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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.

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Principal component analysis (PCA) of population structure of P. vivax. Plots show the three first principal components. Each circle or square represents a parasite isolate or strain and the color is assigned according to the geographic origin of parasites: green circles, Granada; red circles, Plácido de Castro; open circles, Porto Velho (all samples from Brazil are represented with circles); pink squares, Cambodia; blue squares, Sri Lanka; light brown squares, Vietnam (all samples from Asia are represented with squares). The strains Salvador I and Belém are denoted by orange and black circles, respectively. The number of circles or squares plotted in the panels does not correspond to the total number of parasite samples analyzed (Additional file 1 Table S1) because some of them had identical haplotypes and, therefore, had identical PCA coordinates. Upper panel, plot of the first two principal components; Lower panel, plot of the first and third principal components.
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Figure 6: Principal component analysis (PCA) of population structure of P. vivax. Plots show the three first principal components. Each circle or square represents a parasite isolate or strain and the color is assigned according to the geographic origin of parasites: green circles, Granada; red circles, Plácido de Castro; open circles, Porto Velho (all samples from Brazil are represented with circles); pink squares, Cambodia; blue squares, Sri Lanka; light brown squares, Vietnam (all samples from Asia are represented with squares). The strains Salvador I and Belém are denoted by orange and black circles, respectively. The number of circles or squares plotted in the panels does not correspond to the total number of parasite samples analyzed (Additional file 1 Table S1) because some of them had identical haplotypes and, therefore, had identical PCA coordinates. Upper panel, plot of the first two principal components; Lower panel, plot of the first and third principal components.

Mentions: Not surprisingly, principal component analysis (PCA) [18] defined two major clusters that reflect the continental origin of samples (Figure 6). The first major cluster, characterized with the first and second principal components (which, together, explain 38% of the variance), comprised all Brazilian samples, the monkey-adapted strains Belém (from Brazil) and Salvador-I (from El Salvador), and two samples from Sri Lanka, whereas the second clusters comprised the remaining Asian samples. By combining the first and third principal components (35% of the variance explained), we observed a greater dispersal of Brazilian samples, a few of which clustered together with Asian samples (Figure 6). We repeated the analysis with a set of 29 SNPs selected to minimize intermarker LD, with quite similar results (Additional file 4 Figure S2), indicating that the observed clustering pattern was not an artifact arising from the interdependence of segregating sites. We also repeated the analysis after excluding the populations with the smallest sample size, Porto Velho and Vietnam, but observed the same clustering pattern, with two isolates from Sri Lanka grouped with those from Granada and Plácido de Castro (data not shown).


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)

Principal component analysis (PCA) of population structure of P. vivax. Plots show the three first principal components. Each circle or square represents a parasite isolate or strain and the color is assigned according to the geographic origin of parasites: green circles, Granada; red circles, Plácido de Castro; open circles, Porto Velho (all samples from Brazil are represented with circles); pink squares, Cambodia; blue squares, Sri Lanka; light brown squares, Vietnam (all samples from Asia are represented with squares). The strains Salvador I and Belém are denoted by orange and black circles, respectively. The number of circles or squares plotted in the panels does not correspond to the total number of parasite samples analyzed (Additional file 1 Table S1) because some of them had identical haplotypes and, therefore, had identical PCA coordinates. Upper panel, plot of the first two principal components; Lower panel, plot of the first and third principal components.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Principal component analysis (PCA) of population structure of P. vivax. Plots show the three first principal components. Each circle or square represents a parasite isolate or strain and the color is assigned according to the geographic origin of parasites: green circles, Granada; red circles, Plácido de Castro; open circles, Porto Velho (all samples from Brazil are represented with circles); pink squares, Cambodia; blue squares, Sri Lanka; light brown squares, Vietnam (all samples from Asia are represented with squares). The strains Salvador I and Belém are denoted by orange and black circles, respectively. The number of circles or squares plotted in the panels does not correspond to the total number of parasite samples analyzed (Additional file 1 Table S1) because some of them had identical haplotypes and, therefore, had identical PCA coordinates. Upper panel, plot of the first two principal components; Lower panel, plot of the first and third principal components.
Mentions: Not surprisingly, principal component analysis (PCA) [18] defined two major clusters that reflect the continental origin of samples (Figure 6). The first major cluster, characterized with the first and second principal components (which, together, explain 38% of the variance), comprised all Brazilian samples, the monkey-adapted strains Belém (from Brazil) and Salvador-I (from El Salvador), and two samples from Sri Lanka, whereas the second clusters comprised the remaining Asian samples. By combining the first and third principal components (35% of the variance explained), we observed a greater dispersal of Brazilian samples, a few of which clustered together with Asian samples (Figure 6). We repeated the analysis with a set of 29 SNPs selected to minimize intermarker LD, with quite similar results (Additional file 4 Figure S2), indicating that the observed clustering pattern was not an artifact arising from the interdependence of segregating sites. We also repeated the analysis after excluding the populations with the smallest sample size, Porto Velho and Vietnam, but observed the same clustering pattern, with two isolates from Sri Lanka grouped with those from Granada and Plácido de Castro (data not shown).

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