Genetic Structure of Camelus dromedarius Populations through Genome-Wide RAD Sequencing

The development of cost-effective high-throughput SNP technologies for most of our livestock species has tremendously advanced genomic research for a (sustainable) food production. Despite its worldwide relevance the dromedary (Camelus dromedarius) has been relatively left out from the livestock ”genomic revolution”, until recently with the release of two reference draft genomes assembled at scaffold level. However, no complete chromosome assembled genome and no genome-wide screening tools are yet available. We adopted a double-digest genome-wide Restriction site Associated DNA (ddRAD) sequencing approach, a method that combines traditional DNA shearing via endonucleases with the Illumina Next Generation Sequencing technology to simultaneously genotype tens to hundreds of thousands of single nucleotide polymorphism (SNP) markers in hundreds of individuals. The technology has the major advantages of not requiring substantial prior knowledge of both genome sequence and variability, while achieving per-site and per-individual costs below that of current SNP chip technology. A total of 122 C. dromedarius animals from a wide geographic sampling area, plus 1 C. bactrianus subject, were screened with 200k genomic regions for each animal, at a theoretical coverage of 6X. From an initial set of 88K SNPs, we obtained 53K SNP genotypes after stringent filtering for a minor allele frequency (MAF) of 0.05 and locus missingness of 0.25 using PLINK. ADMIXTURE analysis highlighted clear evidence of C. bactrianus introgression into dromedaries from Kazakhstan and Iran. After removal of admixed animals, consistent phylogeographic clustering was observed using ADMIXTURE, Neighbor-Joining and Neighbor-Net analysis, pointing to a (weak) differentiation between African and Asian dromedaries, with long-range admixture signals also being detected in several populations at various extent. This population genomic study will hopefully open the way to a larger collaborative effort for a more comprehensive characterization of the relationship between genetic and phenotypic diversity in the Camelus dromedarius species.