Last year, Team SUNY Oneonta interviewed local farmers to identify a focus for our project, which became developing a detection system for a specific allele of beta-casein in cattle. In 2021, as we sought to expand the utility of our Flappase-based SNP detection system, our iGEM team deemed it necessary to do more in-depth investigations into cattle breeding and genetic testing. We spoke with two academic experts in cattle genetics, Dr. Chad Dechow (Penn State University) and Dr. Heather Huson (Cornell University), as well as several cattle breeding and genetics companies. From our interviews with the professors and email exchanges with Premier Select Sires, Inc. and Champion Genetics, we gained key information that helped guide the direction of our project.
Interviews with Cattle Geneticists
Our team decided that if we wanted to create a genotyping panel to detect multiple genetic variants in cattle, we should contact cattle geneticists who could give us some insight on the topic. We were able to interview experts Dr. Chad Dechow and Dr. Heather Huson. Dr. Dechow has a Ph.D. in Animal Science, and is an Associate Professor of Dairy Cattle Genetics at Pennsylvania State University. He focuses primarily on the improvement of dairy cow health, and the well-being of the cattle as they continue to be bred for higher levels of milk yield and milk production efficiency. Dr. Huson has a Ph.D. in Molecular Genetics, and is an Associate Professor of Animal Science at Cornell University. Dr. Huson focuses primarily on improving overall dairy cattle performance and genetic evaluations. After conducting both interviews, we learned that there are many specific cattle traits that we should include within our genotyping panel that could aid small-scale farmers within our area. Both experts explained to us that it would be ideal to focus on genetic traits that are desired by breeders that are dictated by fewer SNPs.
Chad Dechow gave us some very helpful insight to start off our search for specific traits to include within our genotyping panel. Dr. Dechow told our team that the best type of sample to use for the genetic testing of cattle would either be a tissue sample from an ear, or a hair sample from the tail. We learned that 60% of cows within the United States are artificially inseminated, and that artificial insemination (AI) companies rely on progeny testing to identify bulls with high genetic merit. Significant SNPs in cows that Dr. Dechow told us to look into include cows that don’t grow horns, angus cows, and the SNP that causes cholesterol deficiency in cattle. Dr. Dechow also mentioned that we should reach out to a multitude of companies, including large-scale cow genotyping companies and breeding companies. Even though our current project no longer surrounds A1/A2 milk, Dr. Dechow also provided some insight on the A2 milk industry. He stated that the A2 gene has no negative impact on the cattle, and that it would take around 2 generations to replicate the A2 gene in order for 100% of a population to display this trait.
Dr. Huson was able to help us narrow down our search for SNPs by giving us a list of proteins to further investigate. This list consists of various Beta-Casein and Kappa-Casein proteins that deal with milk production and efficiency. She also showed our team how to read a colored SNP distribution chart to detect which traits are dictated by fewer SNPs. Dr. Huson explained to us that not all farmers conduct whole genome testing, as it depends on the size of the farm and the value of the cattle. Therefore, our project direction should continue to focus on genetic testing that can help small-scale farmers with less than 300 animals.
We also learned that on a large-scale farm, progeny testing is required and performed by breeding companies as part of their marketing strategy. On a small-scale farm, progeny genetic testing requires huge resources both financial and infrastructural – large scale artificial insemination, data collection and advanced analysis systems. Because we are focused on helping the small family farms in our area, we are expanding our system to detect these types of useful breeding characteristic that are essential to obtain high value cattle in an economical way to help these farms with limited resources remain competitive. The resource differences between large- and small-scale farms are highlighted in Figure ES-01.
Our team was inspired after talking to both cattle geneticists, and we set off to investigate cattle genetic trait locations and polymorphisms. We wanted our iGEM project to include a multitude of genes that small-scale farmers could test for on the field. The insight gained from these experts guided us in a more productive direction.
The questions we asked our experts and more detailed interview summaries can be found here.
Figure 1: Differences between large- and small-scale dairy farms. Large scale farms have more resources and can obtain greater efficiencies than small scale farms, which face numerous challenges in order to bring their product to market.
Cattle Breeding and Genetic Testing Companies
The academic experts that we interviewed encouraged us to contact companies that were in the business of cattle breeding or genetic testing. We communicated with two companies, Premier Select Sires, Inc. and Champion Genetics. These companies reinforced some of the information provided by Dr.’s Dechow and Huson. They also provided us with a better understanding of selective breeding in cattle. We learned that genetic testing became prevalent about 10 years ago. As to whether farmers actually use genomic information when breeding, we discovered that about 20-25% of the farms that do business with Premier Select currently use direct genomic testing before making breeding decisions. These tests provide an overview of 20 core traits, including stature, udders, milk, fat, protein production, and mastitis or metabolic disease resistance. We also increased our understanding of the varied reasons why a farmer may want to genetically test their cattle. These might include wanting to produce the genetically strongest herd possible, identifying the weakest cattle so they can be eliminated, or to identify traits that are specific but important. An example of this would be the A2 gene in milk, which was the sole focus of our 2020 project. Testing for A2 was provided as an example of a producer trying to “develop a herd that meets their marketing goals.” (Premier Select Sires, Inc.)
The detailed responses to our inquires can be found here.