Analysis of genetic relatedness among Indian cattle (Bos indicus) using genotyping-by-sequencing markers.

Genetic relatedness of 24 animals belonging to seven Indian cattle breeds was studied using high throughput genotyping-by-sequencing (GBS) markers. GBS produced 93.6 million reads with an average of about 3.9 million reads per animal. A total of 107 488 SNPs were identified in these individuals. When only one SNP per read was considered, a total of 60 261 SNPs representing independent reads were identified with an average SNP-to-SNP distance of 45 kb across the bovine reference genome. About 24% of the GBS-SNP markers were more than 100 kb apart. Of these, 58 322 SNPs mapped to autosomes, 1645 to the X chromosome and 28 to the Y chromosome. The average SNP-to-SNP distance on the X chromosome was 91.3 kb, whereas on the Y chromosome it was 1546.4 kb. The minor allele frequency within the Indian cattle varied from 0.103 (Ongole) to 0.177 (Siri), whereas Holstein cattle had the lowest value of 0.089. This is the first application of GBS in cattle of South Asia. The baseline information generated in this study might prompt implementation of GBS in breeding of cattle belonging to this region.