Research Accomplishment Reports 2007

National Animal Genome Research Program (From NSRP-8)

E. Bailey,T. Lear, J. MacLeod, E.G. Cothran, K. Graves, B. Webb
Department of Veterinary Sciences

 

Project Description

Objective: 1. Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation. The whole genome sequence of the horse was completed by the Broad Institute (MA) in 2006 however the assembly of the sequences was conducted during 2007. A first assembly was reported based on computer alignments but without consideration of mapping, BAC contig construction or fish mapped markers. A major activity in our program was to support the second assembly by fish mapping clones at the request of the Broad Institute in support of determining an accurate second assembly.

Objective: 2. Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits. The availability of the horse genome map and the horse genome sequence made ITG possible to use the information for investigation of problems and hereditary traits in horses. Below is a list of activities conducted during the past year in connection with this objective: Investigate equine laminitis based on gene expression of potential therapeutic targets. Investigate genetics of epidermolysis bullosa in American Saddlebred horses. Investigate genetics of lordosis in American Saddlebred horses. Investigate the genetics of dwarfism in miniature horses. Reported inversion that appears to be responsible for tobiano hair color patterns. Reported on the genetics of dominant white among different horse breeds. Identified chromosomal translocations that resulted in reduced fertility of mares. Investigate articular cartilage maturation. Investigate the repair of articular cartilage lesions. Investigate glucocorticoid efficacy and safety in synovial joints.

Objective: 3. Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information. The completed horse genome sequence makes it possible to make predictions about the organization and function of horse genes based on previous work with the human genome. One of the primary computational tools, in this regard, is a program called Compass, developed at the University of Illinois for comparison of genomic information between species. We used gene expression information to test in silico mapping of ESTs using the program Compass.

Impact

Diagnostic tests can be provided for epidermolysis bullosa in Saddlebred horses and for the Tobiano and White hair color in horses. The cytogenetic work identifying translocations was of immediate benefit to the horse owners who were attempting to use affected mares as breeding stock. For a broader application, the work demonstrated the importance of considering translocations in cases of reduced fertility. Work on gene expression in association with laminitis and arthritis will lead to prognostic tests and therapeutic treatments. The work on objectives 1 and 3 make genomic research more productive.

Publications

Coleman, S.J., Gong, G., Faile, D.P., Chowdhary, B.P., Bailey, E., Liu, L., and MacLeod, J.N. (2007). Evaluation of COMPASS as a Comparative Mapping Tool for ESTs Using Horse Radiation Hybrid Maps, Animal Genetics, 38: 294-302.

Haase, B., Brooks, S.A., Schlumbaum, A., Azor, P,J,, Bailey, E., Alaeddine, F., Mevissen, M., Burger, D., Poncet, P.-A., Rieder, S., and Leeb, T. (2007). Allelic Heterogeneity at the Equine KIT Locus in Dominant White (W) Horses, PLoS Genetics, 3(11), e195 doi:10.1371/journal.pgen.0030195.