Properties of Runs of Homozygosity as a Measure of Identity by Descent.

[en] Runs of Homozygosity (ROH) are commonly used to quantify autozygosity/identity-by-descent (IBD) in an individual or population. However, the method's accuracy at the segment level in livestock populations has only been evaluated in a few studies. Thus, the aim of this study was to determine to what extent ROH are truly IBD and estimate the proportion of IBD segments that go undetected in a simulated livestock population. We simulated a population of randomly mating animals for 100 generations. The genome consisted of a single chromosome with a SNP density of either 46 or 92 SNPs per mega base (Mb). In addition, a set of founder markers tracing IBD was recorded. ROH were detected using four different parameter combinations. Using the two sets of markers, we calculated the true positive rate, power, and overall correlation between true (FIBD) and estimated inbreeding (FROH). Additionally, a new measure for within-ROH inbreeding (F|ROH) was introduced and calculated the level of homozygosity within a ROH compared to the general expectation in the genome. The results indicate that ROH longer than 2 Mb are a reliable indicator of IBD, with the F|ROH being over 0.9 for all ROH lengths and parameter combinations. True positive rates only exceeded 0.9 consistently for ROH over 9 Mb, indicating that many of the identified ROH may be associated with common ancestors more ancient than the base population. The power was mainly controlled by the parameter stringency, that is, allowing for shorter ROH increased the power. The ROH-based individual measure of inbreeding FROH was highly correlated to FIBD while also having regression coefficients close to 1 (i.e., a 1% variation in FROH corresponded to a 1% variation in FIBD). Using stringent ROH parameters resulted in underestimation of the rate of inbreeding in the population. Increasing marker density improved predictions, including a higher true positive rate, power, higher correlations, and less underestimation of inbreeding rates.

Disciplines :

Animal production & animal husbandry
Genetics & genetic processes
Veterinary medicine & animal health

Author, co-author :

Wæge, Oda B ; Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway

Druet, Tom ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA) ; Université de Liège - ULiège > GIGA > GIGA Molecular & Computational Biology - Unit of Animal Genomics

Berg, Peer ; Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway

Meuwissen, Theo; Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway

Language :

English

Title :

Properties of Runs of Homozygosity as a Measure of Identity by Descent.

Publication date :

27 August 2025

Journal title :

Journal of Animal Breeding and Genetics

ISSN :

0931-2668

eISSN :

1439-0388

Publisher :

John Wiley and Sons Inc, Germany

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://onlinelibrary.wiley.com/doi/pdf/10.1111/jbg.70013

Funders :

Norges miljø- og biovitenskapelige universitet

Funding text :

Funded by a PhD grant from the Norwegian University of life sciences. Funding:We are very grateful to two anonymous reviewers for their helpful comments. The authors acknowledge the Orion High Performance Computing Centre (OHPCC) at the Norwegian University of Life Sciences (NMBU) for providing computational resources that have contributed to the research results reported within this paper. Tom Druet is Research Director from the Fonds de la Recherche Scientifique\u2014FNRS (F.R.S\u2010FNRS).

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since 24 November 2025

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