TY - JOUR
T1 - Efficient linkage mapping using exome capture and extreme QTL in schistosome parasites
AU - Chevalier, Frédéric D.
AU - Valentim, Claudia L.L.
AU - LoVerde, Philip T.
AU - Anderson, Timothy JC
N1 - Funding Information:
This study was supported by R01 AI097576-01 and R21 AI096277 grants to T. J.C.A. and WHO HQNTD1206356 grant to P.T.L. The molecular work at TBRI was conducted in facilities constructed with support from Research Facilities Improvement Program Grant C06 RR013556 from the National Center for Research Resources, NIH. The AT&T Genomics Computing Center supercomputing facilities were supported by the AT&T Foundation and the National Center for Research Resources Grant No. S10 RR029392. Biomphalaria glabrata snails were supplied by Fred Lewis (Biomedical Research Institute, Rockville, MD) under NIH-NIAID Contract No. HHSN272201000005I. We thank Matt Berriman at the Wellcome Trust Sanger Institute for providing the repeat masked sequence, Guilherme Oliveira for supplying the LE line, Marina McDew-White, Lai Zhao and Dawn Garcia for library preparation, Roy Garcia for Illumina sequencing, Ian Cheeseman for statistical advice and discussions, and Maria-Celeste Ramirez, Holly Barnes, and Yong Yi from Agilent for the bait design and technical advice.
PY - 2014/7/21
Y1 - 2014/7/21
N2 - Background: 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.Results: 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: Z = 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.Conclusions: 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.
AB - Background: 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.Results: 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: Z = 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.Conclusions: 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.
KW - Exome capture
KW - NGS
KW - Oxamniquine resistance
KW - Schistosoma mansoni
KW - X-QTL
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U2 - 10.1186/1471-2164-15-617
DO - 10.1186/1471-2164-15-617
M3 - Article
C2 - 25048426
AN - SCOPUS:84904883075
SN - 1471-2164
VL - 15
JO - BMC genomics
JF - BMC genomics
IS - 1
M1 - 617
ER -