Genetic characterization of Ladakhi donkeys using microsatellite markers

Abstract

The donkeys of Ladakh region of Jammu and Kashmir, are well adapted to the cold, arid and hypoxic conditions of this region. The genomic DNA, isolated from 25 blood samples collected from these donkeys, were amplified by PCR using FAM and HEX labeled primers and resolved for alleles on automatic DNA sequencer. Total 20 loci of the horse origin were tested and only 13 loci gave scorable results. Rest of the loci either did not amplify well (HMS3, HMS7, ASB17 and COR22) or showed less than four alleles (HMS5, HMS6, HTG4), in the studied population. At the 13 loci included in the final analysis, the PCR product size ranged from 79–85 bp at locus HTG6 to 257–275 bp at locus COR18. The observed number of alleles varied from 4 (HTG15, HTG6, HTG10 and VHL20) to 9 (HTG7 and COR71) with a mean of 5.92±1.80. The observed heterozygosity ranged from 0.44 (VHL209) to 0.90 (AHT5) with a mean of 0.76±0.13. The mean genetic diversity estimate (FIS) was –0.076. The cumulative exclusion probability (PE) of these loci was 0.999838 indicating their suitability for parentage testing in these donkeys. The sign test, standardized differences test, the Wilcoxon test using the allelic frequency data under two phased mutation model and sequential mutation model at the studied loci as well as normal ‘L’ shaped distribution of the allelic frequency indicated the absence of any recent genetic bottleneck in donkeys of Ladakh region. When these donkeys were compared to Spiti donkeys of Himachal Pradesh and Brown type donkeys of Andhra Pradesh on the basis of allelic frequency data at these loci, they showed Nei’s minimum genetic distances of 0.115 and 0.165, respectively, from these population.