[en] 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 neighbouring classes. Overall, the new version of the package offers improved computational efficiency and interpretability when characterizing inbreeding, IBD and relatedness levels.
Disciplines :
Genetics & genetic processes Animal production & animal husbandry Environmental sciences & ecology Veterinary medicine & animal health
Author, co-author :
Forneris, Natalia ; Université de Liège - ULiège > GIGA > GIGA Molecular & Computational Biology - Unit of Animal Genomics
Faux, Pierre ; GenPhySE, Université de Toulouse, Toulouse INP, INRAE, ENVT, Castanet Tolosan, France
Gautier, Mathieu ; CBGP, INRAE, CIRAD, IRD, L'institut Agro, Université de Montpellier, Montpellier, France
Druet, Tom ; Université de Liège - ULiège > GIGA > GIGA Molecular & Computational Biology - Unit of Animal Genomics
Language :
English
Title :
Updating the RZooRoH Package for the Analysis of Inbreeding, Identity-By-Descent and Relatedness From Genomic Data.
Publication date :
2026
Journal title :
Molecular Ecology Resources
ISSN :
1755-098X
eISSN :
1755-0998
Publisher :
John Wiley and Sons Inc, England
Volume :
26
Issue :
6
Pages :
e70186
Peer reviewed :
Peer Reviewed verified by ORBi
Tags :
CÉCI : Consortium des Équipements de Calcul Intensif
SPW - Service Public de Wallonie F.R.S.-FNRS - Fonds de la Recherche Scientifique
Funding text :
This work was supported by the Fonds de la Recherche Scientifique - FNRS, ROAGE T.0102.24 and by the Service Public de Wallonie, BEWARE FitSel project - convention no. 2110192.We acknowledge Thibault Leroy for sharing the original honey bee whole-genome sequencing data set. We would like to thank the editor as well as Samuel Speak and three anonymous reviewers whose valuable comments helped us to improve the manuscript. Tom Druet is Research Director from the Fonds de la Recherche Scientifique - FNRS (F.R.S- FNRS). Computations were carried out using the supercomputing facilities of the Consortium d'Equipements en Calcul Intensif en Fédération Wallonie-Bruxelles (CECI), funded by the F.R.S.-FNRS.
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