Genetic diversity and breed proportions of Indian stud cattle

Genetic diversity and breed proportions of Indian stud cattle India is the world's leading milk producer, however, average milk yield per animal is low. Most of India's cattle milk is produced by indigenous breeds, followed by crossbred cows. Crossbreeding intensified in the 1960s and 70s with a large influx of Holstein Friesian and Jersey bulls, and an increased use of artificial insemination. Based on genotypes generated from the 50K v2 BovineHD BeadChip assay, we analysed the genetic diversity and breed composition of 242 breeding cattle sampled from the BAIF breed herds, including indigenous, exotic dairy, and crossbred animals. We compared these animals to indigenous and animals used in smallholder systems in East Africa. Key findings were: confirmation that Indian Zebu breeds are pure Bos indicus in contrast to African Zebu and Sanga breeds, which are admixtures of Bos indicus and African Bos taurus; as found elsewhere, many apparently pure animals contain some admixture from imported breeds; crossbred animals exhibit a wider range of breed composition than intended, reflecting the lack of pedigree when sampling bull mothers from smallholder farms; breed composition of purebred and crossbred animals can in future be tested using SNP data, and only those meeting the desired composition retained for breeding.