Genetic diversity analysis by using Heterologous Microsatellite markers among cattle and buffalo breeds

Microsatellite markers have become a reliable technique for genetic diversity studies, parentage analysis, and breed characterization in animals. The 18 amplified heterologous microsatellite markers out of 20 microsatellites were used for studying the genetic variation among cattle and buffalo. The estimated mean allelic diversity for cattle breeds was 12.50 for Sahiwal, 10.94 alleles in HF crossbred, and 10.444 and 10.944 alleles for Murrah and Nili Ravi breeds of buffalo, respectively. The Sahiwal breed had the highest allelic diversity compared to other studied breeds. A high level of genetic variability was observed for the observed heterozygosity (0.857±0.027) and expected heterozygosity (0.811±0.017) between the Sahiwal and HF crossbred breed of cattle. A low level of genetic variability was observed between the Murrahand Nili Ravi breeds of buffalo. The FIS values -0.156 to 0.065 depicted low inbreeding in the breeds. The Nei's genetic distance was measured for all the breeds which showed the genetic distance/divergence between the HF crossbred and Sahiwal was 1.070. The genetic difference based on Nei's genetic distance between the cattle HF crossbred and Nili Ravi breed of buffalo was 2.456. The genetic difference between the Nili Ravi breed of buffalo and the HF crossbred was the highest. The principal component analysis accurately reflected genetic distances, forming distinct groups for HF crossbred, Sahiwal, Murrah, and Nili Ravi. The HF crossbred and Sahiwal appeared in different coordinates, indicating the notable genetic distance between these breeds, while Nili Ravi and Murrah clustered together in a single coordinate. These groups showcased clear genetic distinctiveness. The bottleneck analysis exhibited the typical L-shaped pattern, implying that all breeds did not undergo a recent bottleneck and were not at risk of potential extinction.