Genomic diversity and population structure analysis of four geographically distinct Holstein cattle populations using...

Holstein cattle are the world's most widely distributed dairy breed, present in more than 150 countries. Despite their large population and widespread presence, the genomic diversity of Holstein subpopulations across the globe is surprisingly low; therefore, genetic monitoring of these populations, especially in countries that import their genetic material, is crucial. This study aimed to compare the genomic diversity of Iranian Holstein cattle with populations from France, Poland, and Sweden, providing a comprehensive overview of the Holstein breed's genetic structure. In total, 399 Holstein cattle from four geographically distinct countries, namely, Iran ( $n=25$ ), France ( $n=153$ ), Poland ( $n=198$ ), and Sweden ( $n=23$ ), were selected for analysis. Quality control and data filtering were conducted using PLINK 1.9. After quality control, a pruning process was applied to the genomic data, resulting in 10 822 single-nucleotide polymorphism markers for genomic diversity analysis. Due to limitations in the software used for population structure analysis, missing data were imputed using Beagle 5.2. To analyze the genetic structure of the populations, discriminant analysis of principal components (DAPC) and population admixture analysis were performed using the adegenet package in R. Moreover, genomic diversity and distances were assessed using Weir and Cockerham's unbiased differentiation index ( $F_{\mathrm{ST}}$ ) and Nei's genetic distance. The results were visualized using R software. The DAPC analysis revealed minimal genetic differences among the studied populations. Based on the findings, the studied populations from Iran, France, Sweden, and Poland formed a single genetic group with no significant differentiation. These results were further confirmed through $F_{\mathrm{ST}}$ and Nei's genetic distance statistic and population admixture analysis. Overall, a high genetic similarity was found between Iranian Holstein cattle and Holstein cattle populations in other countries, particularly in Europe and North America. This similarity is likely due to the extensive importation of genetic material and the absence of an effective breeding and selection program in Iran. Future studies may investigate the precise influence of these factors on the genomic diversity and population structure of the Holstein breed. The results of this study can be used to explore the structure of the Holstein population. Likewise, they can be beneficial in national breeding schemes and planning for the importation of genetic material (especially semen).