Genetic Diversity and Bottleneck Analysis of Indigenous Grey Cattle Breeds of India Based on Microsatellite Data

Bovine microsatellite data of 21 loci was used for the assessment of genetic diversity and bottleneck analysis of 10 indigenous grey cattle breeds from different agroclimatic regions of India. A total of 448 alleles were observed across 21 loci and the observed number of alleles varied from 11 (INRA 05) to 35 (ILSTS-05). The overall observed and expected heterozygosity was 0.722 and 0.802, the PIC and Shannon index values were 0.779 and 2.065 indicating high genetic diversity. The mean number of alleles was 12.33 across 10 grey cattle breeds. The maximum observed heterozygosity was observed in Hariana and minimum in Hill Cattle breed. The FST estimates revealed 92.5% of the total genetic variation within breed, while 7.5% of the total genetic variation was among breeds. Three different tests, viz., Sign rank, Standardized differences and Wilcoxon tests using 3 models of microsatellite evolution (IAM, SMM and TPM) were employed to investigate whether any of the ten Indian grey cattle populations have undergone recent bottleneck or were in mutation drift equilibrium. The tests revealed no genetic bottleneck in recent past and this was confirmed by mode shift test which gave L-shaped distribution for proportion of alleles.