How does parent verification work?

The November issue of the Register contained a Down to the Genes article focused on parentage testing.  Here we republished a blog post with more in depth information on how the parentage analysis works and a hands-on example where readers can work through who is the correct sire.

By Jackie Atkins, Ph.D., Director of Science and Education

Originally published on the ASA Science blog, Mar 7, 2016.

Whether you use parent verification to confirm your breeding records, distinguish between AI and pasture bred calves, or to sort through progeny from a multi-sire pasture, parental validation is an important test for breeders.  Roughly 10% of pedigrees reported across all breed associations are inaccurate.  These are frequently honest mistakes but never-the-less, vital to fix and make informed breeding decisions.  The theory behind parental validation is to determine if an animal could have inherited specific DNA markers from their reported parents.  If the animal could not inherit a specific DNA Marker from the sire or dam, then the parent is excluded.  With enough qualified markers, an animal is confirmed as the sire or dam of the offspring.

In the past, 15 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 validation is 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).

Let’s work through a hypothetical example using SNPs for parental validation.  We have test results for SNPs on a calf, two possible sires, and the likely dam.  We look at each SNP and see if the calf could have inherited that SNP from the possible parents and also if the mating (the parents analyzed together) could have passed along those SNPs.  The following diagram and table show four SNP markers for the individuals and the conclusions drawn.

Slide1

Example of 4 SNP markers for a calf and his potential parents.  See the table and text for explanation of the analysis.

Slide2

Hypothetical SNP markers at 4 locations for a calf and his potential parents.  See text for further explanation for the conclusions drawn.

Working through each SNP marker, we look if the calf could have inherited his DNA markers (genotype; options are A, T, C, or G) from the potential parents.  At SNP 1, the calf has a genotype of A/T.  This means the calf inherited an “A” from one parent and a “T” from the other parent.  Both the Dam and Sire 1 are homozygous T and SNP1.  This means they could only have passed along a T at this location.  The potential dam and Sire 1 could not have conceived the calf together as neither could have passed along an “A” at this location.  However, we can’t exclude either the dam or Sire 1 based on this information, we just know that they can’t be confirmed as the parents together.

Continuing through our analysis, we cannot exclude any of the parents with SNPs 2 and 3 because the pairing of both sires with the dam could pass on the calf’s SNP markers.  Looking at SNP 4 is helpful.  The calf has two “T”s at SNP 4, one from his dam and one from his sire.  Sire 1 has two “A”s at SNP 4 so he could not have passed along a T at this location.  Sire 1 is excluded based on this comparison.  If Sire 1 is excluded, then the potential Dam and Sire 2 work for the remaining SNP locations.  The parental validation at the lab uses the same logical progression as this simple example except it uses approximately 100 SNP markers for the analysis.

 

Top Tips for Taking Blood and TSU Samples

Sample failure can often be prevented by ensuring the sample collection process is correct.

With mail time, DNA testing can take around 2 months. FedEx’ing kits from ASA to members, and from members to the lab, can cut down this time. However, if a sample fails this time is doubled.

Below are tips for taking blood and TSU samples.

Please find the Down to the Genes article, “Common Reasons for Delays in DNA testing”, in the October issue of the Register for more information.

 

DNA Timeline, Requirements, and Top Tips

By Lilly Platts, Jackie Atkins, Riley Foster, and Leoma Wells

Everything you need to know about ASA’s DNA Services & more. This is an extended version of the first installment of ‘Down to the Genes’ published in the September 2018 issue of the Register.  This article covers frequently asked questions and offers tips for a smooth DNA process. For additional FAQ’s and information, see the September issue of the Register.

When do I have to DNA test an animal?

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I purchased semen, are those selling semen monitored by ASA to ensure HD/150K testing?

No. Breeders are responsible for completing ASA’s testing requirements. It is strongly suggested that buyers of semen ensure a bull has all required testing prior to purchasing semen and breeding cows.

Do ASA’s genetic defect testing requirements match those put in place by sales management and bull tests?

Not always. Sales managers and bull tests may require additional testing depending on their requirements. It is always best to follow up with the specific sales manager or bull test on the testing requirements prior to ordering DNA kits from ASA to ensure the animal can be sold through that venue.

Do other associations require the same testing?

Each association has different requirements. If a sire/dam is registered with ASA from another breed certificate, additional testing may be required to register progeny. Make sure to contact ASA with any questions prior to progeny being born to avoid delays at registration time.

