Genomic Inbreeding Coefficient (GIC, g-COI)
The genomic inbreeding coefficient (GIC) which is also called genomic coefficient of inbreeding (g-COI) quantifies the extent of inbreeding within an individual by directly evaluating the genome of the animal being analysed. In general, the ‘inbred proportion of the genome’ is the proportion that is homozygous as a result of descent from common ancestors. Direct insight into the genome using SNP arrays or whole genome sequencing (WGS) reveals the affected areas independently of pedigree data, which only cover a limited number of generations and are based on unverified ancestry data.
Alongside heterozygosity values and ROH profiles, the GIC is one of the building blocks of genome-based assessment for inbreeding & fitness.
Determining genomic inbreeding coefficients
Genomic inbreeding coefficients are best determined by analysing SNP (single nucleotide polymorphism) arrays or by whole genome sequencing (WGS) with as many individual SNPs as possible that are evenly distributed across the genome.
In the first step, the ROH (‘Runs Of Homozygosity’) are determined from the SNP marker values. The lengths of all ROH areas are added together and set in relation to the size of the entire genome. The result is a percentage value, the GIC, or g-COI. The larger the GIC, the more hereditary characteristics are present as a result of inbreeding.
Informations GIC can provide
The genomic inbreeding coefficient directly reflects the probability that hereditary characteristics are present in a homozygous state due to inbreeding. This applies both to hereditary traits for desirable performance parameters and breed-specific traits, as well as to the inheritance of deleterious, recessive predispositions. The higher the GIK value, the greater the inbreeding and the higher the probability that rare harmful, recessive hereditary defects will also come together in a homozygous state and have an effect. The GIK value itself provides an indication of the relationship between the parents of the animal being analysed, provided that these parents were not themselves the result of inbreeding.
Examples:
| GIC of investigated animal: | 12,5% | 25% | |
|---|---|---|---|
| Relatedness of parents of investigated animal: | like a Half siblings mating | like a Full siblings mating like a Parent - child mating |
Purebred dogs consistently have population average GIC values of around 20%. Individual breeds can also be far higher in their average GIC.
These values show that the individual breeds have been established through inbreeding and then the breed-typical characteristics have been continuously consolidated through continued more or less intense inbreeding.
GIC and genomic Heterozygosity
Both the genomic inbreeding coefficient and genomic heterozygosity are building components for assessing genetic diversity and health, but provide different information that complement each other and each offer their own advantages.
The value of heterozygosity shows the general genetic diversity of the analysed individual, but does not explicitly measure its degree of inbreeding and thus its risk of harmful recessive alleles taking effect.
The GIC together with the ROH profile is the basis for the development of breeding strategies to prevent inbreeding in defined mating or to reduce it in a population with already existing threatening levels of inbreeding.
Useful links - Literature
SHOP: Inbreeding & Fitness (Genetic Diversity)
Lexikon:
Literature:
- Nishio, M., Inoue, K., Ogawa, S. et al. Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle.BMC Genomics 24, 376 (2023). https://doi.org/10.1186/s12864-023-09480-5