Geographical genomics of human leukocyte gene expression variation in southern Morocco

• Published in: Nature genetics Vol. 42; no. 1; pp. 62 - 67
• Main Authors: Idaghdour, Youssef, Czika, Wendy, Shianna, Kevin V, Lee, Sang H, Visscher, Peter M, Martin, Hilary C, Miclaus, Kelci, Jadallah, Sami J, Goldstein, David B, Wolfinger, Russell D, Gibson, Greg
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.01.2010; Nature Publishing Group
• Subjects: Agriculture; Analysis; Animal Genetics and Genomics; Arab people; Arabs - genetics; Biological and medical sciences; Biomedical and Life Sciences; Biomedicine; Biosynthesis; Cancer Research; Chronic illnesses; Disease; Diverse techniques; Environmental factors; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling - methods; Gene Function; Genetic aspects; Genetic Predisposition to Disease; Genetic Variation; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genetics, Population; Genome-Wide Association Study; Genomics; Genomics - methods; Geography; Human Genetics; Humans; Leukocytes; Leukocytes - metabolism; Methods; Molecular and cellular biology; Morocco; Physiological aspects; Polymorphism, Single Nucleotide; Population structure; Principal Component Analysis; Morocco; Africa; United States; Human; Gene expression; Leukocyte; Genomics
• ISSN: 1061-4036; 1546-1718; 1546-1718
• DOI: 10.1038/ng.495

Greg Gibson and colleagues report an analysis of gene expression variation in relation to environmental geography and ethnicity in blood leukocyte samples from individuals in rural and urban southern Morocco. The study determined the contributions of geography and ethnicity to associations between genotypes and transcript abundance. Studies of the genetics of gene expression can identify expression SNPs (eSNPs) that explain variation in transcript abundance. Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco. Gene expression differed between pairs of locations for up to a third of all transcripts, with notable enrichment of transcripts involved in ribosomal biosynthesis and oxidative phosphorylation. Robust associations were observed in the leukocyte samples: cis eSNPs ( P < 10 −08 ) were identified for 346 genes, and trans eSNPs ( P < 10 −11 ) for 10 genes. All of these associations were consistent both across the three sample locations and after controlling for ancestry and relatedness. No evidence of large-effect trans -acting mediators of the pervasive environmental influence was found; instead, genetic and environmental factors acted in a largely additive manner.