Genetic gain & Inbreeding

Impact of using different coancestry matrices in optimal contribution management on effective population size

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Abstract

The effective population size (Ne) is a key parameter in animal genetic conservation programs, where the main objectives are to preserve genetic diversity and prevent inbreeding depression. Ne reflects the extent of genetic drift and the rate of inbreeding within a population, and is proportional to the loss of genetic variation. In conservation programs, the Optimal Contribution (OC) method is recognized as the preferred strategy to minimize genetic diversity loss and maximize Ne by optimizing the contributions of parents to the next generation. This is achieved by minimizing the global coancestry among potential parents weighted by their respective contributions. Thus, coancestry matrix lies at the core of the OC methodology. Both pedigree-based and genomic coancestry matrices can be used within the OC framework; however, the impact of using different matrices on the resulting Ne remains unknown. This study evaluated, through stochastic simulations, the true identity-by-descent (IBD) coancestry-based Ne obtained after applying OC over 20 generations in a population composed of N = 100 individuals, using different coancestry matrices. These matrices included the pedigree-based matrix (θPED), the linkage-based genomic relationship matrix (θGLA) and those described by Li and Horvitz (θLH1, θLH2), VanRaden (θVR1, θVR2) and Yang and colleagues (θYA1, θYA2). Genomic matrices were constructed using approximately 55,000 biallelic markers (SNPs). The different management strategies were compared based on the reference IBD-based Ne achieved across generations. The Ne was obtained using 10,000 multiallelic loci simulated at the base population to estimate IBD probabilities. Each of these loci was assigned two unique alleles per individual to represent fully informative markers, enabling the estimation of true coancestry and inbreeding coefficients and Ne. Among evaluated strategies, management based on θGLA produced the highest Ne values across generations, reaching 220 in later generations. Management using θPED resulted in a slightly lower Ne (~200), but still was higher than that achieved with most genomic matrices other than θGLA. Among the remaining genomic matrices, θVR2 and θYA2 led to the highest Ne (~185 for both matrices), followed by θVR1 and θYA1 (~170 for both matrices). The lowest Ne values were observed with genomic matrices θLH1 and θLH2 (~100 and ~50, respectively). Regarding inbreeding coefficients, management based on θGLA and θPED produced estimates nearly identical to the true IBD-based inbreeding. In scenarios where pedigree information is unavailable, management based on θYA2 would be preferred over θVR2 as θVR2-based management led to inbreeding coefficient estimates that were substantially underestimated and even showed a decreasing trend across generations, whereas the true IBD-based inbreeding increased as expected. In conclusion, management based on θGLA consistently produced the highest Ne and closely followed the trajectory obtained under IBD-based management, making it the most suitable strategy for maximizing Ne in conservation programs.

Keywords: 2026

How to Cite:

Caballero, A., Fernández, A., Fernández, J., Garcà­a-Ballesteros, S., López de la Torre, R., Meuwissen, T., Morales-González, E., Toro, M. & Villanueva, B., (2026) “Impact of using different coancestry matrices in optimal contribution management on effective population size”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285452. doi: https://doi.org/10.31274/wcgalp.23713

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