Low Differentiation despite High Genetic Diversity in Five Zebu Cattle (Bos Indicus) Breeds Native to North and Western Parts of India

Information on genetic structure and variability of livestock breeds is critical for efficient conservation plans. Here we present molecular characterization of 5 Indian grey colored cattle breeds from northern and western parts of India on the basis of 21 FAO recommended microsatellite markers. Kankrej breed has its native tract in the state of Gujarat, Tharparkar, Nagori and Mewati in Rajasthan and Hariana in the state of Haryana. All the five breeds had high diversity values. The average number of alleles per locus varied between 9.00 (Tharparkar) to 11.81 (Hariana). Gene diversity (expected heterozygosity) was high and varied from 0.707 in Tharparkar to 0.777 in Hariana. FIS values were very low (almost zero) in all the five breeds, with mean FIS values ranging from 0.00 to 0.007. Phylogenetic analysis by Neighbour Joining tree based on Nei’s genetic distance and Cavalli-Sforza Edwards chord distances generated identical phylogenies, which are in accordance with historical and geographical data. The two breeds from Rajasthan viz., Tharparkar and Nagori clustered together and were joined by the third breed from Rajasthan (Mewati). Hariana breed from adjoining Haryana state joined the tree last while Kankrej from Gujarat state was quite distinct in the cluster. AMOVA revealed very low breed differentiation among the five breeds. Only 1.57% variation was due to between breed differences and the remaining 98.43% due to individuals within breeds. PCA, MDS and STRUCTURE analysis revealed no breed structure. A very high migration (average 11.26 (DHR-IJBLS), Vol. 4, Issue 2, 2013 (DHR-IJBLS) ISSN: 2278-8301 249 immigrants per generation) was estimated between the five breeds. The study thus reveals very low genetic differentiation despite high genetic variability in the five investigated breeds.