Comparative evaluation of di-nucleotide and tetra nucleotide repeat microsatellite markers in generating polymorphism in chicken

A total of 19 di-nucleotide repeats (Ca or GT repeats) and 11 tetra-nucleotide repeat markers (CTTT/GAAA/GGAAGAAA) were evaluated for their comparative efficiency in detecting polymorphism in chicken. Average number of alleles per locus across all the tetra nucleotide repeat markers was more (14.72) in comparison to that across di-nucleotide markers (9.41). Similarly, higher PIC estimates (0.883 vs 0.796) and high expected heterozygocity (0.904. vs 0.828) was observed for tetra nucleotide repeat microsatellite markers as compared to the di-nucleotide repeat markers and the differences were significant (P>0.05). Further, the tetra-nucleotide repeat markers showed much wider allelic size range at a particular locus (116 bp to 526 bp) in comparison to di-nucleotide repeats (18 bp to 126 bp). Hence, the tetranucleotide repeat markers seemed to be more informative than the di-nucleotide repeats in polymorphism studies.