Down to the Genes_November 2018.qxp_Founding Trustee Dies.qxd 10/25/18 1:48 PM Page 2
Down to the Genes
Everything you need to know about ASA’s DNA Services and more. Focus on Parentage By Jackie Atkins Ph.D., Lilly Platts, Leoma Wells and Riley Foster Whether you use parent verification to confirm breeding records, distinguish between AI and pasture bred calves, or to sort through progeny from a 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
Interpretation of SNP parentage results/reports
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.
The following tables provides parentage results, their interpretation, and Herdbook abbreviations, when no further action is needed.
Report
No further action needed: Interpretation Herdbook Abbreviation
Animal qualified through DNA to both sire and dam
Animal matched to both sire and dam
PQB = parentage qualified to both
Animal qualified through DNA to sire
Animal matched to sire. Dam does not have DNA on file for comparison
PQS = parentage qualified to sire
Animal qualified through DNA to dam
Animal matched to dam, sire does not have DNA on file for comparison
PQD = parentage qualified to dam
Animal qualified through DNA to sire, dam waived
Animal matched to sire, dam DNA outdated (microsatellites) and unable to make comparison
PQS
Animal qualified through DNA to dam, sire waived
PQB
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.
Animal matched to dam. Sire DNA markers outdated (microsatellites) and unable to make comparison
Parentage qualifications waived
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.
Both the sire and dam have outdated (microsatellites) markers and unable to compare to their parentage markers
Animal DNA placed on file
Sire and dam do not have DNA on file for comparison
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.
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BTF = blood type on file, this animal has SNP DNA on file but not able to compare to its parents DNA BTF