Genetic structure analysis in several populations of cattle using SNP genotypes

Parameters such as effective population size (Ne), runs of homozygosity (ROH), and inbreeding based on ROH (FROH) can give new insight into the level of genetic diversity for the population under selection. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), Haplotype Block Structure, and runs of homozygosity (ROHs) in several populations of cattle using SNP genotypes. In this study, that the average r(2) decreased with the increasing distance of SNP pairs. A general decrease in Ne can be seen for all four populations, indicating a loss of genetic diversity. The Iranian Holstein had the lowest level of genomic inbreeding at an ROH of 1, 5, 10 Mb, while the French Holstein had the highest. The maximum number of ROH is seen at a distance of less than 1 Mb, and the lowest number of ROH is seen at a distance of 10 Mb. The number of ROH decreases with increasing distance due to the increased recombination rate. This is a concern as an increase in inbreeding leads to a reduction in the effective population size, which was also evident in the study populations.

Automated summary

This research measured the extent of linkage disequilibrium, effective population size, haplotype block structure, and runs of homozygosity in several cattle populations using SNP genotypes. The results showed a decrease in genetic diversity with increasing distance between SNP pairs. The Iranian Holstein population had the lowest level of genomic inbreeding, while the French Holstein population had the highest. The number of runs of homozygosity decreased with increasing distance due to the increased recombination rate. This is concerning as it leads to a reduction in the effective population size.