Limits...
Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies.

Orjuela-Sánchez P, Karunaweera ND, da Silva-Nunes M, da Silva NS, Scopel KK, Gonçalves RM, Amaratunga C, Sá JM, Socheat D, Fairhust RM, Gunawardena S, Thavakodirasah T, Galapaththy GL, Abeysinghe R, Kawamoto F, Wirth DF, Ferreira MU - BMC Genet. (2010)

Bottom Line: We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed.Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax.We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil.

ABSTRACT

Background: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized.

Results: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for ~40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance.

Conclusion: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

Show MeSH

Related in: MedlinePlus

Population divergence revealed by mutations at the pvmdr-1 locus of P. vivax. The map on the top panel shows pairwise estimates of FST (with 95% confidence intervals derived from bootstrapping in parentheses) for three populations within Brazil, while the lower panel shows pairwise estimates of FST for three populations across South and Southeast Asia. Pie charts represent the population-level frequencies of the Y976F and F1076L mutant alleles of pvmdr-1 as follows: green, wild type; salmon, F1076L single mutant; yellow, Y976F single mutant; dark blue, Y976F-F1076L double mutant.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2910014&req=5

Figure 8: Population divergence revealed by mutations at the pvmdr-1 locus of P. vivax. The map on the top panel shows pairwise estimates of FST (with 95% confidence intervals derived from bootstrapping in parentheses) for three populations within Brazil, while the lower panel shows pairwise estimates of FST for three populations across South and Southeast Asia. Pie charts represent the population-level frequencies of the Y976F and F1076L mutant alleles of pvmdr-1 as follows: green, wild type; salmon, F1076L single mutant; yellow, Y976F single mutant; dark blue, Y976F-F1076L double mutant.

Mentions: We next explored between-population differentiation patterns revealed by loci putatively affected by natural selection. We scored SNPs at two loci, pvcrt-o and pvmdr-1, encoding digestive-vacuole membrane proteins that can be involved in chloroquine (CQ) resistance in P. vivax (Additional file 7 Figure S5). None of the five nonsynonymous SNPs assayed in the pvcrt-o gene was found to segregate in any of the parasite populations examined. In contrast, the six SNP sites analyzed within the pvmdr-1 gene segregated in most populations. Allele frequencies at pvmdr-1 varied markedly between locations, with an overall FST of 0.705. We found very little differentiation between neighboring locations within Brazil (Granada versus Plácido de Castro) and Asia (Cambodia versus Vietnam) (Figure 8), with large differentiation in intercontinental comparisons (Brazil versus Cambodia, FST = 0.746; Brazil versus Vietnam, FST = 0.755; Brazil versus Sri Lanka, FST = 0.528). The low FST value estimated for the comparison between Cambodian and Vietnamese parasites is particularly noteworthy, given the long time interval between dates of sample collection in these sites.


Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies.

Orjuela-Sánchez P, Karunaweera ND, da Silva-Nunes M, da Silva NS, Scopel KK, Gonçalves RM, Amaratunga C, Sá JM, Socheat D, Fairhust RM, Gunawardena S, Thavakodirasah T, Galapaththy GL, Abeysinghe R, Kawamoto F, Wirth DF, Ferreira MU - BMC Genet. (2010)

Population divergence revealed by mutations at the pvmdr-1 locus of P. vivax. The map on the top panel shows pairwise estimates of FST (with 95% confidence intervals derived from bootstrapping in parentheses) for three populations within Brazil, while the lower panel shows pairwise estimates of FST for three populations across South and Southeast Asia. Pie charts represent the population-level frequencies of the Y976F and F1076L mutant alleles of pvmdr-1 as follows: green, wild type; salmon, F1076L single mutant; yellow, Y976F single mutant; dark blue, Y976F-F1076L double mutant.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2910014&req=5

Figure 8: Population divergence revealed by mutations at the pvmdr-1 locus of P. vivax. The map on the top panel shows pairwise estimates of FST (with 95% confidence intervals derived from bootstrapping in parentheses) for three populations within Brazil, while the lower panel shows pairwise estimates of FST for three populations across South and Southeast Asia. Pie charts represent the population-level frequencies of the Y976F and F1076L mutant alleles of pvmdr-1 as follows: green, wild type; salmon, F1076L single mutant; yellow, Y976F single mutant; dark blue, Y976F-F1076L double mutant.
Mentions: We next explored between-population differentiation patterns revealed by loci putatively affected by natural selection. We scored SNPs at two loci, pvcrt-o and pvmdr-1, encoding digestive-vacuole membrane proteins that can be involved in chloroquine (CQ) resistance in P. vivax (Additional file 7 Figure S5). None of the five nonsynonymous SNPs assayed in the pvcrt-o gene was found to segregate in any of the parasite populations examined. In contrast, the six SNP sites analyzed within the pvmdr-1 gene segregated in most populations. Allele frequencies at pvmdr-1 varied markedly between locations, with an overall FST of 0.705. We found very little differentiation between neighboring locations within Brazil (Granada versus Plácido de Castro) and Asia (Cambodia versus Vietnam) (Figure 8), with large differentiation in intercontinental comparisons (Brazil versus Cambodia, FST = 0.746; Brazil versus Vietnam, FST = 0.755; Brazil versus Sri Lanka, FST = 0.528). The low FST value estimated for the comparison between Cambodian and Vietnamese parasites is particularly noteworthy, given the long time interval between dates of sample collection in these sites.

Bottom Line: We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed.Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax.We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil.

ABSTRACT

Background: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized.

Results: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for ~40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance.

Conclusion: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

Show MeSH
Related in: MedlinePlus