PRJNA227358
Schistosoma mansoni: Efficient linkage mapping using exome capture and extreme QTL
Extreme QTL (X-QTL) methods promise to increase the power and simplify logistics of linkage mapping in experimental crosses, because many 1000s of progeny can be analysed, and progeny pools rather than individuals are genotyped. We explored the utility of this method for mapping a drug resistance gene in the human parasitic fluke Schistosoma mansoni. We staged a genetic cross between oxamniquine sensitive and resistant parasites, then between two F1 progeny, to generate multiple F2 progeny. One group of F2s infecting hamsters was treated with oxamniquine, while a second group was left untreated. We used exome capture to reduce the size of the genome (from 363Mb to 15Mb) and exomes from pooled progeny (treated males, untreated males, treated females, untreated females) and the two parent parasites were sequenced to high read depth (mean = 95-366x) and allele frequencies at 14,489 variants compared. We observed dramatic enrichment of alleles from the resistant parent in a small region of chromosome 6 in both treated male and female pools (combined analysis: Z = 11.07, p = 8.74 x10-29). This region contains Ssmp_089320 a gene encoding a sulfotransferase recently implicated in oxamniquine resistance using classical linkage mapping methods. These results (a) demonstrate the utility of exome capture for generating reduced representation libraries in Schistosoma mansoni, and (b) provide proof-of-principle that X-QTL methods can be successfully applied to an important human pathogen. The combination of these methods will simplify analysis of biomedically important traits such as virulence and host specificity in this parasite.