Selection strength and hitchhiking around two anti-malarial resistance genes.

Hdl Handle:
http://hdl.handle.net/10144/66034
Title:
Selection strength and hitchhiking around two anti-malarial resistance genes.
Authors:
Nash, D; Nair, S; Mayxay, M; Newton, P N; Guthmann, J P; Nosten, F; Anderson, T J C
Journal:
Proceedings. Biological sciences / The Royal Society
Abstract:
Neutral mutations may hitchhike to high frequency when they are situated close to sites under positive selection, generating local reductions in genetic diversity. This process is thought to be an important determinant of levels of genomic variation in natural populations. The size of genome regions affected by genetic hitchhiking is expected to be dependent on the strength of selection, but there is little empirical data supporting this prediction. Here, we compare microsatellite variation around two drug resistance genes (chloroquine resistance transporter (pfcrt), chromosome 7, and dihydrofolate reductase (dhfr), chromosome 4) in malaria parasite populations exposed to strong (Thailand) or weak selection (Laos) by anti-malarial drugs. In each population, we examined the point mutations underlying resistance and length variation at 22 (chromosome 4) or 25 (chromosome 7) microsatellite markers across these chromosomes. All parasites from Thailand carried the K76T mutation in pfcrt conferring resistance to chloroquine (CQ) and 2-4 mutations in dhfr conferring resistance to pyrimethamine. By contrast, we found both wild-type and resistant alleles at both genes in Laos. There were dramatic differences in the extent of hitchhiking in the two countries. The size of genome regions affected was smaller in Laos than in Thailand. We observed significant reduction in variation relative to sensitive parasites for 34-64 kb (2-4 cM) in Laos on chromosome 4, compared with 98-137 kb (6-8 cM) in Thailand. Similarly, on chromosome 7, we observed reduced variation for 34-69 kb (2-4 cM) around pfcrt in Laos, but for 195-268 kb (11-16 cM) in Thailand. Reduction in genetic variation was also less extreme in Laos than in Thailand. Most loci were monomorphic in a 12 kb region surrounding both genes on resistant chromosomes from Thailand, whereas in Laos, even loci immediately proximal to selective sites showed some variation on resistant chromosomes. Finally, linkage disequilibrium (LD) decayed more rapidly around resistant pfcrt and dhfr alleles from Laos than from Thailand. These results demonstrate that different realizations of the same selective sweeps may vary considerably in size and shape, in a manner broadly consistent with selection history. From a practical perspective, genomic regions containing resistance genes may be most effectively located by genome-wide association in populations exposed to strong drug selection. However, the lower levels of LD surrounding resistance alleles in populations under weak selection may simplify identification of functional mutations.
Affiliation:
Southwest Foundation for Biomedical Research (SFBR), San Antonio, TX 78245, USA.
Issue Date:
7-Jun-2005
URI:
http://hdl.handle.net/10144/66034
DOI:
10.1098/rspb.2004.3026
PubMed ID:
16024377
Submitted date:
2009-03-13
Type:
Article
Language:
en
ISSN:
0962-8452
Sponsors:
Epicentre
Appears in Collections:
Malaria

Full metadata record

DC FieldValue Language
dc.contributor.authorNash, D-
dc.contributor.authorNair, S-
dc.contributor.authorMayxay, M-
dc.contributor.authorNewton, P N-
dc.contributor.authorGuthmann, J P-
dc.contributor.authorNosten, F-
dc.contributor.authorAnderson, T J C-
dc.date.accessioned2009-04-23T14:48:41Z-
dc.date.available2009-04-23T14:48:41Z-
dc.date.issued2005-06-07-
dc.date.submitted2009-03-13-
dc.identifier.citationSelection strength and hitchhiking around two anti-malarial resistance genes. 2005, 272 (1568):1153-61 Proc. Biol. Sci.en
dc.identifier.issn0962-8452-
dc.identifier.pmid16024377-
dc.identifier.doi10.1098/rspb.2004.3026-
dc.identifier.urihttp://hdl.handle.net/10144/66034-
dc.description.abstractNeutral mutations may hitchhike to high frequency when they are situated close to sites under positive selection, generating local reductions in genetic diversity. This process is thought to be an important determinant of levels of genomic variation in natural populations. The size of genome regions affected by genetic hitchhiking is expected to be dependent on the strength of selection, but there is little empirical data supporting this prediction. Here, we compare microsatellite variation around two drug resistance genes (chloroquine resistance transporter (pfcrt), chromosome 7, and dihydrofolate reductase (dhfr), chromosome 4) in malaria parasite populations exposed to strong (Thailand) or weak selection (Laos) by anti-malarial drugs. In each population, we examined the point mutations underlying resistance and length variation at 22 (chromosome 4) or 25 (chromosome 7) microsatellite markers across these chromosomes. All parasites from Thailand carried the K76T mutation in pfcrt conferring resistance to chloroquine (CQ) and 2-4 mutations in dhfr conferring resistance to pyrimethamine. By contrast, we found both wild-type and resistant alleles at both genes in Laos. There were dramatic differences in the extent of hitchhiking in the two countries. The size of genome regions affected was smaller in Laos than in Thailand. We observed significant reduction in variation relative to sensitive parasites for 34-64 kb (2-4 cM) in Laos on chromosome 4, compared with 98-137 kb (6-8 cM) in Thailand. Similarly, on chromosome 7, we observed reduced variation for 34-69 kb (2-4 cM) around pfcrt in Laos, but for 195-268 kb (11-16 cM) in Thailand. Reduction in genetic variation was also less extreme in Laos than in Thailand. Most loci were monomorphic in a 12 kb region surrounding both genes on resistant chromosomes from Thailand, whereas in Laos, even loci immediately proximal to selective sites showed some variation on resistant chromosomes. Finally, linkage disequilibrium (LD) decayed more rapidly around resistant pfcrt and dhfr alleles from Laos than from Thailand. These results demonstrate that different realizations of the same selective sweeps may vary considerably in size and shape, in a manner broadly consistent with selection history. From a practical perspective, genomic regions containing resistance genes may be most effectively located by genome-wide association in populations exposed to strong drug selection. However, the lower levels of LD surrounding resistance alleles in populations under weak selection may simplify identification of functional mutations.en
dc.description.sponsorshipEpicentreen
dc.language.isoenen
dc.rightsArchived with thanks to Proceedings. Biological sciences / The Royal Societyen
dc.subject.meshAnimalsen
dc.subject.meshAntimalarialsen
dc.subject.meshChloroquineen
dc.subject.meshChromosomesen
dc.subject.meshDrug Resistanceen
dc.subject.meshGenetic Variationen
dc.subject.meshGenotypeen
dc.subject.meshHeterozygote Detectionen
dc.subject.meshLaosen
dc.subject.meshLinkage Disequilibriumen
dc.subject.meshMembrane Proteinsen
dc.subject.meshMembrane Transport Proteinsen
dc.subject.meshMicrosatellite Repeatsen
dc.subject.meshMutationen
dc.subject.meshPlasmodium falciparumen
dc.subject.meshProtozoan Proteinsen
dc.subject.meshPyrimethamineen
dc.subject.meshSelection (Genetics)en
dc.subject.meshTetrahydrofolate Dehydrogenaseen
dc.subject.meshThailanden
dc.titleSelection strength and hitchhiking around two anti-malarial resistance genes.en
dc.typeArticleen
dc.contributor.departmentSouthwest Foundation for Biomedical Research (SFBR), San Antonio, TX 78245, USA.en
dc.identifier.journalProceedings. Biological sciences / The Royal Societyen

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