Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (?± s.e.) allelic diversity was 5.9 (?± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (?± s.e.) effective number of alleles (3.3 ?± 1.27), observed heterozygosity (0.5306 ?± 0.22), expected Levenea€?s heterozygosity (0.6612 ?± 0.15), expected Neia€?s heterozygosity (0.6535 ?± 0.14), and polymorphism information content (0.6120 ?± 0.03). Low values of Wrighta€?s fixation index, $F_{ ext{IS}}$ (0.2433 ?± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal a€?La€? shaped distribution of modea€“shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant e?‘€ ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.
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