Inbreeding and Genetic Gain in the Presence of Random Mating and Mate Allocation Using Genomic-Pedigree Relationships in Chickens: A Simulation Study

In this simulation study, Mate Allocation (MA) strategy using combined genomicpedigree information was compared with Random Mating (RM) aiming at controlling the level of inbreeding (ΔF) with minimum impacts on the amounts of Genetic Gain (ΔG) in poultry breeding programs. Five equally-sized subpopulations of chickens (P1 to P5) were simulated. A genome encompassing five chromosomes involving 15,000 bi-allelic markers was defined for each bird. Potentially, 500 QTL impacted a trait, which had a heritability of 0.1. Only pedigree information was assumed to be available in P1 while the percent of genotyped birds were 10% in P2, 20% in P3, and 50% in P4 and P5. Estimated Breeding Values (EBVs) were computed using the traditional approach (PBLUP) and the Single- Step method (SSGBLUP). In P5, early predictions were applied to estimate GEBVs. Comparisons were made based on the reductions in ΔF and changes in ΔG between two mating scenarios and two evaluation methods within and across subpopulations, respectively. After seven generations, MA resulted in 20 to 30% less ΔF within subpopulations compared with RM with negligible impacts on ΔG. Furthermore, in both mating scenarios, SSGBLUP brought about 11 to 61% less ΔF compared to PBLUP across subpopulations. Results indicated that the benefits of using combined genomicpedigree relationships could be more than improving the accuracy of EBVs through the SSGBLUP as they can also be used in mating designs to restrict ΔF with a minimum impact on ΔG. Also, this study verified that SSGBLUP could bring about lower ΔF compared with PBLUP.