Pakistan is rich in Animal Genetics Resource (AnGR) and has various breeds of sheep and goat but the genetic data in these different breeds is lacking which needs to be established for their genetic identification. The advent of molecular techniques has led to an increase in the studies that focus on the genetic characterization of domestic breeds using genetic markers. Due to their reliability and availability, the microsatellites have become preferred method for the genome mapping. Microsatellites or STRs are the 1-6 nucleotide tandem repeats present in both coding and non coding regions of both prokaryotes and eukaryotes. Microsatellites are powerful tools in genome mapping, forensic DNA studies, paternity testing, population genetics and conservation! management of biological resources. The present study was conducted on the molecular diversity analysis of sheep and goat breeds of Pakistan using FAQ recommended unlabelled microsatellites. Blood samples of unrelated true representative animals of two sheep and goat breeds were selected from their breeding tracts and different Government Livestock Farms throughout the country. DNA was extracted with the standard protocol and amplification of DNA was done with a set of 16 microsatellite markers in Molecular Cytogenetics and Genomics Laboratory in the Institute of Biochemistry and Biotechnology. The products of touch-down PCR were examined on non denaturing Polyacrylamide Gel Electrophoresis (PAGE). Genotyping results were analyzed through the sofiware POPGENE version 3.3 for calculating the number of alleles, expected and observed heterozygosity, homozygosity, Polymorphic Information Content (PlC).

Average observed heterozygosity, average observed homozygosity, observed and effective number of alleles for all loci and populations were 0.8394, 0.1606, 3.6875 and 2.8693 respectively. Almost all of the microsatellite markers showed significant variations in both breeds of sheep and goat. Genotyping results of microsatellite markers were clearly different for four different breeds showing a distinct genetic distance between sheep and goat breed's.

This work provided the genetic data which will be helpful in breed identification and making effective breeding policies and conservational activities in future according to FAO global Farm Anithal Genetic resource data. Moreover this study can become the basis for further research investigations in sheep and goat in Pakistan.