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Take home message:  Do not delay your DNA testing – order your kits today!

Ten things you can do to ensure a smooth DNA testing process:

  1. Familiarize yourself with ASA’s DNA testing requirements.
  2. First contact the sale, bull test, show, etc., you may participate in to be clear of their DNA requirements.
  3. Order kits early (at least two months before you need results) by contacting the ASA – DNA@simmgene.com or 406-587-4531. Please follow instructions and have all required information before calling.
  4. Use a blood card, TSU, or hair card for collection. NEVER send vials of blood, bags of hair, etc. to the lab.
  5. Follow the instructions for collection included with your kits. Failure to collect the samples properly may result in samples failing testing – watch for more information in the October issue.
  6. If you make a mistake, i.e. collect sample from the wrong animal, etc., do NOT send the sample to the lab. If you do, contact ASA immediately.
  7. Never send kits to the lab without either ordering them for specific animals, or if you have blank kits, always complete paperwork with the DNA department first.
  8. Send samples to the lab as soon as they are ready. Getting them out the door ensures faster processing and less time for paperwork to get mixed up.
  9. Check your email for results.
  10. If you have a question, ASA is happy to help. Please have your membership number and information on the animal you are inquiring about (ASA number, tattoo, etc.).

 

When Does ASA Require DNA Testing?

Question – When does ASA require DNA testing on an animal?

Simmental/Simbrah/SimAngus/SimGenetics Animals

1) If you are collecting a bull and using him as an AI sire, yes, even if it’s just for “in herd use only”, he has to be AI approved with ASA. Contact ASA with the sire’s registration number to request a DNA kit.

a. If sire contains at least an 1/8 of a another breed please read below under Genetic Defect Testing Requirements.

2) If you flush a dam, she will need to be approved with ASA as a Donor Dam.  Contact ASA with the dam’s registration number to request a DNA kit.

a. If donor dam contains at least an 1/8 of a another breed please read below under Genetic Defect Testing Requirements.

3) If you purchase an Embryo or a recipient dam carrying an embryo, and are not associated with the owner of the Donor Dam at the time she was flushed, you MUST parent verify your ET calf to both sire and dam prior to submitting a registration request. Contact ASA with the calf tattoo, sex, sire and dam’s registration numbers to request a DNA kit.

a. If sire/donor dam is at least an 1/8 of a another breed please read below under Genetic Defect Testing Requirements.

Foundation Sires and Donor Dams(animals registered with ASA from their other breed certificate)

1) To qualify as an AI sire, the bull must meet the following requirements:

a. If the bull was DNA parentage typed prior to May 1, 2012, he is grandfathered in from ASA’s genomic requirement.  The sire’s DNA parentage SNPs or STRs will need to be forwarded from the respective breed association along with the date the DNA was completed. Once ASA has this information he can be approved for AI use.
b. If the bull was DNA typed after May 1, 2012, in addition to parentage, he needs to have a High Density genomic panel on file.  The sire’s DNA parentage SNPs or STRs will need to be forwarded from his respective breed association along with verification that a High Density(50K or equivalent) genomic panel has been completed.

2) To qualify as an Donor Dam, the dam must meet the following requirements:

a. If the dam was DNA parentage typed prior to May 1, 2012, she is grandfathered in from ASA’s genomic requirement.  The dam’s DNA parentage SNPs or STRs will need to be forwarded from the respective breed association along with the date the DNA was completed. Once ASA has this information she can be approved as a Donor Dam.
b. If the dam was DNA typed after May 1, 2012, in addition to parentage, she needs to have a High Density genomic panel on file.  The dam’s DNA parentage SNPs or STRs will need to be forwarded from her respective breed association along with verification that a High Density(50K or equivalent) genomic panel has been completed.

Genetic Defect Testing Requirements

All sires and Donors Dams identified with a carrier in their lineage (CL, DL) or who come from a risk population (PR) for specified genetic defects MUST be tested for that defect before registration certificates and EPDs are available on new progeny. Please visit the TraitTrac Guide post to learn more about how to check an animal’s defect status.

To recap the above information, you need to submit a DNA sample on AI sires, Donor Dams and ET calves(if you did not own the dam at the time she was flushed) for necessary testing in order to meet ASA requirements. To learn more about how to verify whether an animal is approved for use as an AI sire/Donor Dam, click here.

If you have specific questions or concerns please email dna@simmgene.com or call our office at 406.587.4531.