A fitness assay for comparing RNAi effects across multiple C. elegans genotypes

BMC Genomics

Methodology Article

Ulrike Klemstein¹  Mark Elvin¹  Gino B Poulin¹  Martin Frejno¹  Laurens B Snoek²  Jan E Kammenga² 

[1] Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, M13 9PT, Manchester, UK;Laboratory of Nematology, Wageningen Universiteit, 6708 PB, Droevendaalsesteeg 1, Wageningen, The Netherlands;

关键词: Quantitative Trait Locus;    Recombinant Inbred Line;    Quantitative Trait Locus Mapping;    Relative Optical Density;    RNAi Treatment;   

DOI  :  10.1186/1471-2164-12-510

 received in 2011-08-11, accepted in 2011-10-17,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundRNAi technology by feeding of E. coli containing dsRNA in C. elegans has significantly contributed to further our understanding of many different fields, including genetics, molecular biology, developmental biology and functional genomics. Most of this research has been carried out in a single genotype or genetic background. However, RNAi effects in one genotype do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation.ResultsHere we present a method that allows for rapidly comparing RNAi effects among diverse genotypes at an improved high throughput rate. It is based on assessing the fitness of a population of worms by measuring the rate at which E. coli is consumed. Critically, we demonstrate the analytical power of this method by QTL mapping the loss of RNAi sensitivity (in the germline) in a recombinant inbred population derived from a cross between Bristol and a natural isolate from Hawaii. Hawaii has lost RNAi sensitivity in the germline. We found that polymorphisms in ppw-1 contribute to this loss of RNAi sensitivity, but that other loci are also likely to be important.ConclusionsIn summary, we have established a fast method that improves the throughput of RNAi in liquid, that generates quantitative data, that is easy to implement in most laboratories, and importantly that enables QTL mapping using RNAi.

【 授权许可】

Unknown   
© Elvin et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.