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


RESULTS
After 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).


CONCLUSIONS
The 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.
Gautier
Mathieu
M
INRA, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France. Mathieu.Gautier@jouy.inra.fr
Flori
Laurence
L
Riebler
Andrea
A
Jaffrézic
Florence
F
Laloé
Denis
D
Gut
Ivo
I
Moazami-Goudarzi
Katayoun
K
Foulley
Jean-Louis
JL
D000222:Adaptation, Physiological / Q000235:genetics*; D000354:Africa, Western; D000818:Animals; D001499:Bayes Theorem; D002417:Cattle / Q000033:anatomy & histology / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D006197:Hair / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D012867:Skin / Q000378:metabolism; D049490:Systems Biology; D014329:Tropical Climate