A whole genome Bayesian scan for adaptive genetic divergence in West African cattle.

Mathieu Gautier,Ivo Gut,Jean-Louis Foulley,Florence Jaffrézic,Katayoun Moazami-Goudarzi,Laurence Flori,Denis Laloé,Andrea Riebler

doi:10.1186/1471-2164-10-550

Abstract

BackgroundThe recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposure to new pathogens. West African cattle populations thus represent an appealing model to unravel the genome response to adaptation to tropical conditions. The purpose of this study was to identify footprints of adaptive selection at the whole genome level in a newly collected data set comprising 36,320 SNPs genotyped in 9 West African cattle populations.ResultsAfter a detailed analysis of population structure, we performed a scan for SNP differentiation via a previously proposed Bayesian procedure including extensions to improve the detection of loci under selection. Based on these results we identified 53 genomic regions and 42 strong candidate genes. Their physiological functions were mainly related to immune response (MHC region which was found under strong balancing selection, CD79A, CXCR4, DLK1, RFX3, SEMA4A, TICAM1 and TRIM21), nervous system (NEUROD6, OLFM2, MAGI1, SEMA4A and HTR4) and skin and hair properties (EDNRB, TRSP1 and KRTAP8-1).ConclusionThe main possible underlying selective pressures may be related to climatic conditions but also to the host response to pathogens such as Trypanosoma(sp). Overall, these results might open the way towards the identification of important variants involved in adaptation to tropical conditions and in particular to resistance to tropical infectious diseases.

Highlights

The recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposure to new pathogens
SNP polymorphism In total, 437 individuals belonging to 12 different cattle populations, nine of which originating from West Africa (Figure 1), were genotyped for the BovineSNP50 chip assay containing 54,001 SNPs mainly derived from sequences available in European cattle breeds [9]
Marker polymorphism remained clearly lower in West African taurine populations (ND1, ND2, LAG, SOM and BAO), the proportion of SNPs with a MAF < 0.05 being the highest (36%) in LAG which displayed the lowest average heterozygosity (0.118)

Summary

Introduction

The recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposure to new pathogens. Archaeological, historical and anthropological evidence combined with recent genetic data [1] have provided insights into the complex origins of present day West-African cattle diversity. Their wild ancestor Bos primigenius was not native to sub-Saharan Africa, West African cattle populations are representative of both shorthorn (Bos taurus (page number not for citation purposes). BMC Genomics 2009, 10:550 http://www.biomedcentral.com/1471-2164/10/550 brachyceros) and longhorn (Bos taurus longifrons) humpless taurines, humped zebus (Bos indicus) and zebu/taurine hybrid cattle This early suggested that West African cattle has originated from several successive and recent colonization events [2,3]. Zebu cattle spread even more recently over West Africa with movements of pastoralist people such as the Fulani [1]

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