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Genome-wide association study (GWAS) was used to detect candidate genes affecting economic traits in livestock. GWAS can detect single nucleotide polymorphisms (SNPs) in all chromosome regions. This study aimed to determine the genetic markers for body weight by GWAS in native cattle breeds of Indonesia. The Illumina Bovine 50K BeadChip was used to determine the candidate genes in three mixed-sex Indonesian cattle breeds of Bali (16 animals), Madura (16 animals), and Ongole grade (13 animals). All animals were raised at the Pasuruan Regency, East Java, Indonesia breeding station. The GWAS was performed in pooled sample of animals (45 animals) with the general linear model (GLM) method using SNP markers with minimum allele frequency (MAF) values more than 0.05 by TASSEL 5.0. software. Therefore, the body weight of cattle at 1 to 3 years of age was collected for each animal for computing Manhattan plot graphics. This research found that SUGT1, SF3A3, and DSCAM genes were detected as potential genetic markers for body weight in cattle breeds of Indonesia. The SUGT1 and DSCAM genes were monomorphic in Bali cattle (Bos javanicus). In addition, both genes were significantly associated (P