Genetic signatures of selection in southern Angolan sheep unravel adaptation for maternal and body conformation traits.

Abstract

Natural and artificial selection in African sheep populations has left distinctive genomic signatures. In southern Angola, pastoralist tribes breed fat-tailed sheep adapted to arid and mesic savannas for protein and cultural purposes. This study aims to identify candidate genes associated with productivity and adaptation in these sheep. We sequenced genomes from Namibe (n = 3) and Cunene (n = 5) and compared them with publicly available data from African and commercial breeds. After quality control, mapping (BWA), and SNP calling (samtools, bcftools) with a minimum 10× coverage and observation in at least 3 reads, ~20 million high-confidence SNPs were identified. Selection signatures were detected using the within-breed Integrated Haplotype Score (iHS) and Pairwise Cross Population Extended Haplotype Homozygosity (XP-EHH) methods (R package rehh), followed by gene set enrichment analysis for biological processes (ShinyGO) and QTL overlap analysis. We identified 65 candidate regions (1,052 kb, 39 genes) through iHS and 88–278 regions using XP-EHH, with an average of 51 genes per population. To identify candidate genes under selection exclusively in southern Angolan sheep, we selected the genes identified by both methods for functional analysis. Thus, resulting in a total of 8 genes, revealing enrichment in 65 biological processes grouped into 11 major GO terms, in which growth hormone regulation, maternal process involved in parturition, and neuromuscular junction development were most represented. QTLs for body weight and bone density frequently overlapped with selected regions. In conclusion, we identified novel gene candidates of selection that are related to relevant biological processes that should be further investigated.