Answers To Frequently Asked DNA Questions
by Joe Epperly, Assistant Executive Director and Brittany Barrick, Director of Registry and Performance North American Limousin Foundation
With the recent changes to the DNA testing structure and protocol at NALF, we have had a number of questions arise that deserve to be addressed. The following are a list of the top questions we have received along with an explanation of each.
Why did NALF change the DNA system?
NALF started to handle DNA orders in-house in order to accommodate multiple labs with a more affordable and competitive pricing structure. This will also allow NALF to have more oversight on results and tests with more direct customer service. We will also be able to maintain control over the amount of information available with your animals and samples to control their use in research work.
What do I need to send and where to?
All samples, with the exception of semen, are to be sent directly to the North American Limousin Foundation office and addressed as follows:
ATTN: Brittany Barrick
North American Limousin Foundation
6 Inverness Court East, Suite 260
Englewood, CO 80112-5595
Each sample submitted must also be accompanied by a completed DNA test request form that can be found online under the â€œDNA and Genomicsâ€ section on the NALF website (http://www.nalf.org/dna_genomics.php). Please note the protocol for Proto testing has NOT changed. DO NOT send semen or whole blood samples to the North American Limousin Foundation office.
**DO NOT INSERT SAMPLES INTO PLASTIC BAGSâ€”ONLY INSERT INTO ENVELOPES**
What is the Limousin Genomic Profiler and what will it do for me?
The Profiler offers two distinct advantages in cost and information. By using the Profiler it allows you to cut costs on tests for coat color, polled status or F94L as well as parentage verification (see parentage question below for requirements). The Profiler also yields a bevy of information in the form of molecular breeding values (MBVs). MBVs are a measure of an animalâ€™s genetic merit for any particular trait based on its 50,000 SNP genomic profile. Once the NALF system is updated to accept MBV data this fall, the MBVs will be incorporated into NALFâ€™s EPDs. Incorporating MBVs into an animalâ€™s EPDs is similar in value to that animal having eight to 20 progeny records for that trait.
For example, you have an embryo heifer calf out of an undocumented recipient cow, thus it will be in a contemporary group of one. You pull a hair sample the day the heifer calf is born and run the Profiler with parentage*, coat color and polled status for $130. Not only does it cost $14 less than it did in 2011 ($130 vs. $144) to run parentage, color and polled, the embryo heifer calf will also have EPDs with an accuracy closer to that of a 10-year-old cow. This is also highly beneficial to breeders who have smaller contemporary groups. The Profiler gives smaller breeders the same opportunity for change as an animal in a larger herd.
Note: The Profiler is currently only available for Purebreds and Fullbloods. A Lim-FlexÂ® Profiler will be on the retail market soon.
*Parents must have SNP parentage profiles on file, see parentage question below
How does the pricing structure work on the Genomic Profiler?
If you only want to run the Profiler, it is $60. If you run the Profiler together with any of the qualifying tests (parentage, color, polled, F94L or BVD-PI), you would add the qualifying test price to the discounted bundled Profiler price of $55.
For example, to run the Profiler and test for coat color:
Bundled Profiler price = $55
Coat color add-on = $15
Total Cost = $70
To run the Profiler, coat color, and polled status you would add an additional $40:
Bundled Profiler price = $55
Coat color add-on = $15
Polled add-on = $40
Total Cost = $110
*You can find the DNA Lab Pricing Structure under the â€œDNA and Genomicsâ€ section on the NALF website*
What is the difference between SNP and STR parentage and which should I do?
Microsatellite STR (Short Tandem Repeat) parentage is the platform NALF parentage verification has been done up to this point. Single nucleotide polymorphism (SNP, pronounced â€˜snipâ€™) parentage is newer technology that is more accurate and can be run with a number of other tests, including the Profiler, to enhance the information yielded from one sample. The problem that NALF is currently faced with is that STR and SNP are not compatible. In order for a breeder to take advantage of SNP parentage, the animal being verified must have parents with SNP profiles.
In order to facilitate moving to SNP parentage, the Board of Directors has decided to cost-share with members to get SNP parentage profiles on sires and dams. This means NALF will charge the member a low price of $12 per sire and dam to get SNP parentage profiles on file.
For breeders, this allows you to run SNP parentage profiles on your donor cows and save up to $10 per parentage test on each of their offspring. AI sires that werenâ€™t included in the research population for the Profiler will have to have parentage profiles done on them.
*Contact Brittany Barrick in the NALF office to see if a particular animal needs a parentage profile.*
What genetic defects do I have to test for?
For animals to qualify for registration with NALF, they must be free of known genetic defects from Angus, Red Angus, Shorthorn and Maine-Anjou, including AM, NH, CA, OS, TH and PHA. These genetic defect rules mainly affect the Lim-Flex population. Animals can be verified free either by pedigree or test. The NALF registry department can aid in identifying carriers in your herd and developing strategies for cost-effective testing. NALF generally recommends testing the oldest available potential carrier animal in the pedigree first to save time and resources.
When talking about genetic defects, it is important to remember all of the genetic defects currently tested for by NALF are simple recessive in nature. So even if an animal has a carrier parent, there is a 50 percent chance the animal is clean from genetic defects. Also, these defects have a low occurrence rate in their native populations and an even lower occurrence in the Limousin population. Our policy on genetic defects should only cost breeders in the short term, as carriers are eliminated from the population in the current generation.
If I have an embryo calf that I also want to get tested for black and polled homozygosity, what is the most cost-effective option?
The most cost-effective option is currently the Limousin Genomic Profiler bundled with parentage, color and polled for $130. Please keep in mind that in order to parent verify the animal, we will need SNP parentage profiles on file for both sire and dam. These are available on a cost-share basis with NALF for $12 each.
Where can I find the DNA rules, forms and pricing?
The most up-to-date DNA rules, forms, information on labs, pricing and protocol is available on the NALF website, www.nalf.org under DNA and Genomics. You can click the revolving banner on the homepage or go directly to the page via http://www.nalf.org/dna_genomics.php.
If you have any other questions about NALFâ€™s DNA policy, protocol, or pricing, feel free to contact us at 303/220-1693. We will also have a short educational session on DNA testing and the Genomic Profiler during the NALF Annual Meeting January 14, 2013, at the Renaissance Hotel in Denver, Colorado.