Submitted to: Cold Spring Harbor Press
Publication Type: Abstract Only
Publication Acceptance Date: 3/13/2006
Publication Date: 5/10/2006
Citation: Kuo, A., Fulton, J., Clover, Ashwell, C., McMurtry, J.P. 2006. Identification of 876 new microsatellite markers by using chicken genome sequences [abstract]. Cold Spring Harbor Press Abstract. P18.
Technical Abstract: Microsatellite loci have been used to evaluate associations with economically important traits in commercial poultry populations, but these analyses have been limited by the number of available markers. Specific chromosomal regions located on chicken GGA3, GGA5, GGA8, GGA9, GGA27, GGA28, and GGZ were queried for new microsatellite repeats. Ensembl and UCSC Genome Browsers were used to determine new putative microsatellite markers in each chromosomal region. Primer sequences were obtained from the published genome sequences and used to amplify the microsatellite. Eight hundred-seventy-six new microsatellite biomarkers were identified, and 117 loci were selected for further characterization and re-screened using fluorescent primers to confirm polymorphism. Chicken DNA samples from 8 diverse genetic lines were screened for polymorphism. A small subset of these new markers from 6 chromosomal regions were selected for sequencing to understand the polymorphic differences between Red Jungle Fowl and commercial layers. Sequencing reactions were carried out in both directions from homozygous individuals and multiple alleles for each microsatellite were aligned and compared. The number of base pairs per cM varies between chromosomes, and is related to the size of the chromosome with smaller chromosomes having less base pair per cM. In addition, the number of microsatellites per cM varied, with a greater number of the microsatellite per cM being found for larger chromosome. Preliminary analysis showed variations in allele sizes between samples tested and Red Jungle Fowl published sequences. All types of microsatellite repeats including-, tri-, tetra-, penta-, and complex types exhibited polymorphisms. The study considerably increases the number of microsatellite markers now available for genotype studies.