Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size

Abstract

In populations of small effective size (N_e), such as those in conservation programmes, companion animals or livestock species, inbreeding control is essential. Homozygosity-by-descent (HBD) segments provide relevant information in that context, as they allow accurate estimation of the inbreeding coefficient, provide locus-specific information and their length is informative about the “age” of inbreeding. Our objective was to evaluate tools for predicting HBD in future offspring based on parental genotypes, a problem equivalent to identifying segments identical-by-descent (IBD) among the four parental chromosomes. In total, we reviewed and evaluated 16 approaches using simulated and real data from populations with small N_e. The methods included model-based approaches as well as more computationally efficient rule-based approaches. The accuracy of the methods was then evaluated, including with low-density marker panels, genotyping-by-sequencing data and small groups of individuals, typical features of such populations. Two model-based approaches performed consistently well, while some rule-based approaches proved accurate for genome-wide predictions. The model-based approaches were particularly efficient when genomic information was sparse or degraded. Methods using phased data proved to be more accurate, while some approaches relying on unphased genotype data were sensitive to the assumed allele frequencies. In some settings, pedigree-based predictions ranked high for recent inbreeding levels. Finally, we showed that our evaluation is also informative about the accuracy of the methods for estimating relatedness and identifying IBD segments between pairs of present-day individuals. This study shows that future inbreeding can be accurately predicted, including at specific loci, but not all methods perform equally well.