ROH Profiles - Determination and Applications

The samples are genotyped using SNP (single nucleotide polymorphism) arrays or by whole genome sequencing. Dedicated algorithms identify the ROH and classify them according to their position and length.

Length is given in megabases: 1 Mb = 1,000,000 base pairs (base = single building block of DNA). Depending on the objective and the available data, the ROH are grouped into length classes.

What length reveals: Every time a segment is passed on to the next generation, recombination breaks it up further. The longer a ROH, the fewer generations ago the common ancestor lived. As a rule of thumb (Purfield et al. 2012):

These values are approximations, as the recombination rate varies along the genome. Long ROH (over 10 Mb) therefore indicate recent inbreeding. Very short ROH (under 1 Mb) reflect inbreeding in the distant past and can only be detected unreliably with SNP arrays; they are therefore usually not taken into account when assessing inbreeding.

To ensure that the values are comparable, ROH and the profiles created from them must be generated according to defined parameters (Meyermans et al. 2020):

1. Resolution of the array used: number of SNP markers and their distribution (SNP density).
2. Minimum size: the number of consecutive homozygous SNPs and the minimum length from which a run is classified as a ROH. The threshold depends on the resolution of the array: the higher the resolution, the lower it can be set. Example: with the 170k chip for dogs, a ROH of 1 Mb consists of approximately 70 homozygous markers, with a 60k chip of only approximately 24 markers. If a cut-off of 50 SNP markers is chosen, ROH of 1 Mb length cannot be detected with the 60k chip.
3. Allowed heterozygous and missing calls per 1 Mb: every technical analysis has missing calls and occasional genotyping errors. The tolerance depends on the quality of the laboratory work, the resolution of the available array and the chosen minimum length.

Values from analyses with different parameters or arrays are therefore not directly comparable.

The most important information currently provided by ROH profiles is:

For the individual animal analysed:

1. The individual genomic inbreeding coefficient (GIC): it results from the total length of all ROH, see Genomic Inbreeding Coefficient (GIC).
2. Length of the ROH: it indicates how long ago the inbreeding mating(s) took place (see table above).

At population level:

1. Genetic diversity: the ROH patterns of the animals in a population help to estimate its genetic diversity. A predominance of short ROH with few long ROH indicates a population without notable recent inbreeding. A high proportion of long ROH points to frequent matings between relatives in recent times.
2. Detection of selection signatures: genomic regions that lie within a ROH in a large number of animals of a population (so-called ROH islands) indicate regions that have been under selection. Certain alleles may be fixed in these regions due to selection pressure.
3. Associations with health and disease: certain ROH regions may be associated with genetic disorders, for example when a recessive disease variant lies within them, and can thus provide information on the health of animals and populations.

The knowledge gained from ROH profiles makes it possible to use inbreeding information obtained directly from the animal in question:

• Assessment of the overall extent of inbreeding in the animal analysed, regardless of knowledge of its ancestors.
• Identification of offspring from very close matings (e.g. parent-offspring or full siblings) by several very long ROH.
• Control of inbreeding: monitoring ROH allows breeders to manage the level of inbreeding in a targeted way. This is of great importance for maintaining the vitality and health of breeding populations.
• Use in mating strategies to avoid matings between closely related animals.
• Indications of trait-related regions: ROH islands can point to genomic regions associated with desirable traits. For targeted selection, however, this association must be demonstrated separately.
• Conservation of genetic diversity: understanding the genetic structure of populations through ROH profiles helps breeders and breed associations to manage their breeding stock in a way that preserves genetic diversity.

The determination of runs of homozygosity (ROH) provides important insights into the genetic diversity, inbreeding and health of a population. It is therefore becoming increasingly important in breeding practice.

The determination of an animal's ROH profile is part of the 'Inbreeding & Diversity' assessment. For this purpose, Generatio carries out SNP array genotyping and, in addition to the ROH profile, determines the genomic inbreeding coefficient and the HE value. The assessment is currently available for dogs, horses and camelids (dromedaries, Bactrian camels, alpacas).

Single tests:

• Dog:Inbreeding & Diversity (Fitness) Dog
• Horse:Inbreeding & Diversity (Fitness) Horse
• Camelids:Inbreeding & Diversity (Fitness) Camelids

Bundles including inbreeding analysis:

• Dog:SNP Profile Identity & Inbreeding & Fitness Dog: DNA identity and inbreeding analysis
• Dog:ProLine Bundle Dog: DNA identity, inbreeding and diversity analysis and breed analysis
• Horse:Bundle Breed Analysis, Identity, Inbreeding Assessment
• Horse:MIM-6-Var. plus Inbreeding & Fitness: test for the six MIM variants and inbreeding analysis
• Dromedary:Bundle DNA Identity and Inbreeding Analysis Dromedary

Associated lexicon articles:

• Genomic Heterozygosity (HE)
• Genomic Inbreeding Coefficient (GIC, g-COI)
• Popular Sire Syndrom

Literature:

1. Grilz-Seger, G., Druml, T., Neuditschko, M. et al.: High-resolution population structure and runs of homozygosity reveal the genetic architecture of complex traits in the Lipizzan horse.BMC Genomics 20:174, 2019. DOI: 10.1186/s12864-019-5564-x
2. Purfield, D.C., Berry, D.P., McParland, S., Bradley, D.G.: Runs of homozygosity and population history in cattle.BMC Genet 13:70, 2012. DOI: 10.1186/1471-2156-13-70
3. Meyermans, R., Gorssen, W., Buys, N., Janssens, S.: How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species.BMC Genomics 21:94, 2020. DOI: 10.1186/s12864-020-6463-x
4. Ceballos, F.C., Joshi, P.K., Clark, D.W., Ramsay, M., Wilson, J.F.: Runs of homozygosity: windows into population history and trait architecture.Nat Rev Genet 19:220-234, 2018. DOI: 10.1038/nrg.2017.109