Knowing some of the basics of parentage testing and how it works can help a breeder understand the benefits of testing to make important breeding/management decisions.

The Concept

The concept behind using genetic markers for parentage testing is based on the fact that each animal receives one copy of each gene, called an allele, from each parent.  We can genotype an animal to determine what markers they have and compare that to potential parents to determine if those markers are consistent with that individual being a parent of the offspring in question.

Common Misconception

One common misconception of parentage testing is that the test confirms parentage absolutely based on matching DNA of offspring to their parents.  Rather, parentage testing is about excluding animals that cannot be the parents of a particular offspring, rather than proving that an animal is the parent.  In the simplest terms, we use the genetic markers to exclude animals as a possible parent, leaving those remaining (hopefully only one) as the most likely parent for that offspring.

Ways to improve accuracy

1. Make sure your marker panels are consistent

All of the animals being compared need to be genotyped with the same type of marker panel.  Older animals that might have been genotyped on a microsatellite panel might need to be re-genotyped on a SNP panel if the genotypes are needed for a parentage test on a younger animal.

Also, the quantity of different markers shown on a panel can vary,  so the higher the quantity of markers being compared the greater chance for accuracy. SNP parentage panels include a large number of markers.

2. It is essential to genotype all possible parents

If an individual that could have been a parent is not included in the comparison, it is possible that parentage may be incorrectly assigned. Ideally collect DNA from all herd sires BEFORE they go out with the cows for the breeding season.

3. Don’t include any animals that couldn’t possibly be the sire or dam of the individual in question due to their location or other factors

Because parentage testing is about excluding animals that could not possibly have been the sire or dam of the individual in question, you risk an inconclusive result if two or more individuals cannot be excluded.  This is more likely to occur if the animals are close relatives.  Even if you have run parentage panels on all of your herd sires, do not include all of them just because you possess the information.

4. It is harder to resolve parentage when using related sires/animals

Because related animals tend to share the same chromosomes, and thus have the same genotype at genetic marker loci, it is harder to resolve parentage when potential sires are related.  This may be especially important to remember when using related sires in a multi-sire pasture if your intention is to parent-verify the calves.  Because their genotypes are often similar, it becomes more difficult to exclude close relatives as potential sires, especially in the absence of dam genotypes.

References:

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.  Accessed 12/16/2016.