title: Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii.
abstract: The rodent malaria parasite Plasmodium yoelii is an important model for studying malaria immunity and pathogenesis. One approach for studying malaria disease phenotypes is genetic mapping, which requires typing a large number of genetic markers from multiple parasite strains and/or progeny from genetic crosses. Hundreds of microsatellite (MS) markers have been developed to genotype the P. yoelii genome; however, typing a large number of MS markers can be labor intensive, time consuming, and expensive. Thus, development of high-throughput genotyping tools such as DNA microarrays that enable rapid and accurate large-scale genotyping of the malaria parasite will be highly desirable. In this study, we sequenced the genomes of two P. yoelii strains (33X and N67) and obtained a large number of single nucleotide polymorphisms (SNPs). Based on the SNPs obtained, we designed sets of oligonucleotide probes to develop a microarray that could interrogate ∼11,000 SNPs across the 14 chromosomes of the parasite in a single hybridization. Results from hybridizations of DNA samples of five P. yoelii strains or cloned lines (17XNL, YM, 33X, N67 and N67C) and two progeny from a genetic cross (N67×17XNL) to the microarray showed that the array had a high call rate (∼97%) and accuracy (99.9%) in calling SNPs, providing a simple and reliable tool for typing the P. yoelii genome. Our data show that the P. yoelii genome is highly polymorphic, although isogenic pairs of parasites were also detected. Additionally, our results indicate that the 33X parasite is a progeny of 17XNL (or YM) and an unknown parasite. The highly accurate and reliable microarray developed in this study will greatly facilitate our ability to study the genetic basis of important traits and the disease it causes.
authors.affiliation: Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Sethu C
authors.initials: SC
authors.lastname: Nair
authors.affiliation: Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
authors.forename: Sittiporn
authors.initials: S
authors.lastname: Pattaradilokrat
authors.affiliation: Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Martine M
authors.initials: MM
authors.lastname: Zilversmit
authors.affiliation: Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Dommer
authors.affiliation: Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Vijayaraj
authors.initials: V
authors.lastname: Nagarajan
authors.affiliation: The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
authors.forename: Melissa T
authors.initials: MT
authors.lastname: Stephens
authors.affiliation: Metabolism Branch, National Cancer Institutes, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Wenming
authors.initials: W
authors.lastname: Xiao
authors.affiliation: The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Tan
authors.affiliation: Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: xsu@niaid.nih.gov.
authors.forename: Xin-Zhuan
authors.initials: XZ
authors.lastname: Su
mesh_terms: D016054:DNA, Protozoan / Q000235:genetics; D018503:Genome, Protozoan; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D057166:High-Throughput Screening Assays / Q000379:methods; D046228:Microarray Analysis / Q000379:methods*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010274:Parasitology / Q000379:methods; D010967:Plasmodium yoelii / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D016054:DNA, Protozoan
keywords: Genome sequencing; High-throughput genotyping; Malaria; Rodent; Single nucleotide polymorphism