A Steak in Genomics™

Christian P. Lewis South Dakota State University undergraduate student Rapid advances in science and technology are appearing throughout agriculture. One of the newest technologies that has worked its way into the cattle industry is DNA testing and the use of genomic data. Practical Uses of Genomic Data Genetic abnormalities are not a common problem in beef cattle production, but they do appear if precautions are not taken. Most frequently, a genetic abnormality appeared because both the cow and bull were carriers of a recessive allele that causes the abnormality. An animal is termed a “carrier” when they have a dominant allele that is masking the recessive allele. Figure 1 illustrates how an abnormality can appear by mating two carriers. Genetic abnormalities will appear when a calf has two copies of the recessive allele that it got from its sire and dam. A a A AA Aa 50% chance the calf will be a carrier ...

Here are videos from the American Simmental Association's Facebook livestream of my presentation titled "Taking Technology Home to the Farm and Ranch." Tradition Intuition Legacy Seedstock Producers as Educators Decker's Rants EPDs and Environment  Q&A Loading...

I talked about use of high-throughput DNA sequencing to improve fertility by removing DNA variants from a breed that cause embryonic losses during pregnancy. Here is a  link  (Managing Broken Genes in the Age of Genomics) to the PowerPoint presentation I gave. I discussed the development of a genomic EPD based on the number of embryonic lethal variants (broken genes) that an animal carries that causes losses of embryos during pregnancy. DNA Sequencing Costs, Data from the NHGRI Genome Sequencing Program (GSP) http://www.genome.gov/sequencingcosts/  The cost of DNA sequencing has rapidly dropped in the last 15 years. In 2001 it cost about $10,000 to sequence a million base pairs of DNA. In 2014 it costs under 10 cents to sequence a million base pairs. This rapid drop in the price of DNA sequencing has enabled researchers to tackle questions that we previously could not address. With this sequencing data we are identifying loss-of-function variants (broken genes) that...

The American Simmental Association continues to adjust their management and reporting of genetic defects and abnormalities. From their eNews newsletter: At the April board meeting, the ASA Board of Trustees voted unanimously to remove the color system from TraitTrac and add all genetic conditions with available tests into our TraitTrac system (including the most recent condition, developmental duplication). While the existing TraitTrac has worked well for years, it gives a false impression that "green" animals are clear of genetic defects - they are only clear of the ones we know about. Furthermore, this gives us flexibility to add new conditions to TraitTrac relatively simply as they are discovered. In the new TraitTrac system, the main animal page says "TraitTrac" if an animal has no results on any genetic conditions. If the statement "Check for available results" appears under "TraitTrac" then there is additional information on this animal. ...

MAGNUM - AMGV38 Picture from search.gelbvieh.org On January 14th, Dr. Jon Beever of the University of Illinois sent a letter to the Board of Directors of the American Gelbvieh Association informing them that his lab had resolved issues with odd results when testing fullblood Gelbvieh animals with the DNA test for Contractural Arachnodactyly (CA, “fawn calf”). One of the oldest fullblood Gelbvieh bulls, Magnum (AMGV38) tested as a carrier of the CA abnormality, and several other Gelbvieh animals with little Angus influence tested as either affected or carrier. Dr. Beever took several lines of action to evaluate what was producing the odd results and after DNA sequencing the region in the Gelbvieh animals found that the protein sequence was still functional in the Gelbvieh animals. But, the DNA base pair used in the diagnostic test was the same in affected Angus and normal Gelbvieh. Thus, the test was producing false positives in Gelbvieh animals. Dr. Beever originally designed...

One of the focuses of my  extension program  is helping farmers and ranchers understand how to manage genetic defects in their herds and how science is changing how we identify these broken genes. I recently gave a webinar during the NCBEC Brown Bagger series , which can be viewed here . I know each producers is going to have different opinions about managing defects. The point I strive to make is that we need to use optimal strategies to manage these loss-of-function mutations .

In addition to DNA variants' utility in predicting EPDs , disease risk, and other traits, they are also very useful in predicting an individual's ancestry. The most common use of this in livestock is parentage verification or testing. But DNA variants can also be used to look at relationships over much longer time scales. For example, my coauthors and I have used SNPs to look at relationships among ruminant species and breeds of cattle . Last week I sent 10 mL of my saliva to 23andMe to for processing and DNA testing. This is the human equivalent of genomic-enhanced EPDs (although 23andMe uses different statistical methods). In addition to finding out if I carry specific genetic disorders and my risk for common diseases, I will also find out about my ancestry. One of the interesting things we have learned from sequencing ancient genomes is that most humans from Europe or Asia have Neanderthal ancestry . So, as part of my 23andMe results I will learn what percent of ...

Here is a link to my article in the BEEF Cow-Calf Weekly. I know there may be some questions (and disagreement) about my article. Please comment with questions or contact me by email. Luckily, we now have the tools to manage these broken genes.

by Alan Levine I had a great conversation with Tom Steever at the Missouri State Fair Simmental Event . Listen to the interview . Then, post your thoughts in the comments section. In the future, how will your operation approach genetic defects?

Come see me tomorrow at the Missouri State Fair!

As you may know, both Zoetis and GeneSEEK have updated their genomic tests. Zoetis still uses about 50,000 SNPs, but have now trained their data set with more animal records and genotypes. The genetic correlations for the Zoetis test range from 0.38 to 0.73. See  this Angus Journal article  for more information. GeneSeek now use about 80,000 SNPs in its genomic test. The genetic correlations for the GeneSeek test range from 0.60 to 0.70 for most traits, except milk which is at about 0.4 and calving ease direct which is at 0.34. See this explanation  from the American Angus Association. So, the accuracy differences appear to be pretty small. Both tests cost $75. If you add genetic abnormality tests, such as AM, NH, or CA, to the Zoetis test, you pay $23.00 per test. If you add an the same genetic abnormality tests to the GeneSeek test, you pay $8.00 per test. See the Angus Genetics Inc.  website  or  https://www.angusonline.org/AGI/AgiDnaPricing.aspx...