strategy. POCS and GOCS schemes realised similar true genetic gains from generations t = 4, …, 10. POCS and GOCS schemes realised 12% more true genetic gain from generations t = 4, …, 10 than truncation selection schemes. We advocate for OCS schemes with pre-selection against the LRA that cause animal suffering and high costs. At LRA frequencies of 0.10 or lower, OCS schemes in which male carriers are culled reduce the frequency of LRA, control rate of inbreeding, and realise no significant reduction in true genetic gain compared to OCS schemes without pre-selection against LRA.