Assessment of Mutation Drift Equilibrium and the Occurrence of a Recent Genetic Bottleneck in South Indian Zebu Cattle

SIMPLE SUMMARY: This study was conducted on eight Indian zebu breeds with an objective to reveal any cryptic genetic bottlenecks in the population. The alarming reduction in the effective population size of these breeds was the major reason for conducting this study. Genotyping of 27 FAO/ISAG-recommended microsatellite markers and further statistical analysis using allele frequency data under three different models of mutation revealed the absence of recent genetic bottlenecks in any of the populations under study. The results from the qualitative test of mode shift distortion were in accordance with the above findings. Even though the results of the present study indicated little or no critical loss of rare alleles in any of the breeds understudy, the chances of this happening cannot be completely ignored. One of the plausible explanations for this scenario could be the potential gene flow from commercial taurine cattle through indiscriminate crossbreeding in the native tract of these breeds. Thus, we here emphasize the need of further initiatives for improving selective breeding practices in order to conserve and effectively utilize the existing South Indian zebu cattle genetic diversity. ABSTRACT: During the last few decades, the effective population size of indigenous zebu cattle breeds has declined drastically, resulting in the classification of some of them into the vulnerable, endangered, or critically endangered category. Drastic reductions in the effective size of a population may result in genetic bottlenecks and can affect within-breed genetic variability and its viability. The present study was undertaken with the objective of evaluating South Indian zebu cattle populations for mutation drift equilibrium and to detect the occurrence of recent genetic bottleneck events. A total of 293 cattle from eight indigenous breeds were genotyped at 27 FAO/ISAG-recommended microsatellite marker loci. Three different statistical tests, viz., the sign test, standardized differences test, and Wilcoxon sign rank test were performed using allele frequency data to detect loci with heterozygosity excess under the infinite alleles, stepwise, and two-phase mutation models. Under the infinite alleles model, the observed number of loci with heterozygosity excess (He > Heq) ranged between 10 and 19 among the investigated cattle breeds. However, the observed heterozygosity excess was not statistically significant (p > 0.05) in any of the studied breeds. Similarly, the standardized differences test and Wilcoxon sign rank test revealed no concrete evidence for the occurrence of a recent genetic bottleneck in South Indian zebu cattle breeds. The qualitative test for mode-shift distortion revealed a normal L-shaped distribution of allele frequencies, suggesting a lack of evidence for the loss of low-frequency alleles in all the investigated South Indian zebu cattle breeds.