The genetic and evolutionary basis of gene expression variation in East Africans

BackgroundMapping of quantitative trait loci (QTL) associated with molecular phenotypes is a powerful approach for identifying the genes and molecular mechanisms underlying human traits and diseases, though most studies have focused on individuals of European descent. While important progress has been made to study a greater diversity of human populations, many groups remain unstudied, particularly among indigenous populations within Africa. To better understand the genetics of gene regulation in East Africans, we perform expression and splicing QTL mapping in whole blood from a cohort of 162 diverse Africans from Ethiopia and Tanzania. We assess replication of these QTLs in cohorts of predominantly European ancestry and identify candidate genes under selection in human populations.ResultsWe find the gene regulatory architecture of African and non-African populations is broadly shared, though there is a considerable amount of variation at individual loci across populations. Comparing our analyses to an equivalently sized cohort of European Americans, we find that QTL mapping in Africans improves the detection of expression QTLs and fine-mapping of causal variation. Integrating our QTL scans with signatures of natural selection, we find several genes related to immunity and metabolism that are highly differentiated between Africans and non-Africans, as well as a gene associated with pigmentation.ConclusionExtending QTL mapping studies beyond European ancestry, particularly to diverse indigenous populations, is vital for a complete understanding of the genetic architecture of human traits and can reveal novel functional variation underlying human traits and disease.

Automated summary

By mapping expression and splicing QTLs in a diverse cohort of 162 Africans, we found that the gene regulatory architecture is broadly shared between African and non-African populations, but individual loci show significant variation across populations. QTL mapping in Africans improves the detection and fine-mapping of expression QTLs compared to European Americans. Integrating QTL scans with signatures of natural selection revealed genes related to immunity, metabolism, and pigmentation that are highly differentiated between Africans and non-Africans.