Abstract
Genetic crosses are most powerful for linkage analysis when progeny numbers are high, parental alleles segregate evenly and numbers of inbred progeny are minimized. We previously developed a novel genetic crossing platform for the human malaria parasite Plasmodium falciparum, an obligately sexual, hermaphroditic protozoan, using mice carrying human hepatocytes (the human liver-chimeric FRG NOD huHep mouse) as the vertebrate host. We report on two genetic crosses—(1) an allopatric cross between a laboratory-adapted parasite (NF54) of African origin and a recently patient-derived Asian parasite, and (2) a sympatric cross between two recently patient-derived Asian parasites. We generated 144 unique recombinant clones from the two crosses, doubling the number of unique recombinant progeny generated in the previous 30 years. The allopatric African/Asian cross has minimal levels of inbreeding and extreme segregation distortion, while in the sympatric Asian cross, inbred progeny predominate and parental alleles segregate evenly. Using simulations, we demonstrate that these progeny provide the power to map small-effect mutations and epistatic interactions. The segregation distortion in the allopatric cross slightly erodes power to detect linkage in several genome regions. We greatly increase the power and the precision to map biomedically important traits with these new large progeny panels.
Highlights
Genetic crosses are most powerful for linkage analysis when progeny numbers are high, parental alleles segregate evenly and numbers of inbred progeny are minimized
We demonstrate that targeted crosses between clinical isolates can be rapidly generated and outperform all previous crosses in their size, mapping power, and precision
The uncloned bulk populations from these controlled genetic crosses provide a powerful and complimentary resource for bulk selection analysis/ linkage group selection (BSA/LGS) to identify loci linked to phenotypes of interest as demonstrated in rodent malaria[38,39,40,41,42] and more recently in P. falciparum[24,43]
Summary
Genetic crosses are most powerful for linkage analysis when progeny numbers are high, parental alleles segregate evenly and numbers of inbred progeny are minimized. To use genetic mapping to elucidate the genetic architecture of emerging drug resistance in P. falciparum we need to be able to rapidly create genetic crosses with large numbers of progeny from recent field isolated parasites which exemplify relevant clinical traits such as drug resistance. We report on the production of large numbers of unique recombinant progeny utilizing human liver-chimeric FRG huHep mice infused with human red blood cells These mice were previously reported as an option for P. falciparum genetic crosses[23], until now they have failed to produce more progeny than historic crosses. We report on two genetic crosses that were carried out using recent clinically derived P. falciparum isolates with emerging drug resistance phenotypes This effort was aided by a progeny characterization bioinformatics framework that filters single nucleotide polymorphisms (SNP) and identifies clonal unique recombinant progeny. We show that while segregation distortion (SD) can locally reduce power we are still able to detect major effect loci in our expanded progeny panels
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