Artemisinin resistance genetics. A, Genome-wide scans of LGS of AS-30CQ × AJ backcross (under ART treatment) with quantitation of parental alleles by pyrosequencing . Comparative Index (AJ) is the proportion of alleles in the population from sensitive parent AJ, after drug-selection, relative to the proportion measured in untreated hosts. Absence of selection would be represented by a Comparative Index of 1. Genome position indicates the mapped position (kb) of ~90 markers in the genome of P. chabaudi (Additional File 1). Data points (open green squares) are each mean of 3 independent determinations. Horizontal line (blue) indicates the threshold for rejecting null hypothesis in simulation analysis (p < 0.05, Additional File 2). Positions of mutations appearing in both AS-30CQ and AS-15MF as defined by Solexa genome re-sequencing are indicated at the bottom (x = point mutation; circle = indel). Note one sole point mutation on chr02 (ubp1) and one point mutation on chr07 (dhfr). Chromosome numbers are indicated (top). B, Position of ART-selection valley on chr02 as determined from two independent LGS scans of two genetic crosses (AS-30CQ × AJ, red; AS-15MF, × AJ blue) and the position of the mutated gene (ubp1, PCHAS_020720, green arrow). Pyrosequencing assays shown for whole chromosome (pcpfxx-yyyy, denotes P. chabaudi-specific assays at loci homologous to P. falciparum chrxx, location yyyy Kbp).