Whole genome sequencing reveals signals of adaptive admixture in Creole cattle

Abstract

The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock.

Figure 1

Genetic diversity and population structure and genetic diversity of Creole cattle from Guadeloupe (GUA). Population names and locations are described in supplementary table S13 (supplementary material). (a) Genome-wide distribution of nucleotide diversity (Pi) estimated in 1-Mb nonoverlapping window. AFI African indicine, AFT African taurine (b) Principal component analysis, PC 1 against PC 2. CRIO Criollo (Colombian and venezuelan cattle breeds), IBER Spanish breeds, AMASI American-Australian and Asian indicine breeds (c) Results of admixture analysis for K 3–5.

Figure 2

Manhattan plots showing the results of Extended Haplotype Homozygisty-based tests. (a) Rsb test AFT versus GUA cattle. (b) Rsb test EUT versus GUA cattle (c) Rsb test IND versus GUA cattle. (d) XP-EHH test AFT versus GUA cattle. (e) XP-EHH test EUT versus GUA cattle (f) XP-EHH test IND versus GUA cattle. (g) iHS test for GUA cattle. Horizontal dashed lines mark the significance threshold applied to detect the outlier SNPs (− log10 (p value) = 6).

Figure 3

Nucleotide diversity and Pairwise Fst values [EUT vs. GUA (blue) and AFT vs. GUA (green)] calculated for each 50-kb window around the candidate regions on chromosomes 2 and 5. (a) Nucleotide diversity on chromosome 2. (b) Nucleotide diversity on chromosome 5. (c) Pairwise Fst values between GUA and EUT on chromosome 2. (d) Pairwise Fst values between GUA and EUT on chromosome 5. (e) Pairwise Fst values between GUA and AFT on chromosome 2. (f) Pairwise Fst values between GUA and AFT on chromosome 5.