Footprints of selection in the ancestral admixture of a New World Creole cattle breed

Admixed populations represent attractive biological models to study adaptive selection. Originating from several waves of recent introduction from European (EUT), African (AFT) and zebus (ZEB) cattle, New World Creole cattle allow investigating the response to tropical environmental challenges of these three ancestries. We here provide a detailed assessment of their genetic contributions to the Creole breed from Guadeloupe (CGU). We subsequently look for footprints of selection by combining results from tests based on the extent of haplotype homozygosity and the identification of excess/deficiency of local ancestry. To tackle these issues, 140 CGU individuals and 25 Brahman zebus from Martinique were genotyped at 44 057 SNPs. These data were combined to those available on 23 populations representative of EUT, AFT or ZEB. We found average proportions of 26.1%, 36.0% and 37.9% of EUT, AFT and ZEB ancestries in the CGU genome indicating a higher level of African and zebu ancestries than suggested by historical records. We further identified 23 genomic regions displaying strong signal of selection, most of them being characterized by an excess of ZEB local ancestry. Among the candidate gene underlying these regions, several are associated with reproductive functions (RXFP2, PMEPA1, IGFBP3, KDR, PPP1R8, TBXA2R and SLC7A5) and metabolism (PDE1B and CYP46A1). Finally, two genes (CENTD3 and SAMD12) are involved in cellular signalization of immune response. This study illustrates the relevance of admixed populations to identify footprints of selection by combining several tests straightforward to implement on large data sets.

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