Efficient linkage mapping using exome capture and extreme QTL in schistosome parasites
Efficient linkage mapping using exome capture and extreme QTL in schistosome parasites
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DOI：
10.1186/1471-2164-15-617
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发表时间：
2014-07-21
期刊：
影响因子：
4.4
通讯作者：
Anderson, Timothy J. C.
中科院分区：
文献类型：
--
作者：
Chevalier, Frederic D.;Valentim, Claudia L. L.;Anderson, Timothy J. C.
背景资料：利用经典的连锁作图方法来鉴定寄生虫的耐药性和宿主特异性等特征的基础基因是具有挑战性的。极端QTL（X-QTL）方法，最初由啮齿动物疟疾和酵母研究人员开发，承诺增加能力和简化物流连锁图谱在实验杂交的寄生虫（或其他蠕虫寄生虫），因为许多1000后代可以分析，表型是不需要的，和后代池，而不是个人的基因型。我们探讨了这种方法的实用性，在人类寄生吸虫曼氏血吸虫Schistosoma mansoni.Results的耐药基因定位：我们分期之间的遗传杂交？一组感染仓鼠的F2用奥曲喹处理，而第二组不处理。我们使用外显子组捕获来减小基因组的大小（从363 Mb到15 Mb），并且对来自合并的F2后代（处理的雄性、未处理的雄性、处理的雌性、未处理的雌性）和两个亲本寄生虫的外显子组进行测序以达到高读取深度（平均值= 95- 366 x），并比较14，489个变体的等位基因频率。我们观察到在药物处理的雄性和雌性池中，6号染色体的一个小区域中来自抗性亲本的等位基因显著富集（组合分析：Z = 11.07，p = 8.74 x 10（-29））。该区域包含Smp_ 089320一个基因编码的磺基转移酶最近牵连在oxidopquine resistance using classical linkage mapping methods.Conclusions：这些结果（a）表明外显子组捕获的效用产生减少代表性库曼氏血吸虫，和（B）提供的原则证明，X-QTL方法可以成功地应用于一个重要的人类蠕虫。这些方法的结合将简化这种寄生虫的生物医学或生物学重要特征的连锁分析。
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 = 95-366x) 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 drug-treated male and female pools (combined analysis: Z = 11.07, p = 8.74 x 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.