Genetic Diversity and Population Structure of Saudi Arabia

Saudi Arabia is the largest country in the Arabian Peninsula, yet its genetic diversity and population structure has been little studied. This project has used analysis of forensic DNA markers, typed both conventionally (by capillary electrophoresis, CE) and by massively parallel sequencing (MPS), to characterise its genetic diversity. Ychromosomal haplotypes based on 27 STRs (short tandem repeats) were generated in 597 unrelated Saudi males, classified into five geographical sub-regions. This showed marked population structure with low diversity in the Central and Northern regions, and high diversity in the East and West. Haplogroup J1 was very predominant and showed signals of recent expansion. Comparing geographically-matched males recruited in the UK with those recruited in Saudi Arabia showed significant haplotype differences, pointing to social structure. Variation in 21 autosomal STRs was also investigated. As in the Y chromosome study, this revealed population structure, but with a different geographical pattern. Heterozygote deficiency was observed at nearly all loci, probably as a consequence of high levels of consanguineous marriage. MPS analysis (via the Verogen ForenSeq™ DNA Signature Prep Kit) of 27 autosomal STRs and 91 identity-informative single nucleotide polymorphisms (iiSNPs) revealed sequence variation that reduced both the STR-based and iiSNP-based random match probabilities. As with the autosomal CE data, evidence of consanguinity was apparent from both marker types. A global comparison showed that the Saudi sample was typical of Middle Eastern populations, with higher inbreeding than is seen in most European, African and Central/South Asian populations. Y-STR and X-STR sequence data from the same experiments revealed sequence variation in both types of markers. A population-level comparison of the Saudi Arabian X-STRs with a global sample demonstrated affinity with other Middle Eastern populations. This study has revealed population structure and the influence of consanguinity in Saudi Arabia, and provides valuable reference datasets for forensic analysis.