Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep

Abstract

The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (-13910(∗)T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene LCT is responsible for lactase persistence and appears to have been under strong directional selection in the last 5,000 years, evidenced by the widespread occurrence of this allele on an extended haplotype. In Africa and the Middle East, the situation is more complicated and at least three other alleles (-13907(∗)G, rs41525747; -13915(∗)G, rs41380347; -14010(∗)C, rs145946881) in the same LCT enhancer region can cause continued lactase expression. Here we examine the LCT enhancer sequence in a large lactose-tolerance-tested Ethiopian cohort of more than 350 individuals. We show that a further SNP, -14009T>G (ss 820486563), is significantly associated with lactose-digester status, and in vitro functional tests confirm that the -14009(∗)G allele also increases expression of an LCT promoter construct. The derived alleles in the LCT enhancer region are spread through several ethnic groups, and we report a greater genetic diversity in lactose digesters than in nondigesters. By examining flanking markers to control for the effects of mutation and demography, we further describe, from empirical evidence, the signature of a soft selective sweep.

Figure 1

Transfection Experiment Showing the Effect of the −14009^∗G Variant on the Enhancer Activity in Caco-2 Cells Promoter/enhancer constructs containing either the ancestral sequence, the −14009^∗G variant, or the −14010^∗C variant LCT enhancer sequence were transfected into Caco-2 cells together with a CMV-driven β-galactosidase expression plasmid. The cells were harvested and analyzed for luciferase and β-galactosidase activities 9 days after transfection. The luciferase expressions were corrected for transfection efficiency via the β-galactosidase activities. The −14010^∗C construct was used as a positive control. The bar chart shows luciferase expression relative to the “promoter only” construct (lacking the enhancer) and the error bars represent SDs (n = 8). Both the −14009^∗G and −14010^∗C enhancer sequences lead to an increased luciferase expression, which is significantly different from the ancestral sequence (−14009^∗C/−14010^∗G; p = 0.000032 and 0.000038, respectively).

Figure 2

Phased Haplotypes for the Lactase Enhancer and Two Flanking Regions, in Intron 4 of MCM6 and 1 kb Upstream of LCT in a Cohort of 422 Ethiopian Individuals with No Known Shared Ancestry to the Grandparental Level, for whom Full Sequencing Data Were Available Haplotypes that occurred <3 times (n = 21) are omitted. The variable sites are numbered and refer to the following chromosome positions relative LCT; 1, −30210^∗C; 2, −30203ins; 3, −30182^∗G; 4, −29949^∗C; 5, −14010^∗C; 6, −14009^∗G; 7, −13957^∗G; 8, −13915^∗G; 9, −13913^∗C; 10, −13910^∗T; 11, −13907^∗G; 12, −13806^∗G; 13, −13730^∗G; 14, −13603^∗T; 15, −958^∗T; 16, −942del; 17, −875^∗A; 18, −678^∗G. n indicates the number of chromosomes for which that haplotype was inferred. The lettered haplotypes that are shown refer to the haplotypes previously reported by Hollox et al. Those that are shown in bold are the most likely haplotype according to previously reported distributions and examination of additional alleles (unpublished data).

Figure 3

Comparison, in Nondigesters and Digesters, of Nucleotide Diversity π Measured across the Three Sequence Regions Data points show the five ethnic groups tested: Amhara, Tigre, Oromo, Wolayita, Somali, and “other Ethiopians” as a single group. Red horizontal bars show median values. See Table 2 for n values. Abbreviations are as follows: D, digester; ND, nondigester.