DNA TESTING
All DNA submissions must have either a registration number or performance number in order for them to be processed and sent to the lab. Please allow 6 weeks for DNA Processing. For questions email BBUDNA@beefmasters.org.
DNA Sample Collection
Collecting a DNA sample is easy, but collecting a good DNA sample is crucial to receiving prompt and accurate results. As a Beefmaster breeder it is required that DNA samples be collected and processed through NEOGEN on all embryo donor dams and semen sires, as well as A.I. and E.T. calves. The process of collecting quality DNA blood, hair or tissue samples is important to understand for all Beefmaster breeders. If a bad DNA sample is provided then the DNA-testing lab cannot efficiently extract the DNA. If you currently, or plan to in the future, collect DNA samples please become familiar with the instructions below.
DNA Frequently Asked Questions
- STRs - The proper name for STR is Short Tandem Repeat analysis. This is the old type of marker analysis that was used previously before the industry transitioned to the new SNP analysis in 2012. When a sample is tested with STR analysis there are 11-14 NUMBER markers that the lab looks at and can compare with another animal’s markers to determine parent verification. As the labs have now moved to SNP analysis, STR analysis is no longer used except on a case-by-case basis.
- SNPs - The proper name for SNP is Single-nucleotide Polymorphism (often referred to as snip). This is the new type of marker analysis that is currently used in today’s genetic market. Every sample submitted to NEOGEN for a Genotype panel or Parentage Analysis is run on SNPs. Contrary to the STR analysis, when a sample is tested with SNPs there are 80-110 LETTER markers that the lab looks at and can compare with another animal’s markers to determine parent verification.
- When a sample is submitted for genotyping or parent verification it is run on a SNP analysis. If the sire or dam of this animal was DNA typed back several years ago and only has STRs on file they cannot be compared to the SNPs as this is two different types of markers (explained above). If possible, it is in your best interest to either submit a new sample for that parent so it can be run on SNPs, or if the sample on file is viable for additional testing to have that sample pulled and run on SNPs. If that sire or dam is no longer alive to have an additional sample submitted for SNPs and the sample on file is not viable for additional testing, then that parent cannot be compared back to the calf using SNPs.
- The 100K Genotype is a panel of 100,000 SNP markers. When your animal is run on an 100K Genotype it will receive Genomic-Enhanced EPDs (GE-EPDs) and parent verification if the parents have DNA on file. All A.I. sires and embryo donor dams are required to be run on the 100K Genotype and must be parent verified back to both sire and dam.
- The Ultra-Low Density (uLD) Genotype is a panel of 30,000 SNP markers at NEOGEN. When your animal is run on the uLD panel it will receive parent verification as well as GE-EPDs. All A.I. and E.T. calves are required to be run on the uLD (30K) Genotype.
- The first and most important thing that your animal will receive when genotyped on the 100K or uLD panel is GE-EPDs. GE-EPDs have increased accuracy over the general EPDs and ONLY animals that have been genotyped will receive these enhanced EPDs. Parentage Analysis is also included when having your animal genotyped, as long as the parents have DNA on file.
- Unlike when having an animal parent verified, there is no official report that you will receive when an animal is genotyped. Again, you will see the results of this test when the GE-EPDs are available. BBU will send you a confirmation report that simply states that your animals have successfully been genotyped and the information has been recorded with our geneticist.
- When you receive a DNA report that states that your animal is DNA excluded this means that the animal either did not qualify to the dam, to the sire or to both parents. When comparing SNP markers only 1-2 DNA exclusions are allowed and if there are any more than this the animal is considered excluded to that parent. This means that the sire or dam provided is not the correct parent of the calf. Animals with DNA exclusions are placed on hold in the registry.
- After receiving a DNA report that shows a DNA exclusion the first step is to contact BBU. You will need to inform us of an alternate sire or dam to have the lab test against. If that parent has DNA on file to compare back to, BBU can run a recheck on your animal. If it does qualify back to that parent your next step would be to then return the certificate for the animal to have it corrected in the system. If that parent does not have DNA on file but you believe it is the only other possible option we can make the correction per the breeder’s authorization but cannot record the animal as parent verified as the parent does not have DNA on file to compare back to. In this case, you would still need to return the original certificate of that animal to have the parentage corrected.
- If you have multiple sires that your calf could possibly be out of, DNA is the best way to accurately decipher which sire is the correct sire. You can submit a DNA sample for the calf and have it tested to the multiple sire options to see which sire qualifies.
- When submitting the DNA sample for the calf, on the submission paperwork you would list ALL possible sire options the calf could be out of. When the sample is submitted to the lab they will test the calf against two options, as long as that sire has DNA on file, and can tell you which sire is correct. Additional sire options can be checked by BBU.
- This can happen in rare cases where the calf will qualify to the sire on an individual basis and the dam on the individual basis but will exclude at the mating pair. This means when the sire and dam were compared TOGETHER against the calf there were exclusion markers present. As this is a rare occurrence, it is handled on a case-by-case basis. Normally this happens because the actual sire or dam is closely related to the sire or dam that the calf was tested against. It could be a full sibling, half sibling, etc.
- The first step is that an alternate sire or dam option should be given to test against to see if we can get it to qualify. If the dispute is still not cleared up after trying several other options, it would be recommended that a new sample be submitted for the calf and possibly the sire and dam, if necessary.
