Characterization of Erythrocyte Receptor Polymorphisms in a Malaria Endemic Population in Kilifi, Kenya

Abstract

Malaria is a strong selective force in the human genome, selecting genes for resistance to disease in human populations living in malaria endemic areas. Selection by malaria has generated genetic variations, providing evolutionary driving force mediating polymorphisms such as Glucose-6-Phosphate Dehydrogenase deficiency and sickle-cell anaemia. Genes encoding erythrocyte receptors of Plasmodium falciparum especially the sialoglycoproteins, glycophorins A, B and C, which are the main parasite receptors, have been shown to be under selection, with Single Nucleotide Polymorphisms (SNPs) and exon deletions being detected. This study analyzed SNPs in glycophorins A, B, and C genes in a population living in the malaria endemic area of Kilifi, Kenya. DNA samples were obtained from malaria positive individuals. Regions encompassing extracellular coding domains of the genes were amplified using gene specific primers. These regions are either putative or confirmed binding domains of the malaria parasite. PCR products were cleaned using EXOSAP-IT enzymatic clean-up procedure and sequenced using BigDye v3.1 terminator chemistry. Genes were analyzed separately for polymorphisms using DNASTAR software. Tajima’s D, Fu and Li’s D* and F* statistics were calculated to establish if polymorphisms detected were under selection. Elevated haplotype diversity was detected, with glycophorin A having the highest number of haplotypes. Statistically significant (p<0.05) SNPs were detected in the second and third exons of glycophorin A, and the fourth exon of glycophorin B. A single polymorphism that was not statistically significant (p>0.10) was detected in exon 2 of glycophorin C. Glycophorin A had an excess of intermediate frequency polymorphisms, indicative of balancing selection, while glycophorin B showed significantly higher proportions of low frequency polymorphisms relative to expectation within this population, indicating a population size expansion or purifying selection. The results indicate that the population is under selection, possibly caused by malaria, as the glycophorins are the main receptors for P. falciparum.