Genetic Diversity based on SNP markers

Genetic diversity within a population forms the basis for maintaining fitness of its individuals.

In contrast to the unique characteristics typically associated with specific breeds, the overall health and adaptability of an organism tend to decline as its genetic makeup becomes more homogeneous. This decrease in genetic diversity ultimately leads to what is known as inbreeding depression, where harmful genetic alterations accumulate and manifest themselves.

By taking into account the individual diversity metrics of an animal's genetic material, informed decisions can be made during the selection of mating pairs. This approach helps to reduce the potential risks associated with inbreeding depression.

generatio offers a specialized test portfolio in the field of routine diagnostics based on SNP-chip technology (SNP = Single Nucleotide Polymorphism). This approach allows the simultaneous examination of 60,000-230,000 (depending on the species) SNP-markers, that are evenly distributed throughout the genome.

Heterozygosity serves as a valuable metric for quantifying genetic diversity. It allows us to measure the proportion of gene loci in an animal's genome where there exists heterozygosity, meaning the presence of two different alleles. In contrast, homozygosity refers to gene loci where the alleles are identical. While heterozygosity alone may not provide a comprehensive assessment of an animal's inbreeding status, it can indicate a substantial loss of genetic diversity. This underscores the importance of considering heterozygosity as a factor when evaluating an animal's genetic makeup.

In addition, the mean value of the population is displayed. This value represents the average of all tested animals of the same species or breed. It provides a reference for the individually tested animal.

The genomic inbreeding coefficient (GIK) is a measure that quantifies the proportion of a descendant's genome that is identical due to the relatedness of the parent animals. It identifies allele pairs at a specific gene locus that originate from a common ancestor of the parent animals.

In the past, the inbreeding coefficient was estimated based on pedigree records. However, inbreeding events that occurred before the evaluated generations were neglected. generatio determines the actual inbreeding status of an animal using genomic information obtained from SNP-array analysis. This approach queries the variability of an animal's genome across its species and can indicate the level of inbreeding, including background inbreeding (such as resulting from breed or ecotype formation). This value is referred to as the genomic inbreeding coefficient. As a result, it is also possible to determine the genetic inbreeding status of an animal without precise knowledge of the relatedness of the parent animals or other ancestors.

Please note: High GIK values in individual animals do not automatically result in exclusion from breeding and do not diminish the individuals breeding value. However, it is important to find a breeding partner for these animals that possess complementary gene variants for these inbred regions in the genome in order to increase the genetic variability of the offspring. This can prevent the long-term loss of genetic material in the population and the resulting inbreeding depression.

This shows the distribution of GIK values in a population, for example in one's own herd or in the entire population. The individual animal is depicted there in comparison to the other animals.