- To request DNA sample cards, TSU applicators, or TSU boxes you can contact BBU at (210) 732-3132 or you can email bbudna@beefmasters.org. When requesting DNA sampling supplies we need to know your BBU Membership number, the item(s) you would like, and the quantity. When the supplies are mailed out we also include the DNA Submission Paperwork. This is what needs to filled out, signed and submitted with the DNA samples after the samples have been collected.
Use a new needle, syringe or pin prick device for each animal. When collecting, packaging and submitting samples for DNA testing, it is critical to eliminate cross-contamination. Rinsing needles is not enough to prevent possible DNA residue. Please follow these simple steps to improve accuracy of test results:
- Verify the animal's tattoo and/or tag number and clearly record it on the blood card in the space provided. This ID will be used for reporting results, so it's important to double-check it for accuracy.
- Using a new needle or piercing device for each animal, prick a vein in the animal's ear. As blood forms at the site of the prick, open the blood card and touch it to the drop on the indicated square. Apply only enough blood to the card to fill the circle outline, but not so much that the card is soggy and overly saturated. Two or three heavy drops of blood per circle is plenty. A syringe may also be used to collect and spot the blood cards.
- Next, bend the top flap of the card up so that the sample dries while the card is in an open position.
- Set the blood card aside with the top flap open until dry. Make sure that blood cards do not touch this is a possible source of DNA cross-contamination. Also, do not dry blood cards in direct sunlight, as UV radiation destroys DNA.
- Once dry, rubber band closed blood cards together in batches of 10-15.
- Record the Animal ID, sample barcode, test type, and other animal information on the NEOGEN DNA Submission Form, such that each sample can be correctly matched with each animal.
- Send DNA sample to: Beefmaster Breeders United, P.O. Box 3790, Bryan, TX 77805.
- Samples can also be shipped directly to NEOGEN upon request.
Collecting good hair root samples is crucial for reliable test results because bulbs are a reliable source of DNA. Proper collection will reduce the number of samples that fail in the lab due to insufficient quantity and quality of DNA.
Getting Started
To help assure the safety of the animal and the handler, properly restrain the animal with a halter, headlock, chute or whatever is most appropriate for the animal's size. Always wash your hands or use clean gloves. If you are using a device (e.g., hemostats), be sure to wipe it clean between animals. Additional attention must be used when collecting hair roots from calves under four (4) months of age, as adequate hair roots might be difficult to obtain.
Collecting The Hair Samples
Steps:
- Record the animal's tag number on the hair sample collector in the space provided. This animal ID will be used for reporting test results, so it's important to doublecheck for accuracy.
- While holding the end of the tail switch, pull a pencil-thickness tuft of hair (at least 20 ' 25 hair roots) from the tail switch, making sure hair roots are attached. Roots are under the skin of the tail and extract easily when pulled correctly. Pull the hair 'up and away' from the way it lays to get as many roots as possible. Always collect dry hair samples and make sure the roots are not contaminated with feces. Hair root samples also may be obtained from other sources, such as ears or tailhead.
- Open the hair sample collector completely. Place the hair on the back of the printed flap of the collector as shown, with roots close to the joined end. Peel off the backing paper, starting from the joined end, to expose the sticky backing of the flap.
- Press the sticky plastic side down on top of the hair roots. Make sure the edges of the plastic are sealed around the collector. Also, verify that the roots are covered.
- Trim the excess hair to the edges of the sample collector. Place the collectors in bundles of 10 ' 15 in a resealable plastic storage bag.
- Record the Animal ID, sample barcode, test type, and other animal information on the NEOGEN DNA Submission Form, such that each sample can be correctly matched with each animal.
- Send DNA sample to Beefmaster Breeders United, P.O. Box 3790, Bryan, TX 77805.
- Samples can also be shipped directly to NEOGEN upon request.
- Remove a TSU punch from the packaging. Punches should be assembled as one piece; if they have come apart, reassemble. Open the tube retainer at the base of the applicator by pushing the retainer clip.
- Insert the punch into the applicator. Release the clip to lock punch into the device. Carefully squeeze the applicator handles together, guiding the punch tip into place if necessary. When the gun bolt rests flush against the red plastic clip, release the handle.
- Remove the red plastic clip by pulling it outward. Be careful as the metal cutter above the clip is very sharp. Ensure the applicator is loaded with an unused punch (if the red plunger is visible, the punch is used and should be replaced with one that is unused).
- Slide the applicator over the animal’s ear and position the metal cutter one inch from the edge of the ear, making sure to avoid any obvious veins or ridges. Squeeze handles together to take a sample and then release to free the ear. Try to do this in one swift, fluid motion.
- Remove the punch from the applicator and check that sampling has been successful. If not, discard the sample and proceed with a new punch. Remove the used cutter from the applicator by pulling the handles apart. Discard carefully as the cutter is very sharp.
- Record the Animal ID, sample barcode, test type, and other animal information on the NEOGEN DNA Submission Form, such that each sample can be correctly matched with each animal.
- Send DNA sample to Beefmaster Breeders United, P.O. Box 3790, Bryan, TX 77805.
- Samples can also be shipped directly to NEOGEN upon request.
DNA Testing Supplies
Blood cards for NEOGEN are $1.50/blood card. Hair cards for NEOGEN are $2.00/hair card and a $7.00 processing fee per sample. This is an additional fee to the actual DNA test, not included. Along with blood and hair samples, we also accept tissue samples. We do have the Allflex Tissue Sampling Unit (TSUs) available in the office for purchase. The Allflex tissue applicator is $95.00. The Allflex TSU Kits are $35/per box and there are 10 punches in each box. Postage fees are applicable and vary by order. To place a Supplies order, please email BBUDNA@Beefmasters.org.