Linkage disequilibrium between two chromosomally distinct loci associated with increased resistance to chloroquine in Plasmodium falciparum

Chloroquine-resistance in Plasmodium falciparum is associated with polymorp hisms in a locus on or near the cg2 gene on chromosome 7, and in the pfmdr1 gene on chromosome 5. In this study we typed P. falciparum DNA from uncomp licated malaria cases in The Gambia in 1990, 1995 and 1996 for size polymor phism in the omega repeat of cg2, for sequence polymorphisms in pfmdr1 at c odons 86 and 184, in dhfr at codon 108 and in the msp2 gene. Chloroquine se nsitivity tests were conducted in vitro. A significant but incomplete assoc iation was found between the presence of the cg2 Dd2-like omega repeat size polymorphism and in vitro resistance, and between the tyr-86 allele of pfm dr1 and in vitro resistance. Furthermore there was strong linkage disequili brium between the pfmdr1 asn-86 allele and the cg2 not Dd2-like omega repea t allele located on different chromosomes. In contrast, no linkage disequil ibrium was found between these alleles and either the dhfr ser-108 allele o r the msp2 IC sequence polymorphism. No significant linkage was measured be tween pfmdr1 asn-86 and phe-184 although these loci are separated only by 2 96 base pairs. Our results suggest that genetic elements linked to the cg2 and the pfmdr1 genes are important determinants of chloroquine resistance. It can be concluded that the observed linkage disequilibrium is maintained epistatically through selection by chloroquine.