Parentage verification has always been a bit of a struggle between the science and recordkeeping, and in recent months members have had some parentage issues they were not seeing previously. There have been numerous changes in the last few years that have led to some of these issues. In order to help alleviate some of those issues, it’s best to make the membership aware of them and their history, and provide some solutions to help make the process better for everyone involved.
For many years, MMI Genomics was an authorized lab and genetic services provider for NALF and the American Angus Association (AAA), as well as many other breeds. Parentage was verified based on 11 STR (microsatellite) markers at MMI. In 2010, MMI Genomics (now known as Scidera Genomics) became subject to an involuntary bankruptcy action and no longer had a contract with AAA. NALF continued to do parentage exclusively with MMI through August of 2013 when we began contracts with both GeneSeek (formerly Igenity) and Zoetis (formerly Pfizer).
In January 2013, GeneSeek’s parent company, Neogen, acquired Scidera and in April transitioned all of their cattle testing to GeneSeek’s Lincoln, Nebraska, location. Additionally, during this time, AAA made a switch in their parentage verification technology from STR to SNP (single nucleotide polymorphism) verification.
Needless to say, all of these corporate changes have caused some problems and confusion on the customer’s end.
Scidera used 11 markers for parent verification and would qualify animals with a minimum of nine matches with no exclusions. GeneSeek runs 14 markers which include the 11 Scidera markers plus three other markers. SNP markers include a minimum of 100 markers which are quite different from STR. Although there is research to impute SNP markers from STR markers, current methods haven’t proven accurate enough for commercial use, so the technologies cannot be used together.
Here is an example of an issue that we encounter frequently and the solution we are implementing at NALF. If parents of a new embryo calf were verified at Scidera with nine of the 11 markers and the calf only has eight of those same markers when run at GeneSeek, we end up with a short call. A short call means the information we have says the mating works, but we lack enough information to definitively verify it. This is one of the main reasons why some members have been asked for new samples on parent animals or have been delayed while we run STR markers on the parents again—if samples are available at the lab.
In Lim-Flex, we have the issue that the newest crop of Angus bulls genotyped after the AAA switch to SNP has no STR markers on file. The Limousin and Lim-Flex dams of these animals only have STR markers on file. So we end up with a delay in parentage while we find a sample on the sire or dam and run it for either SNP or STR markers, and if moving to SNP, rerun the progeny’s DNA on SNP markers.
SNP verification is more accurate as we have seen with problem cases at NALF. NALF’s board and staff are currently working with the labs to develop a strategy to move our parentage to SNP to improve accuracy and decrease cost to you. In the meantime, NALF is still running a $12 special for any historical animal (AI sires and donor-dams) that you would like to have SNP markers run on.
There have also been a few logistical issues as historical samples are moved from Scidera in Davis, California, to GeneSeek in Lincoln, Nebraska. These are mainly lab issues with keeping IDs consistent when moving them into GeneSeek’s new system.
As members, it is important to remember to send all samples (first time or resubmits) to NALF rather than directly to the lab, excluding semen (contact Brittany for semen instructions). All samples are preprocessed at NALF and given a reference number before being sent to the labs. This is to protect the breeders’ information from being used in research by the labs without NALF or the breeder consent, and to give members more competitive pricing. Without this information, the lab doesn’t know what information (tests, parents, etc.) to link the sample to.
One other major problem we see at NALF is poor samples being sent for testing, especially when dealing with hair. GeneSeek prefers hair samples, but samples should be large enough and in the correct container to ensure sample integrity. Hair cards are available from NALF and NALF has to send the samples to GeneSeek on the cards. Incorrect sample containers include plastic bags and large envelopes. These can allow mold growth and manure from the bottom of the hair sample to pollute the follicle, as well as allowing the follicles to be damaged.
When taking a hair sample, take the sample from the animals switch and pull upward to be sure to remove the follicle. The sample should be about the width of your thumb when flattened in your hand especially when requesting multiple tests.
At NALF, we are committed to using the best technology and processes in order to provide you with the most accurate breeding tools in the industry. We are here to assist you and if you have any questions on DNA testing, contact Brittany Barrick in the office (ext. 57). The more we can work together, the better the results for you and for the breed.