Knowledge of population structure is essential for planning and interpreting genomic selection as well as genome-wide association studies. For this purpose, the structure of linkage disequilibrium (LD) and the genetic relationship of three Merino sheep populations, including Australian Merino, Chinese Merino and Merinolandschaf, were investigated. In total, genotypic data included 97 genotyped animals with 50k marker chips. To check the LD trend, r2 between every 2, 5, 10 and 20 adjacent markers and check the genetic relationship, the genomic matrix was considered. The results showed that the degree of linkage disequilibrium between adjacent markers in the three breeds of Australian merino, Chinese Merino, and Merino landscape was 0.142, 0.183, and 0.181, respectively. With the increase in the number of markers, the amount of LD decreased and reached the values of 0.059, 0.103 and 0.103, respectively. The range of genomic relationships for the three mentioned breeds were (-0.010 to 0.521), (-0.149 to 0.344) and (-0.132 to 0.433), respectively. Also, the highest inter-breed genetic relationship was observed between Australian and Chinese Merino (0.24). The results showed that the amount of LD and the average genetic relationship between these breeds allows the use of multi-breed populations for genomic selection programs.

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