Plant & Animal Genomes XIII Conference Plant & Animal Genomes XIII ConferenceJanuary 15-19, 2005
Town & Country Convention Center
San Diego, CA
To facilitate research on cartilage and osteoarthritis in horses, an expressed sequence tag (EST) and cDNA microarray has been generated from equine articular cartilage. A total of 16,319 clones were partially sequenced from a normalized cDNA library generated from the articular cartilage of a 15-month-old Thoroughbred gelding. These sequences were processed to yield 13,962 high quality ESTs. Clustering analysis, based on a match length of at least 200 nucleotides with 98% or greater identity, defined 9,322 unique sequences (7,228 singlets and 2,094 clusters). A comparison of these 9,322 equine ESTs to the human/mouse/rat refseq database at NCBI using a threshold (E) value of 1x10-5 identified 44.6% matches by BLASTX and 72.1% matches by BLASTN. A similar comparison by BLASTN to the full GenBank nt database identified 91.2% matches. Functional assessment using five broad GO categories yielded a pattern of relative distribution similar to that observed for all refseq database proteins, suggesting broad representation of expressed genes. The microarray was constructed using the 9,322 element clone set, 26 additional equine cDNAs, two positive control mammalian genes (EFTu and G3PDH), and two negative control plant genes (soy Rubisco small chain 1 and soy chlorophyll ab binding protein). In initial experiments, the microarray is being used to study cell/matrix interactions by examining the differential regulation of gene expression by a cartilage-restricted isoform of fibronectin. A second set of experiments is investigating articular cartilage maturation by comparing chondrocyte gene expression between superficial and deep layers of articular cartilage from neonatal and mature horses.