Studying the structure and effective population size of the Holstein, Holstein and their hybrids using whole genome scanning

The purpose of this research was to determine the population structure and effective population size of Najdi, Holstein and their hybrids in the herds of Khuzestan province. For this purpose, the genomic information of 329 cattle samples including 141, 60 and 128 samples from Holstein, mixed and Najdi breeds were used. The samples were genotyped with Illumina SNP30K genomic arrays. Population analysis was done using PCA and plotNJ, and in both methods the populations were somewhat separated. The range of r2 is from 0.150 ± 0.359 in chromosome 26 to 0.244 ± 0.450 in chromosome 20 for the Holstein breed and 0.130 ± 0.319 in chromosome 28 to 0.271 ± 0.462 in chromosome 20 in were mixed livestock, while the highest value of r2 was observed in the Najdi breed from the range of 0.120 ± 0.311 in chromosome 28 to 0.271 ± 0.483 in chromosome 20. The effective size of the populations in the fifth generation for the populations of this study was 45 Najdi heads, 101 mixed heads and 110 Holstein heads. These numbers for Najdi cattle are far from the recommended values for the protection of populations, and this indicates a serious risk of eliminating native Najdi cattle in the near future. Reducing the effective size will increase the sensitivity of this population to the upcoming environmental changes.