University of Kentucky College of Agriculture, Food & Environment


Gluck Center > Directory > Gluck Faculty >MacLeod, JN > Research Projects


Gene Mapping, SNP Genotyping, Association Studies,
and Transcriptional Profiling

James N. MacLeod, VMD, PhD
(859) 218-1099

In a manner similar to other domestic species, horses have been selectively bred for hundreds of years with careful maintenance of pedigree data. Unlike other domestic species, however, selective breeding practices in horses have been based primarily on athletic performance traits. As such, horses provide an opportunity to investigate genetic determinants related to exercise physiology and diseases that compromise athletic performance. Genome sequence data and informative polymorphisms will permit the identification and characterization of quantitative trait loci for disease traits of the musculoskeletal, neuromuscular, cardiovascular, and respiratory system that appear very similar in clinical presentation and pathogenesis to diseases in humans. Specific examples include osteochondrosis dessicans, angular limb malformation, trauma induced osteoarthritis, tendon and ligament injury, stenosis and other malformations of the vertebral canal, exercise associated cardiac arrhythmias and conduction abnormalities, and exercise induced pulmonary hemorrhage.

map of cartilage

Analysis of gene expression is widely performed in experimental biology to investigate cell and tissue function, cellular differentiation, disease pathogenesis, and the molecular mechanisms of different therapies. The basic premise is that valuable insight about a tissue or cell type can be obtained from studying qualitative and quantitative changes in the pattern of gene expression. New technology is becoming available to make this scientific strategy much more powerful and efficient. Traditionally, gene expression was studied one gene at a time and scientists were quite limited in the number of genes they could evaluate in any given experiment. As a result, it was necessary to make an educated prediction about which genes should be important to study. With approximately 30,000 genes in the total genome, this was an inefficient process. The new methods allow scientists to initially take a much broader perspective, screening expression across large subsets of genes in a single experiment. This enables an informed decision to be made subsequently on which individual genes or encoded proteins should be most interesting to focus on at greater detail. Essentially, the scientist can evaluate the “forest” before making a decision on which individual “trees” should be investigated further. To take advantage of these experimental “genomic” strategies, we have been working over the past three years to develop a cDNA clone set representing 9,322 different genes expressed by chondrocytes in equine articular cartilage. This will enable gene expression profiling of our experimental samples on a broad scale, generating data from thousands of genes not routinely studied in cartilage and hundreds of transcripts that do not match any functionally annotated genes in the databases from any species. The availability of equine-specific DNA sequences is very important, because it enables expression profiling experiments to be performed with specificity and sensitivity on samples isolated from equine tissues. Overall, this approach holds the promise of identifying both novel genes that are functionally important in equine joint cartilage and quantitative changes in gene expression that will provide valuable insight into disease pathogenesis and molecular mechanisms (both positive and negative) of therapeutic agents.

Equine Articular Cartilage cDNA Microarray. Fluorescent Scan (A), Scatter Plot (B), and Volcano plot (C) illustrating differential gene expression in an experiment that using our 9,322 element equine cartilage cDNA microarray.



Maxwell H.Gluck Equine Research Center
Department of Veterinary Science, University of Kentucky
Lexington, Kentucky 40546-0099

Main Office (859) 257-4757
Fax (859) 257-8542