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This study was conducted to investigate genetic variability and to develop the breed-specific DNA markers of Hanwoo (Korean cattle) and to estimate phylogenetic relationships among Hanwoo, Chinese Yanbian cattle and other foreign cattle breeds (Holstein, Angus, Charolais and Hereford) using AFLP markers as a new DNA fingerprinting technique. Genomic DNA was digested with a particular combination of two restriction enzymes with 4 base (Mse I and Taq I) and 6 base (EcoR I and Hind III) recognition sites, ligated to restriction specific adapters and amplified using the selective primer combinations. In the Hanwoo breed, the number of scorable AFLP bands detected per primer combination varied from 37 to 102, with an average of 66.1 using 13 primer combinations. A total of 859 markers were generated and 568 bands were polymorphic (66%). Among the primer combinations, E35/H12, M11/T32, E38/H13 and E32/H11 primer combinations showed a high level of polymorphism with 0.93, 0.89, 0.86 and 0.83, respectively. Therefore, these primer combinations were effective for AFLP analysis of Hanwoo. The level of polymorphism of Hanwoo was similar to that of Chinase Yanbian cattle (65%) and higher than those of other foreign cattle breeds (48% to 55%). E35/H32 and T32/M13 primer combinations generated AFLP fingerprinting showing individual-specific of Hanwoo. M13/H13 and T32/M13 primer combinations produced breed-specific DNA markers when compared AFLP DNA bands between breeds. Three bands (0.84kb, 0.70kb and 0.64kb) identified in M13M13 primer combination and two bands (0.25kb and 0.24kb) identified in T32/M13 primer combination were found to be unique in Hanwoo. Therefore, these AFLP DNA bands could be used as putative breed-specific DNA markers for Hanwoo breed identification. In comparison of genetic distances, Hanwoo was the most closely related to the Chinase Yanbian cattle, followed by the Hereford and Holstein breeds. AFLP fingerprints may be useful for parentage testing, pedigree analysis, genetic variability and relationships and for the development of DNA markers linked to economic traits in Hanwoo.
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