The tropically adapted Brahman breed (Bos indicus) was developed from four Indian cattle breeds in the United States, and is now widely used for beef production in harsh environments in Northern Australia, South Africa, Namibia, the United States and Columbia. Identifying mutations in Brahman genomes associated with adaptation, fertility, meat quality and growth rates would facilitate genome selection and therefore accelerate genetic gain for these traits, in both Brahman cattle and composite cattle with Brahman ancestry. With this ultimate aim, fifty Brahman bulls were selected for Illumina sequencing at between 12X and 30X. The bulls were selected using an algorithm that identified fifty bulls that captured the highest proportion of genetic variation in the breed, based on an analysis of an extensive pedigree and a stepwise regression procedure to avoid double counting of ancestral genomes. The 50 bulls selected captured 17% of the variation represented in the pedigree. Among the bulls selected, many were grand sires or great grandsires of very large numbers of bulls now used in the Northern Australian industry. The oldest bull in the sequence data set had a birth year of 1959. Initial analysis of the sequence data revealed the Brahman genomes had a much higher rate of polymorphism than that observed in Bos taurus breeds. This is likely a reflection of a larger ancestral population size for Bos indicus cattle than Bos taurus cattle (pre-domestication), and the fact there was some infusion of Bos taurus breeds into Brahmans during breed formation.
