Comparative genetic diversity analysis among six Indian breeds and English Thoroughbred horses

Genetic diversity analysis, population structure and relationship among six Indian horse (Kathiawari, Marwari) and pony breeds (Manipuri, Spiti, Zanskari and Bhutia), along with English Thoroughbred horses as an out group was carried out using 284 DNA samples with 48 polymorphic microsatellite markers. Allele number, observed and expected heterozygosity, polymorphism information content were estimated. These values were higher for all Indian breeds except Spiti ponies in comparison to Thoroughbred horses which indicated high genetic diversity in them. Mean number of alleles was maximum in Marwari horse breeds (10.06±0.36) followed by Bhutia, Zanskari, Manipuri, Kathiawari and Thoroughbred. The allelic count was the lowest in Spiti (5.52±0.42). Similar pattern was observed in terms of allelic richness also. An overall significant deficit of heterozygote (Fis) equal to 0.066 was observed in Indian horse and pony breeds. The mean values of Fis ranged from 0.003 in Spiti to 0.132 in Marwari with mean of 0.065±0.040. The Fst values ranged from 0.0512 (TKY394) to 0.2724 (COR018) with an overall genetic differentiation of 9.8% among breeds. The overall global deficit of heterozygote across populations (Fit) amounted to 15.98%. The estimates of Fst between each pair of breeds revealed that genetic differentiation between Spiti and Thoroughbred (0.1729) was the maximum followed by Spiti and Kathiawari (0.1725) while Zanskari and Manipuri were the least differentiated (0.0379). Individual assignment indicated admixture in all the breeds except Thoroughbred horses. The neighbor-joining dendrogram using the allele sharing distance clearly defined clusters for most of the breeds, Indian horse and pony breeds clustered separately while Thoroughbred formed a separate out-group. The Bayesian analysis using STRUCTURE revealed three distinctive clusters of Indian horse and pony breeds, Kathiawari the most prominent cluster as horse breed, second of Zanskari, Spiti and Manipuri ponies and third one having Bhutia and a sub-population of Marwari horses. Clustering of one sub-population of Marwari with Bhutia indicated their common ancestries which need further investigations as both these are distinct at phenotypic level and geographically isolated. Kathiawari represents the oldest stock and has contributed in other Indian breeds. Similarity of Kathiawari and Marwari horses is attributed to contiguity of their breeding tracts.