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Background  Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. While many studies investigated the adaptation of overall African cattle, genetic characteristics of each breed have been poorly studied.    Results  We performed the comparative genome-wide analysis to assess evidence for subspeciation within species at the genetic level in trypanotolerant N’Dama cattle. We analysed genetic variation patterns in N’Dama from the genomes of 101 cattle breeds including 48 samples of five indigenous African cattle breeds and 53 samples of various commercial breeds. Analysis of SNP variances between cattle breeds using wMI, XP-CLR, and XP-EHH detected genes containing N’Dama-specific genetic variants and their potential associations. Functional annotation analysis revealed that these genes are associated with ossification, neurological and immune system. Particularly, the genes involved in bone formation indicate that local adaptation of N’Dama may engage in skeletal growth as well as immune systems.    Conclusions  Our results imply that N’Dama might have acquired distinct genotypes associated with growth and regulation of regional diseases including trypanosomiasis. Moreover, this study offers significant insights into identifying genetic signatures for natural and artificial selection of diverse African cattle breeds.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3742-2) contains supplementary material, which is available to authorized users.

Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N’Dama