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Background  Peranakan Ongole (PO) is a major Indonesian  Bos indicus  breed that derives from animals imported from India in the late 19 th  century. Early imports were followed by hybridization with the  Bos javanicus  subspecies of cattle. Here, we used genomic data to partition the ancestry components of PO cattle and map loci implicated in birth weight.    Results  We found that  B. javanicus  contributes about 6-7 % to the average breed composition of PO cattle. Only two nearly fixed  B. javanicus  haplotypes were identified, suggesting that most of the  B. javanicus  variants are segregating under drift or by the action of balancing selection. The zebu component of the PO genome was estimated to derive from at least two distinct ancestral pools. Additionally, well-known loci underlying body size in other beef cattle breeds, such as the  PLAG1  region on chromosome 14, were found to also affect birth weight in PO cattle.    Conclusions  This study is the first attempt to characterize PO at the genome level, and contributes evidence of successful, stabilized  B. indicus  x  B. javanicus  hybridization. Additionally, previously described loci implicated in body size in worldwide beef cattle breeds also affect birth weight in PO cattle.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-015-0229-5) contains supplementary material, which is available to authorized users.

Evidence of Bos javanicus x Bos indicus hybridization and major QTLs for birth weight in Indonesian Peranakan Ongole cattle