Genome-wide analysis reveals fine scale population structure in the thin-tailed Sudanese Desert sheep

Abstract

Currently found in North and West Africa, the thin-tailed sheep were the earliest to be introduced into the continent and therefore represent the most primitive sheep in Africa. Although they are categorized into different breeds/populations within which there are several ecotypes and strains, their genetic distinctness remains poorly understood. Here, we genotyped, using the Ovine HD SNP Chip, five ecotypes of the thin-tailed Sudanese Desert sheep to investigate their genetic diversity and structure. We included in our analysis SNP genotypes of four breeds of fat-tailed sheep from China. The analysis revealed moderate to high levels of genetic diversity in the Sudanese Desert sheep but with low levels of genetic differentiation between the ecotypes. Principal component and phylogenetic tree analysis revealed Al-Ahamda ecotype to be genetically distinct. Structure analysis supported the genetic distinction of Al-Hamda ecotype but also identified a number of individuals who were defined by a unique genetic background for 2 ≤ K ≤ 5 values tested. These results demonstrate for the first time the existence of substructure within an African indigenous population of sheep and calls for further studies to determine the possible cause of the fine-scale sub-structure in the breed/population. This would provide valuable but yet unknown insights into the evolutionary dynamics and history of African indigenous livestock populations.