ABSTRACT A concrete way to map genotypes that cause drug resistance phenotypes is by performing a well thought out experimental genetic cross between drug resistance and drug susceptible Plasmodium falciparum strains, isolating recombinant progeny and then using quantitative trait loci mapping to link genotype to phenotype. Three P. falciparum genetic crosses were carried out in splenectomized chimpanzees over 23 years and one of the great achievements of these crosses was the genetic determinant of chloroquine resistance – point mutations in the pfcrt gene. The NIH has now banned chimpanzee research for financial and ethical reasons but we have developed a human-liver chimeric mouse model (the FRG huHep mouse) to replace the chimpanzee for the generation of recombinant progeny from P. falciparum genetic crosses. The FRG mouse lacks the fumaryl acetoacetate hydrolase gene (F designation) and this causes hepatocyte cell death. However, hepatocyte death is controlled with the drug nitisinone. Since only mouse hepatocytes lack fumaryl acetoacetate hydrolase, this enables repopulation of the mouse with human hepatocytes over time with on-off drug use to control the death of mouse hepatocytes and their replacement with human hepatocytes. In close collaboration with the Yecuris Corporation, who creates the FRG huHep mouse, we ensure that the mice we use for our studies have maximal human hepatocyte chimerism and are susceptible to P. falciparum sporozoite infection. Additionally, the mice are able to maintain a human red blood cell (huRBC) population after huRBC infusion and this allows for P. falciparum liver stage-to-blood stage transition in the mouse. Following blood removal, the in vitro expansion of asexual P. falciparum blood stages allows for downstream cloning and then –omics analyses and phenotypic analyses of recombinant progeny. We have already demonstrated our ability to use the FRG huHep/huRBC mouse for the generation of recombinant progeny from experimental crosses and Core A will isolate recombinant progeny from a further eight well conceived experimental genetic crosses between P. falciparum drug resistant and drug susceptible strains as part of this P01. The success of Core A will be aided by RP01 in efforts to maximize the number unique progeny from each cross. Additionally, RP01 will work closely with Core A to determine if bulk segregant analysis coupled with whole genome sequencing can speed the time taken to link genotype to phenotype. The phenotyping of progeny supplied by Core A and downstream mapping of genetic loci responsible for observed phenotypes are integral parts of RP01, RP02 & RP03 and such Core A is the linchpin of this P01. Successful creation of progeny for this P01 will further our understanding of the spread of artemisinin drug resistance and the emergence of piperaquine drug resistance.