Polymorphism identification within 50 equine gene-specific sequence taggedsites

The continued discovery of polymorphisms in the equine genome will be impor tant for future studies using genomic screens and fine mapping for the iden tification of disease genes. Segments of 50 equine genes were examined for variability in 10 different horse breeds using a pool-and-sequence method. We identified 11 single nucleotide polymorphisms (SNPs) in 9380 bp of seque nced exon, and 25 SNPs, six microsatellites, and one insertion/deletion in 16961 bp of sequenced intron. Of all genes studied 52% contained at least o ne polymorphism, and polymorphisms were found at an overall rate of 1/613 b p. Several of the putative SNPs were tested and verified by restriction enz yme analysis using natural restriction sites or ones created by primer muta genesis. The lowest allele frequency for a SNP detected in pooled samples w as 10%. Three of the SNPs verified in the diverse horse pool were further t ested in six breed-specific horse pools and were found to be reasonably var iable within breeds. The pool-and-sequence method allows identification of polymorphisms in horse populations and will be a valuable tool for future d isease gene and comparative mapping in horses.