Genetic gain & Inbreeding

Evaluating a multi-sire joining approach as a practical alternative to full mate allocation for balancing genetic gain and inbreeding in a simulated chicken breeding program

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Abstract

Optimizing genomic selection programs requires strategic mating allocation to balance genetic gain with control of inbreeding. Full mate allocation approaches generally achieve this balance most effectively; however, their implementation can be constrained by biological limitations, housing logistics, and resource availability. This study examines an alternative approach: multi-sire joining, in which a group of sires is allocated to mate with a group of dams while aiming to maximize genetic gain and control inbreeding. We assessed the impact of three mating strategies on genetic gain, inbreeding, and conversion efficiency, defined as the ratio of genetic gain to inbreeding (ΔG/ΔF), within a simulated chicken breeding program. Simulations were performed using the Modular Breeding Program Simulator (MoBPS; Pook et al., 2020) within an overlapping-generation scheme covering three traits: production, reproduction, and survival. At each selection, two subsequent cohorts of 2000 animals each were considered candidates. Approximately 30 males and 100 females were selected to sire and dam the next cohort of 2,000 offspring (selection proportions of 0.015 for males and 0.050 for females). The scenarios included random selection, multi-sire group mating, and a full mate allocation. Random selection was implemented in MoBPS, whereas multi-sire group and full mate allocation strategies were implemented in MateSel (Kinghorn, 2011) with coancestry control. Breeding values were estimated using MiXBLUP (Vandenplas et al., 2024). The simulation comprised an initialization period, followed by 5 cycles of pedigree-based selection and 10 cycles of genomic selection. Results were based on 25 replicates from each scenario across the 10 cycles of genomic selection. Random selection achieved a ΔG of 0.008 (±0.029) genetic standard deviations and a mean ΔF of 0.002 (±0.002) per cycle, resulting in a conversion efficiency of 4.0 (±13.1). Full mate allocation produced a mean ΔG of 0.295 (±0.045) genetic standard deviations and a mean ΔF of 0.012 (±0.002) per cycle, resulting in a conversion efficiency of 24.6 (±4.7). Multi-sire joining delivered a mean ΔG of 0.258 (±0.032) genetic standard deviations and a mean ΔF of 0.008 (±0.001) per generation, resulting in a conversion efficiency of 32.3 (±4.8). Full mate allocation proved to be the best strategy regarding genetic gain, performing significantly better than random selection and multi-sire joining. Multi-sire joining performed the best in terms of conversion efficiency, however, this is mainly due to lower inbreeding. Observed trends were consistent across production, reproduction, and survival traits, although the magnitude of efficiency differences varied among trait categories. Multi-sire joining delivered 86% of the genetic gain achieved by full mate allocation with a lower rate of inbreeding. These findings suggest that multi-sire joining represents a practical and effective alternative to full mate allocation, enabling optimization of conversion efficiency while reducing the logistic complexity associated with full mate allocation strategies.

Keywords: 2026

How to Cite:

Bink, M., Jamieson, D., Perez, B., Pook, T. & Veninga, G., (2026) “Evaluating a multi-sire joining approach as a practical alternative to full mate allocation for balancing genetic gain and inbreeding in a simulated chicken breeding program”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286332. doi: https://doi.org/10.31274/wcgalp.23933

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