Helpful tips to remember when collecting DNA samples
DNA samples from cattle can be used for parentage verification, identifying genetic defects, carcass composition or testing for persistently infected bovine viral diarrhea (BVD-PI). But before any of those results can be made, a quality DNA sample needs to be collected.
Jon Beever, University of Illinois associate professor in molecular genetics, has dealt with his fair share of poor DNA submission samples. Aside from being a leading researcher in bovine genetic defects, he and a colleague operate a DNA testing laboratory, AgriGenomics, as a way to oversee the technologies produced at the university.
Beever says the most common errors in submission samples are producer specific. He recommends producers understand the four most common DNA collection methods and the challenges associated with each.
Regardless of the method used, make sure to verify the animal's individual ID, either by recording its unique form of ID (tag, tattoo, freeze brand). Put this number on the sample for submission. This ID will be used for reporting results.
Always contact the DNA testing lab of your choice before collecting a sample for DNA analysis. Keep in mind, the better the quality of the sample, the more efficient the lab will be in providing results.
DNA is present in any nucleated cell in the body, which, according to Beever, means any cell except red blood cells contains DNA.
Beever explains that various DNA collection methods stem from “the ease of which a producer can collect the sample in his own way without any assistance…and what kind of sample is the preferred sample for the lab you are working with.”
For example, an anti-coagulated blood sample (whole-blood sample) is an easy and clean sample to work with in the lab, but producers usually aren't trained in drawing the sample. It may require a veterinarian's assistance, making collection more costly.
Hair samples can be gathered quickly and easily, but it's imperative that the hair “bulb,” also known as the root, is collected. Each bulb represents 5,000-10,000 skin cells containing DNA, Beever explains. Because hair is easy to collect, scientists thought producers would have no problem submitting these samples.
What they've found, however, is envelopes filled with hair, some weighing 50% manure by volume. Or, someone took a set of clippers down the middle of a calf's back and submitted the clippings. The first is a pain to work with at the lab and can contaminate the sample; the second didn't have any bulbs attached to the hair.
Hair samples provide a lower quantity of DNA than other sources, but can be of high quality if collected properly, Beever says. He estimates that 30% of submitted hair samples are unusable.
He recommends producers pluck 10, 20 or 30 hairs from the mid-section of the tail switch. Make sure they are fairly coarse hairs with large sized follicles to provide sufficient quantities of DNA to analyze.
Do wash your hands or use clean gloves. Or, if using pliers, clean between each animal.
Do pull the recommended amount of hair from each animal.
• Do pull hair from the mid-section of the switch. Pull up and away from how hair lays to get as many roots as possible. Roots lie under the animal's skin.
Do keep all the hairs aligned when adhering to a “sticky” collection card.
Don't collect hair that is wet or contaminated with feces.
Don't submit hair that is clipped from the animal, as it doesn't contain hair bulbs.
Do clip extraneous manure from samples before submitting.
Producers have two considerations when it comes to blood samples. The first deals with whole blood, which provides ample amounts of DNA to run a variety of diagnostic tests. It's important to keep these samples cool.
The fail rate of whole-blood samples is less than 1%, Beever says. He prefers analyzing blood samples because his lab can prep 100 blood samples in the time it takes to prep 20 hair submissions.
A little known fact: bovine blood is high in fibrin and fibrinogen, which makes it clot extremely fast. Drawing blood into a syringe without anticoagulant in it may render the sample unusable. The preferred anticoagulant is EDTA, which is used in the “purple-topped” blood tubes. Other anticoagulants, such as heparin, should be avoided if possible.
The second option requires a producer to bleed an animal onto an FTA card, or blot paper. It's a chemically treated paper that sequesters DNA and binds anything that would degrade the sample. Beever says it's as simple as taking a regular 16-ga. needle, pricking the animal's ear and putting a few spots on the card. While it won't yield a tremendous amount of high-quality DNA, it's sufficient to run some diagnostics.
Do use new needles or pricking devices for each animal. This eliminates cross-contamination. Rinsing needles is not enough.
Do clean the area on the animal before sampling to avoid contamination from dirt and manure. Clip long tufts of hair that may cause smearing.
Do saturate FTA cards with enough blood to fill the circle outlined on the card, but not so much that the card is soggy.
Don't let FTA cards touch once blood samples have been blotted, as this may cross-contaminate samples.
Do sample from locations with easy-to-find blood vessels such as the ear and the underside of the tail.
Do allow blood to dry quickly on FTA sample cards.
Don't dry FTA cards in direct sunlight.
Semen is a great source of DNA for bulls that are deceased and didn't have hair or blood samples drawn. Beever says it's easy to collect and transport, as semen doesn't need to be shipped in liquid nitrogen. The one downfall — cows don't provide semen.
Do package semen carefully, either surrounded by cardboard or inserted into an inexpensive writing pen with the ink tube removed.
As testing for BVD-PI requires live tissue, samples of hair, blood and semen won't work. Companies have designed devices, such as “tissue tags,” to capture live tissue easily. The tagger-style device punches a small sample of the animal's ear into an individual container that is pre-barcoded and ready to ship (or store) for further DNA analysis.
The result is a fairly large chunk of nucleated cells, with DNA of high quality and quantity.
Don't punch through tattoos, as ink residue may interfere with results.
Do make sure the applicator gun is loaded correctly.
Do place the applicator between ribs in the animal's ear to make sure you're getting a tissue sample and not cartilage.