Genetic structure analysis in several populations of cattle using SNP genotypes

Abstract

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 r² 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.

Keywords:

• Linkage disequilibrium
• effective population size
• haplotype block structure
• runs of homozygosity (ROHs)
• cattle

Acknowledgements

We would like to extend thanks to the Ferdows Pars Agricultural Holding Company for giving us access to the animals.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The original data are available upon request to the corresponding authors

Correction Statement

This article has been republished with minor changes. These changes do not impact the academic content of the article.