Abstract
BackgroundThe history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems.ResultsWe analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds.ConclusionsOur findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent.
Highlights
The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity
We report for the first time the genome characterization of five indigenous African cattle breeds which are representatives of the cattle diversity of the continent: N’Dama, which belong a group of West African taurine with tolerances to multiple infectious diseases; Ankole, which represents African sanga the intermediate crossbreed between zebu and taurine cattle populations, with large and distinctive horns and coat color selected by human; Boran and Kenana, two East African zebu, with beef and dairy characteristics, respectively; Ogaden, an East African zebu living in a hot and dry environment
The comparative genome-wide analysis with three European and one Asian commercial cattle breed across African cattle types allows us to identify the unique genome response of African cattle breed to tropical challenges
Summary
We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. We identify signatures of selection including genes and/ or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds
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