Open Access Open Badges Research article

Efficient linkage mapping using exome capture and extreme QTL in schistosome parasites

Frédéric D Chevalier12, Claudia LL Valentim12, Philip T LoVerde2 and Timothy JC Anderson1*

Author Affiliations

1 Department of Genetics, Texas Biomedical Research Institute, P.O. Box 760549, 78245 San Antonio, Texas, USA

2 Departments of Biochemistry and Pathology, University of Texas Health Science Center, 78229-3900 San Antonio, Texas, USA

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BMC Genomics 2014, 15:617  doi:10.1186/1471-2164-15-617

Published: 21 July 2014



Identification of parasite genes that underlie traits such as drug resistance and host specificity is challenging using classical linkage mapping approaches. Extreme QTL (X-QTL) methods, originally developed by rodent malaria and yeast researchers, promise to increase the power and simplify logistics of linkage mapping in experimental crosses of schistosomes (or other helminth parasites), because many 1000s of progeny can be analysed, phenotyping is not required, 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 363 Mb to 15 Mb) and exomes from pooled F2 progeny (treated males, untreated males, treated females, untreated females) and the two parent parasites were sequenced to high read depth (mean = 95-366×) 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 drug-treated male and female pools (combined analysis: <a onClick="popup('','MathML',630,470);return false;" target="_blank" href="">View MathML</a> = 11.07, p = 8.74 × 10-29). This region contains Smp_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 helminth. The combination of these methods will simplify linkage analysis of biomedically or biologically important traits in this parasite.

X-QTL; Exome capture; Schistosoma mansoni; Oxamniquine resistance; NGS