Forneris, N. S. | bioRxiv Science

bioRxiv2025

Updating the RZooRoH package for the analysis of inbreeding, identity-by-descent and relatedness from genomic data

The RZooRoH R package was implemented to characterize individual inbreeding levels. It identifies DNA segments inherited twice from a common ancestor through different paths, which are known as homozygous-by-descent (HBD) segments. The package accepts different data formats and provides multiple outputs: HBD segments, inbreeding rates and genome-wide and locus-specific HBD probabilities. In addition, it partitions HBD levels into multiple HBD classes. The length distribution varies between these classes, which therefore correspond to distinct groups of ancestors that can be traced back to different generations in the past. This provides information about mating structure and recent demographic history. The computational performance of the package has been substantially improved, enabling, for example, computing times to be reduced when working with whole-genome sequence data and more HBD classes to be fitted. It is now possible to fit one class per past generation, which facilitates interpretation of the results. Since we have previously demonstrated that the ZooRoH model can be used to characterize identity-by-descent (IBD) between haploid individuals or phased haplotypes, this option has been included in the new package version. Estimating kinship by characterizing IBD levels between the four possible pairs of haplotypes from two individuals is another feature we added to the package. Finally, new options allow models to be refined, for instance by defining HBD classes as intervals or constant inbreeding rates for neighboring classes. Overall, the new version of the package offers improved computational efficiency and interpretability when characterizing inbreeding, IBD and relatedness levels.

genomics↗

bioRxiv2024

Genomic prediction of individual inbreeding levels for the management of genetic diversity in populations with small effective size

In populations of small effective size (Ne), such as those in conservation programs, companion animals or livestock species, management of diversity and inbreeding is essential. Homozygosity-by-descent (HBD) segments provide relevant information in that context, as they allow efficient estimation of the inbreeding coefficient, provide locus-specific information and their length is informative about the "age" of inbreeding. Therefore, 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 with small Ne. The methods included model-based approaches, mostly hidden Markov models (HMMs), which considered up to 15 IBD configurations among the four parental chromosomes, 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 in such populations. Two HMMs performed consistently well, while two rule-based approaches proved efficient for genome-wide predictions. The model-based approaches were particularly efficient when information was reduced (low marker density, locus-specific estimation). Methods using phased data proved to be more efficient, while some approaches relying on unphased genotype data proved to be sensitive to the allele frequencies used. In some settings, pedigree information was competitive in predicting 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 individuals.

genomics↗