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Focus on Parentage

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Whether you use parent verification to confirm breeding records, distinguish between AI and pasture bred calves, or to sort through progeny from multi-sire pastures, parental validation is an important test for accurate records and genetic evaluation. Especially in a young unproven animal, knowing the accurate pedigree is a big step in evaluating that animal’s genetics.

Additionally, about 10% of pedigrees reported across all breed associations are inaccurate — cleaning up these errors will have a tremendous impact on evaluating the cattle as seedstock. This “Down to the Genes” segment introduces parentage test descriptions, reported results and interpretations, and member actions to resolve parentage conflicts.

Introduction to the parentage tests   

In the past, microsatellite markers (also called Short Tandem Repeats or STRs) were used to confirm parentage but these were costly and not always reliable tests.  Most new parental validations are completed with single nucleotide polymorphisms or SNPs (pronounced “snips”). The SNPs are locations in the DNA that vary from one animal to another.  The SNP parentage test uses over 100 SNP markers to either qualify or exclude an individual as a parent.  Each animal has two markers at each SNP location (one on each pair of chromosomes representing one from each parent).  The SNP parentage analysis looks at the SNP (DNA variant) at a specific location for an animal and then looks to see if the sire and/or dam were able to pass along that marker to their offspring.  The SNP parentage repeats this logic across all the parentage markers to analyze if the sire and dam could be the parent animals. The default parentage test, called “seek sire” and all the genomic panel parentage tests (uLD, GGPLD, GGPHD) use this SNP method.  To understand more how SNP parentage tests work, and go through an example yourself, check out the Have you Herd blog.   

It is important to note the parentage analysis has to be done on the same platform among all animals in the comparison. You can not compare a calf with SNP DNA markers to a dam with microsatellite markers. 

Definitions

Excluded: The proposed parents had SNP markers that could not have been passed to the calf and are therefore not the parents of the calf.

Qualified: The SNPs from the parents of the animal tested were possible as the parents of the animal.  Note false positives may occur with the parentage test which is why the DNA report says “Qualifies” as there is no evidence that the animals tested are not the parent animal but false positives are possible.

DNA on file:  The SNP parentage markers are completed on an animal but neither of that animal’s parents have the SNP parentage markers for comparison.  In this case, the SNP parentage of said animal is in our system for future progeny comparisons, but the ASA is unable to qualify the parents of this individual as there are no markers on the sire or dam.

 

(Right graphic: Interpretation of SNP parentage results/reports    The following tables provide parentage results, their interpretation, and Herdbook abbreviations when no further action is needed. )

 

DNA Exclusion Procedure

If an animal does not qualify to a parent(s) then the following procedure is executed. The table below describes parentage results that require action from the breeder to resolve.

• Member is notified via email or mail of the animal’s DNA test results

• Animal is automatically suspended in the database.

• It is the member’s responsibility to contact ASA regarding the exclusion.

• Members are advised to submit alternate sire/dam possibilities for the animal. DNA Re-Check Alternate sire/dam possibilities are compared.

• If a qualifying parent is found, the DNA record and pedigree are updated accordingly.

• Animal record is unsuspended.

• If the animal is registered a new certificate is issued and mailed with a copy of the DNA results.

• If the animal has registered progeny, a new certificate is issued on each animal and mailed with a letter explaining the update.

 

Pedigree Update per Member Records

If a qualifying parent is not found we ask the breeder to supply written documentation of their breeding records for the birth year of the animal.

• If the breeder is certain of a pasture sire then the written documentation supplied is used to update the pedigree on the animal.

• Animal record is unsuspended.

• If the animal has registered progeny a new certificate is issued on each animal and mailed with a letter explaining the update. If the breeder is unable to determine a pasture exposure sire then we remove the sire information from the pedigree and unregister the animal.

 

Can ASA look for potential parent animals without direction from the member?     

To parentage test an animal, ASA has to be provided with parent possibilities in writing. A “random survey” type test cannot be run. In addition, any parent possibility must have DNA parentage markers on file with ASA in order to be compared. 

 

 

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