Abstract
BackgroundIndigenous 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.ResultsWe 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.ConclusionsOur 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.
Highlights
Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions
Considering the differential distribution of Single-nucleotide polymorphism (SNP) which led to the larger mutual information (MI) values, we suggest that N’Dama has distinctive SNP patterns which may be related to their breed-specific traits including trypanotolerance
Identification of N’Dama-specific missense and nonsense mutations we looked into variations on a protein level by focusing onto non-synonymous SNPs and investigated whether such variations caused any physiological change in N’Dama cattle
Summary
Indigenous cattle in Africa have adapted to various local environments to acquire superior phenotypes that enhance their survival under harsh conditions. Indigenous African cattle which have inhabited geographically isolated region for a long time have been subjected to the environmental pressure. This imposed strong adaptive constraints to African cattle, and led to selection of the fitter individuals to the harsh conditions [2]. Rapid development of large-scale genetic variant inventories has brought attention to the identification of the genes or loci controlling phenotypic traits [6]. This triggered extensive studies on genome-wide analysis which is expected to improve our understanding in the role of unique genetic signatures for adapting environmental conditions. A genome-wide SNP analysis for the small East
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