Genotypic data are often used for parentage testing for embryo transfer calves, for cases of ambiguous breeding dates, and to establish sire identity of calves for producers who utilize multiple-sire pastures. The concept behind using genetic markers for parentage testing is based on the fact that each animal receives one allele from each parent, which makes up the animal's genotype (i.e. for an animal that is Aa, the A came from one parent, while the a came from the other). Therefore, an animal's genotype at many loci can be compared to genotypes of potential parents at those same loci to determine if those markers are consistent with any sire or dam being a parent of the offspring in question.
One common misconception of parentage testing is that the test determines parentage absolutely. Rather, parentage testing excludes animals that cannot be the parents of a particular offspring. In the simplest terms, we use the genetic markers to exclude animals as possible parents, with the goal of having only two animals (a sire and a dam) left as the most likely parents for that offspring after all others have been excluded. This is why all possible parents must be genotyped and included in the comparison to get accurate results, but the inclusion of animals that can be excluded due to location, color, or other factors is discouraged.
The newest type of parentage panels typically utilize 96 SNP (or single nucleotide polymorphism) markers. To account for genotyping errors, one exclusion out of all the markers in the panel is typically allowed and still determine parentage. Two to three exclusions would indicate a need to re-test the sample to rule out contamination, poor DNA quality, or poor genotyping results. More than three exclusions will lead to a complete exclusion of that animal as a potential parent . Research has shown that parentage can be determined with greater specificity with a larger number of SNP markers (around 400), but at a greater cost. A balance between cost effectiveness and having a reasonable ability to eliminate animals that could not have been the parents must be achieved.
Older parentage panels utilized Microsatelllite markers, and these panels typically had a smaller number of markers. Parentage cannot be determined if animals are not genotyped on the same type of panel, as the markers at the same loci cannot be compared between these panels.
More detailed information on parentage testing along with relevant examples can be found at:
- International Society for Animal Genetics. (2012). Guidelines for cattle parentage verification based on SNP markers. http://www.isag.us/Docs/Guideline-for-cattle-SNP-use-for-parentage-2012.pdf