In order to facilitate better accuracy and faster turnaround times, the NALF board decided to transition NALF required parentage from STR (microsatellite) to SNP (pronounced ‘snip’) technology with the help of GeneSeek. This move will help decrease problems for members and has numerous advantages over current STR technology.
All embryo calves born after January 1, 2014, will need to be parent verified via SNP.
In order to facilitate this move and take the burden off breeders, NALF (with the help of GeneSeek) is offering to run free SNP parentage profiles on current AI sires and donor dams until December 1, 2013. NALF will not be re-verifying the parentage on these AI sires and donor dams. They will be run for an identification SNP parentage profile only.
In August, NALF sent out letters asking members to send in DNA samples on current AI sires and donor cows to have SNP parentage markers run. With the receipt of the letters came a number of questions, so I thought we could answer some of those here.
Q: I’ve already run DNA on my animal, why do you need another sample?
A: The question is two-fold. First, there are two types of parentage verification available. All of NALF’s current parentage validations have been done on a microsatellite (STR) panel. A STR (short tandem repeats) panel yields 11 markers with a numerical value (ex. 57/118) for each marker. It measures the amount of repeats in a particular area on the genome.
SNP parentage is much more precise. It yields the exact nucleotides at 98 markers in the form of (AG, CT, A, etc.). Unfortunately there is no way to generate SNP genotypes from STR genotypes with acceptable accuracy for parentage verification. Numerous advances are being made in SNP technology and panels allowing for the possibility of more economical testing in the future. With some problem parentage verifications over the last year with GeneSeek buying Scidera (formerly MMI), once we get the sire, dam and calf on SNP we then have more definitive answers.
Second, though there are some samples still in storage, it is very time consuming for the lab and we would end up with a number of samples that might not have enough DNA left to run on this panel. Samples in storage can sometimes degrade over time plus there might be little DNA left after previous tests, so new samples work best. GeneSeek requested that we get as many new, fresh samples as possible to alleviate their workload and improve the results on these historical animals.
Q: How did you come up with the list of animals?
A: To start, we pulled all the animals that had either an AI or embryo calf registered in the last two years. We then compared it to the list of animals we already have SNP parentage markers on or have been run on the Limousin Profiler. The remaining animals were compiled and a letter sent to their owners.
Q: What if the animal(s) that NALF requested are dead?
A: If a donor cow is dead, please mark that there is not a sample available. Once we have run tests on all the new samples we receive, we will go back and try to pull old samples on dead animals. If it is a bull, please let us know where we can get semen. If there is no semen left, then we will try to pull an old sample.
Q: What if I have an animal that is a donor or AI sire and it is not on the list?
A: If the animal hasn’t had any AI or embryo calves recorded then it wasn’t included in the group we pulled, please add that animal’s information to your green form and we will add it to the list.
Q: What if a donor on the list is no longer being flushed or is dead, and there are no embryos left, do you still need a sample?
A: If you are absolutely certain a donor cow will have no embryo calves born after January 1, 2014, then there is no need to send a sample. It is helpful to weed out those cows that are no longer needed on the list so we can maximize our testing dollars.
Q: What if I decide not to send you a sample?
A: The new rules on parentage require all AI sires and donor dams born after January 1, 2009, to have a SNP genotype on file. While NALF will work with members on animals born before or animals on which a sample is unavailable, all testing of calves born after January 1, 2014, will be on the SNP platform. The NALF board and GeneSeek are working together to get all the animals that will be needed done free-of-charge for the membership. But if you don’t send a sample into NALF by December 1, 2013, we will assume you do not want to participate in the program and it will cost $12 to get your donor-dams or AI sires on SNP.
Q: What if I am flushing a cow and didn’t get a letter?
A: If the cow is owned in partnership, the letter went to the address on record at NALF so it might have gone to your partner. If not, please send in a sample and a note indicating that it is a donor- dam and you would like SNP run and we will try to get her run for free.
Q: What if I want to send semen?
A: Please send in the form telling us where semen is available. NALF will try to obtain semen from as few sources as possible. If we need you to send it yourself, we will contact you to request it once we have received your form and give you instructions.
Q: Do you want hair or blood samples?
A: The GeneSeek lab prefers hair samples, but we will accept blood. The key to good hair samples is to get a large enough sample out of the switch of the tail (width of your thumb) and put it on the supplied hair card (not in a plastic bag or taped to an index card). If you need hair or blood cards, please contact NALF.
If you have any other questions, feel free to contact Brittany or myself in the NALF office.