Genomic Testing and Its Uses in Beef Cattle

By JOHNNY R. ROGERS & FELIPE A.C.C. SILVA, N.C. State University

Introduction - Beef cattle production in North Carolina is primarily based on cow/ calf grazing systems. In recent years, we have seen advances in all facets of the cow/ calf production system, from the increased adoption of defined breeding seasons to nutritional strategies tailored to wean heavier calves. However, even as these technologies become more common, the demands of the marketplace continue to increase. Buyers are placing greater emphasis on the genetic sources for their cowherds and are seeking cattle (i.e., bulls) with documented genomic testing. The main benefits of genomic testing are parent verification and calculating genomic enhanced EPDs. In addition, genomic companies/breed associations offer other tests called add ons that cover breed related genetic defects and other tests like PIBVD screening.

Parent verification is used to identify a calf’s parents (dam and sire). The main goal of the practice is to establish an accurate pedigree. This allows cattlemen to provide customers with more reliable information. Parent verification can be beneficial for seedstock and commercial operations.

Genetic verification is particularly useful in situations including multi-sire breeding pastures, artificial insemination, or embryo transfer followed by clean up bulls, calves switched at birth, and ambiguous data records. Mistakes can happen (i.e., pulling the wrong straw of semen during A.I.), and parent verification offers the opportunity to clear up any problems. This publication is directed to beef producers, farm workers, and extension agents to guide how to perform successful DNA sample collection and shipping for genomic testing.

How does genomic testing work?

Seedstock producers should contact their breed association for guidance about genomic testing. Each breed will have DNA submission forms available with instructions. Genomic companies and breed associations offer genetic tests for commercial cattle, and many commercial producers are using genomic tests to better understand the genetic makeup of their herds. This information can be valuable when selecting replacement heifers (maternal traits) and used for marketing steers (growth and carcass traits). The sampling process is similar for seedstock or commercial. Samples from the calf and its potential parents must be collected and submitted for genetic comparison. Fortunately, genetic material will remain on file at the testing labs; thus, each animal only has to be submitted once. All A.I. sires will already have genetic material on file, and many seedstock suppliers will have tested their bulls. This will make testing the progeny of their bulls much easier. The same will be true for cows and herd bulls after their initial submission, so genetic material from the calf in question may be the only sample to be submitted.

A blood sample is perhaps the lowest cost and most widely used type of genetic sample; however, other types of tissues such as tail hair, semen, and tissue samples from ear notches can also be used, with the majority of samples being shipped at room temperature. Many producers like the convenience of Tissue Sampling Units (TSU), and more information is available from breed associations. The actual analysis and comparison of the samples are generally handled through the breed association associated with the animals in question (Table 1). Care should be taken when collecting samples. Breed associations and/or genomic companies will reject samples that do not meet their criteria (i.e., excess manure contamination in hair samples). Occasionally, samples will fail, and new samples will need to be submitted. Again, consult your lab or association to ensure success. The testing process can take 4-6 weeks, and the results will be provided over email.

The newest technique used for parent verification is based on single nucleotide polymorphism (SNP) testing, which allows greater accuracy compared to formerly used tests such as single tandem repeat (STR) or microsatellite testing (MIP). One crucial factor is that both calf and parents should be tested using the same DNA technology (e.g., MIP and SNP). Therefore, most breed associations are migrating and retesting their animals to SNPs. SNP based parent testing can vary from $15-$25 per sample. Additional genetic testing using the same blood sample can be included as an added on to parent verification. Add ons can include complete genotyping, single traits, or genetic defects testing. Also, companies and associations have special pricing depending on the number of animals to be tested.

*All three associations allow tissue sampling collections (ear notch); however, the price is increased co™mpared to other sampling options. Refer to your association website for further information on tissue sampling and for current pricing.

**Producers can include add on tests such as Coat Color Test, Arthrogryposis Multiplex (AM) Test, and Neuropathic Hydrocephalus (NH) Test. Refer to your association website for the complete list.

The main idea behind parent verification is that each calf will receive one copy (“allele”) of the potential gene marker from each parent. For example (Figure 1), if a bull carrying the alleles “AA” is crossed with a dam carrying the alleles “BB,” the calf must have the alleles “AB” because the calf must receive a gene copy from each parent. If the calf tested were either AA or BB, then the calf is not compatible, and parentage is excluded. This is done by selecting and testing compatibility based on several unique SNPs (a.k.a. DNA markers).

Take home message - Genomic testing is feasible and can provide tremendous value in both commercial and seedstock operations. The advances in the test procedure allow for an easy and affordable collection with the benefits of adding several genetic tests to the results. Tests can be done through your breed association or private laboratories. Genetic testing allows our industry to make faster genetic progress and improve the conversion of forage to beef.

How to collect and ship blood or hair samples for genomic testing?

To collect blood samples:

• Record animal ID on the DNA card.

• Wipe the ear clean.

• Prick the vein in the animal’s ear with a sterile needle (1).

• Touch the circle on the DNA card to the blood site in the ear (2).

• Fill the circle and allow the card to dry away from sunlight for 24 hours before mailing.

To collect tail hair samples:

• Record animal ID on the DNA card

• Pull from the tail switch “up and away” around 20 hairs with root bulbs (1).

• Place the bulb on the sticky flap. Hair bulbs must be present to perform the test (2).

• Press the side on top of the bulbs to seal the sides and trim excess hair to the edges of the hair card (2).

To Ship the samples (Both blood and tail hair samples):

• Mail samples in an envelope or small box. Do not mail in a sealed plastic bag (3).

• The laboratory will process the sample and compare it with potential parents (4).

• Results will state if the calf matches or not potential parents (5).

Contact these RAAC members to learn more about Red Angus genetics and how they can fit into your herd.

HARDROCK BEEF CATTLE

Ronnie & Donna Holman 4613 Hickory Nut Ridge Road • Granite Falls, NC 828-302-8659 ronnie@hardrockbeefcattle.com

JK RED ANGUS

Jeff Banfield & Madison Adams 331 Tee Jay Farm Road • Aberdeen, NC 910-315-3821 jkredangus@gmail.com

LANGDON RED ANGUS & SIMMENTAL John & Eileen Langdon 7728 Raleigh Road • Benson, NC 919-796-5010 johnlangdon5@gmail.com

ROGERS CATTLE COMPANY

Johnny & Sharon Rogers 945 Woodsdale Road • Roxboro, NC 336-504-7268 rccbeef@gmail.com

PRESNELL RED ANGUS

Jonathan & Jacob Presnell 368 Whitaker Road • Shelby, NC 704-473-2627 (Jonathan) • 704-616-8775 (Jacob)

BULL HILL RANCH

Jim & Alvina Meeks • Raymond Prescott, Manager 1986 Trinity Church Road • Gray Court, SC 864-682-3900 • 864-682-2828 bullhill2@mindspring.com

COUNTRY BOY FARMS

Terry Boyles, President - twinbfarm1@gmail.com

David Miller 316 Key Road • Edgefield, SC 706-840-3709

LMA