Questions

What kind of work does your research group conduct?
If the focus of the research group could be captured in one simple sentence, it would be “We seek to understand the relationship between changes in the DNA molecule of an organism (the genome) and the phenotype of that organism.” Of course, this is oversimplified given the tremendous level and types of variability (SNPs, in-dels, CSV, CNV, etc.) across the genome of a species. In addition, these changes are not limited to changes in the actual DNA sequence, but also additional “marks” (methylation, histone modifications, chromatin structure, etc.) that can be present (i.e., epigenetics). Phenotypes can be even more variable ranging from simply inherited phenotypes such as genetic abnormalities to the complex inheritance of quantitative traits that may be controlled by 100s or 1000s of genes. Furthermore, we have also begun to use intermediate molecular measures (gene expression, chromatin accessibility, metabolites, etc.) as phenotypes. The definition of how each of these variants impacts animal phenotypes allows the possibility of “designing” the genome of an animal through technologies such as genomic selection and gene-editing.

What lead you to your research?
A long, long time ago (the early-80s for those of you that were around), I started raising cattle. One of my greatest interests was the genetic evaluation of animals (e.g., Expected Progeny Differences, EPDS) and how it was used to make breeding decisions. I guess you could have described me as an EPD nerd because I had nearly memorized all the EPDs of any potential AI sire in the Hereford breed. I even talked my dad into driving from Illinois to Idaho to purchase cows at the Twin V and Soldier Mountain dispersals. Fortunately, he indulged me, and we purchased three cows and four heifers. I could not wait to get them back to the farm and start making mating decisions and doing things like MOET, a technique that was just picking up momentum at the time. After examining my mating list (probably long enough to last 10 years) and figuring out what the ET bill would have been, I made the decision that I had to go to veterinary school to save some money by doing it myself. Long story short, I never had the discipline to do what it took to get into veterinary school, so I became a classic first semester senior with no plans. Fortunately, when talking to my undergraduate advisor (Dr. Philip George), we started discussing the potential of using genetic markers to predict breeding values. He and another faculty member (Dr. Harris Lewin) had just received a USDA grant to investigate the concept in beef cattle. I spent the next semester in Dr. Lewin’s lab – and then spent the next 34 years at the University of Illinois as a student, technician, post-doc, and faculty member continuing the same type of work. Even today, one of the most significant papers I have published in my career is the first one from my MS degree, Beever et al. 1989 (doi: 10.2527/1990.682337x). Although it seems exceptionally trivial today, it demonstrated the promise of animal genomics. I will add that the cattle used in that study belonged to a man named Henry Gardiner, the progressive owner of a ranch in southwestern Kansas, called Gardiner Angus Ranch.

Where do you see your field in 10 years?
Given the previous 30 years of experience, I think it may not be wise to speculate too much about what will be happening in the next 10 years. I will say that I expect we will be able to genetically design animals for specific production environments and uses, whether it be through genomic selection or gene-editing. Otherwise, it is hard to predict what type of transformative discoveries might take place between now and then. In the paper I referenced above, I used 6 genetic markers that we generously estimated covered 10% of the genome. Today we routinely use 10s of thousands of markers in animal populations numbering in the thousands. It is already becoming common to use millions of markers in some of these very large populations. Much of these advances were brought about by abrupt shifts in technology. For instance, back in the day, PCR was a novel technique. When added to the discovery of a type of marker called a microsatellite, it completely changed our ability to develop linkage maps for animal genomes. Sequencing of animal genomes was a fantasy as there was no way the animal genomics community could afford to do what the human scientific community had embarked on in 1990. Of course, new sequencing technologies and platforms were again revolutionary. The initial draft of the cattle genome cost ~$50-60 million, today you can generate a high-quality de novo genome assembly for less than $30,000. There is still much to do with technologies we know today, and we are progressing very quickly, I cannot wait for that next transformative discovery. I cannot predict what it will be, but I am sure it will be exciting.

Who are your lab members?

Research Associates
Sonia Moisá

Master’s Students
Bret Gittleson
Beatrice Caiado
Leif Majeres

Undergraduate Students
Emma Brown
Alexis Engelen (post graduate)
Rebecca Finchum
Jana Owen