DNA: Where We’re Headed and Where We’ve Been

By Kelsey Crenshaw

Do you remember the day when you could flip open your handy-dandy flip phone to call someone and you knew exactly what you were doing because this was the only thing your phone could do? Now today you can hold a computer in the palm of your hand, better known as a Smartphone.

DNA is no exception to this fast paced race in today’s ever-changing technology. Genetic providers for the beef cattle industry are constantly coming up with new and improved products to offer their customers. Within the last few months I have witnessed the Beefmaster breed being thrown right in the middle of this huge, ever-changing world of genomics. This territory brings several questions with it. Here are answers to some of the most frequently asked questions about cattle genomics.

• What are STRs?

The proper name for STR is Short Tandem Repeat analysis. This is the old type of marker analysis that was used previously before the industry transitioned to the new SNP analysis in 2012. When a sample is tested with STR analysis there are 11-14 NUMBER markers that the lab looks at and can compare with another animal’s markers to determine parent verification. As the labs have now moved to SNP analysis, STR analysis is no longer used except on a case-by-case basis.

• What are SNPs?

The proper name for SNP is Single-nucleotide Polymorphism (often referred to as snip). This is the new type of marker analysis that is currently used in today’s genetic market. Every sample submitted to either Zoetis or GeneSeek for a Genotype panel or Parentage Analysis is run on SNPs. Contrary to the STR analysis, when a sample is tested with SNPs there are 80-110 LETTER markers that the lab looks at and can compare with another animal’s markers to determine parent verification.

• If one of my animals has STRs on file and another animal has SNPs on file, can they be compared for parent verification?

NO, when comparing STRs versus SNPs, each analysis produces a different marker count and STRs are number markers where SNPs are letter markers, so, these two samples cannot be compared. If you run into this scenario with animals you are DNA testing, there are still ways to compare these two animals. BBU would suggest that a new sample be submitted for the animal with STRs on file and have it run on SNPs, so that the two can be compared. If collecting a new sample is not an option, as a last resort the animal with SNPs can also be run on STRs so the two can be compared at an additional fee. Again, this is a last resort and will require approval from BBU staff. Please note, if the parents have DNA on file and a DNA sample is submitted for their progeny, parent verification will be run, no exceptions.

• What is a High Density genotype?

More commonly known as the HD genotype, this panel can map out the genes of an animal by using a 50K or 150K SNP chip. And better yet, as we grow our population of HD genotypes, our genetic vendors will be able to develop a Beefmaster specific panel that can map out genes that pertain specifically to our breed of cattle. Currently, the only animals REQUIRED to be genotyped with the HD chip are any new AI sires or embryo donors that have not already been previously DNA typed as of January 1, 2016. Although, BBU is encouraging that all animals be genotyped with the HD chip.

• What do I get when I have an animal HD genotyped?

The first and most important thing that your animal will receive when genotyped on the HD panel is Genomic-Enhanced EPDs (GE-EPDs). GE-EPDs have increased accuracy over the general EPDs and ONLY animals that have been genotyped will receive these enhanced EPDs. BBU hopes to have GE-EPDs available in May 2016 after the next genetic run. Parentage Analysis is also included when having your animal genotyped, as long as the parents have DNA on file. There is no additional charge for parent verification when your animal is genotyped unless there is an issue with STR vs. SNP comparison, as discussed above. Only then would there be an additional charge to have that animal parent verified.

• Do I get a report for my animals that have been genotyped?

Unlike when having an animal parent verified, there is no official report that you will receive when an animal is HD genotyped. Again, you will see the results of this test when the GE-EPDs are available. BBU will send you a confirmation report that simply states that your animals have successfully been genotyped and the information has been recorded with our geneticist.

These are just a few of the many questions that come up during the DNA process. If you ever have any questions regarding DNA testing please contact the BBU office. If you need DNA sample cards and submission paperwork in order to submit samples for DNA testing, please contact the BBU office.

Sometimes it is easy to sit back and wish for the more simple times of the past and long to hold that handy-dandy flip phone back in your hand. However, it is pretty cool to be able to access almost anything from just one touch of your Smartphone. As Beefmaster breeders, if we commit to DNA testing and genomics today we will ensure a successful future for our breed and enhance its importance to the cattle industry.