title: Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil.
authors.forename: Pamela
authors.initials: P
authors.lastname: Orjuela-Sánchez
authors.forename: Nadira D
authors.initials: ND
authors.lastname: Karunaweera
authors.forename: Mônica
authors.initials: M
authors.lastname: da Silva-Nunes
authors.forename: Natal S
authors.initials: NS
authors.lastname: da Silva
authors.forename: Kézia K G
authors.initials: KK
authors.lastname: Scopel
authors.forename: Raquel M
authors.initials: RM
authors.lastname: Gonçalves
authors.forename: Chanaki
authors.initials: C
authors.lastname: Amaratunga
authors.forename: Juliana M
authors.initials: JM
authors.lastname: Sá
authors.forename: Duong
authors.initials: D
authors.lastname: Socheat
authors.forename: Rick M
authors.initials: RM
authors.lastname: Fairhust
authors.forename: Sharmini
authors.initials: S
authors.lastname: Gunawardena
authors.forename: Thuraisamy
authors.initials: T
authors.lastname: Thavakodirasah
authors.forename: Gawrie L N
authors.initials: GL
authors.lastname: Galapaththy
authors.forename: Rabindra
authors.initials: R
authors.lastname: Abeysinghe
authors.forename: Fumihiko
authors.initials: F
authors.lastname: Kawamoto
authors.forename: Dyann F
authors.initials: DF
authors.lastname: Wirth
authors.forename: Marcelo U
authors.initials: MU
authors.lastname: Ferreira
mesh_terms: D000818:Animals; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium; D010966:Plasmodium vivax / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic