Amplification of sequence tagged sites in five avian species using heterologous oligonucleotides

Short of a complete genomic DNA sequence, sequence tagged sites (STSs) have emerged as major genomic reagents for the genetic analysis of little-studi ed ecologically and agriculturally important organisms. Here, we report STS developed for the turkey (Meleagris gallopavo), guinea fowl (Numidea melea gris), Japanese quail (Coturnix coturnix) and pigeon using primers specific for reference DNA sequences of two chicken (Gallus gallus) genes, aggrecan (agc1) and type X collagen (col10). Additional STSs were also developed fo r turkey, quail and chicken using primers specific for the human apobec-1 g ene. The total length of the STSs developed was 5990, 2522, 4127, 1539 and 6600 bp for the turkey, guinea fowl, Japanese quail, pigeon and chicken, re spectively. Based on splice site consensus GT and AG sequences, four of the seven agc1-based chicken STS appear to contain introns. The human gene-bas ed STSs showed no significant sequence identity with the reference GenBank sequences. Maximum likelihood, maximum parsimony and neighbour-joining anal ysis of an agc1-based STS that was common to all five species showed phylog enetic relationships consistent with those previously defined using mitocho ndria DNA sequences and nuclear gene restriction maps. Additionally, severa l putative single nucleotide polymorphisms (SNPs) were detected within the STSs, including eight in the turkey, two in the quail, and two in the chick en when multiple sequences were evaluated from each species. This report de scribes new STSs that are resources for genetic and physical mapping and ge nome analysis within and among avian species. These resources should furthe r aid in our understanding of the biology of agriculturally important but l ittle-studied guinea fowl and turkey.