A total of 14 Bos indicus cattle breeds of India (indigenous cattle) were studied to investigate their genetic composition, divergence and admixture. Descriptive statistics on genotype data revealed that Amritmahal, Tharparkar and Kangayam had relatively low expected heterozygosity than other indigenous breeds. Geography and FST were tightly connected. Principal component analysis did not reveal any major substructures within the indigenous breeds; however, more principal components than total number of breeds (30 components were highly significant) were required to explain considerable variability amongst breeds studied. All indigenous breeds except Hariana, Rathi, Khillar and Hallikar had distinct origins in our Admixture analysis. Stable proportions of four populations each in Khillar and Hallikar suggested a distant origin by admixture for these breeds, while Hariana and Rathi showed signs of recent admixture. Patterns of divergence of the selected indigenous breeds of cattle of India have been presented in the paper and compared with other Bos indicus and Bos taurus breeds in other parts of the world by TreeMix analysis. No evidence for migration to or from indigenous breeds of India to other cattle breeds was found. A set of 500 ancestry informative markers for Gir, Sahiwal, Kankrej, Red Sindhi, Holstein Friesian and Jersey breeds were identified and found suitable for tracing ancestries of these purebred as well as their crossbreds. Implications of these studies have been described with emphasis on efficient implementation of breed improvement programs. Keywords: indicus cattle, population structure, admixture, ancestry informative marker
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Challenges - Species Conservation, , 585, 2018
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