Laboratory for Genomics and Bioinformatics

  
 

Lee H. Pratt
Marie-Michèle Cordonnier-Pratt
  
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Project Summary and Objectives
Background:
Currently, little is known about the equine genome, with only a limited number of equine genome sequences (~4,300) having been deposited in GenBank. In this regard the International Equine Genome Project is attempting to address efforts to increase the quality and quantity of equine genome information. As a contribution to this international collaboration we have recently commenced an equine expressed sequence tag (EST) project to provide essential equine cDNA sequences and bacterial clones to the equine research community.

The objectives of this project are:
 

1. To generate ~80,000 equine-specific ESTs by sequencing 40,000 cDNAs (sequenced from both 5’ and 3’ ends) obtained from a number of equine cDNA libraries prepared from different tissues.

2. To analyse these sequences for SNPs and SSRs, archive the all unique cDNAs sequences and establish this information together with the corresponding bacterial clones as a public resource for other investigators.

3. To incorporate the unique ESTs into an equine-specific microarray that can be used to identify changes in gene expression profiles under defined conditions (e.g. endotoxin challenged monocytes versus control, non-stimulated monocyte).

4. To examine selected candidate genes for SNPs that segregate with a specific equine traits (e.g. susceptibility to disease or enhanced endurance).
 

cDNA libraries:
Our collaborators Drs. Sumio Sugano and Yutaka Suzuki at the University of Tokyo are generating full-length cDNA libraries from a variety of equine tissues. To increase the yield of information that will be generated during these studies we have elected to obtain equine tissues from horses representing 6 different breeds (Thorougbred, Quarter Horse, Tennessee Walking Horse, Dartmoor Pony, Belgian Draft and Arabian). This is done to increase the likelihood of polymorphic marker detection (e.g., SNPs and SSRs) during the sequencing and sequence analysis phase of our study as each tissue library constructed will contain genetic information from different horse breeds. Table 1 lists our current and proposed cDNA libraries together with the tissues and horse breeds from which they have or will be prepared.
 

Funding:
Support has been obtained from the Veterinary Medicine Experiment Station at the University of Georgia and from the Grayson-Jockey Club Research Foundation. A research proposal has been submitted to the USDA-NRI program.