Abstract. Crossbreeding using exotic bulls have been developed widely in Indonesia. Ychromosome markers have high value for the evaluation of paternal genetic and phylogeny
history. The aim of this study was to investigate the coding sequence polymorphism of SRY
gene in crossbred cattle using Belgian Blue Bull and Wagyu Bull. Polymerase chain reaction
method was used to identify the target sequence 690 bp of SRY gene coding sequences. Then,
direct DNA sequencing with forward primer was performed to identify the single nucleotide
polymorphism (SNP) differences between individual sample. The results of the alignment
coding sequence of SRY gene from four GenBank data, Brahman cross cattle, Belgian Blue
Bull Cross and Wagyu Bull cross revealed that there are 21 SNPs variation. Six SNPs out of 21
SNPs (29%) was synonymous and 15 SNPs out of 21 SNPs (71%) was change the amino acid
(non-synonymous). Eight out of 21 SNPs (38%) were transition mutation and 13 SNPs out of
21 SNPs (62%) were transversion mutation. Crossbred cattle using Brahman cross cow with
Belgian Blue Bull and Wagyu Bull show the SNP at position 1707TàG (transversion
mutation). This SNP change the amino acid from Phe(TTT) to Cys(TGT). Thus, the result can
be used as molecular marker for identifying the paternal lineage of crossbred cattle which
recently develop in Indonesia