Performing RNAi by feeding was an important step that made loss of function analysis truly high throughput. However, the bottleneck of this technology remains the scoring. Different approaches have been used to bypass the tedious task of sitting at the microscope, but many of these are either expensive or of a lower throughput. Here we will present a strategy that is based on how much bacteria is eaten by the worms in function of the time, which is an indication of the worms fitness. The RNAi is performed in liquid, in a 96-well format and analysed using a plate reader with a 600 nm filter. Readings are taken everyday for a week and a curve of OD in function of the time is derived for every experiment. Here, we s how that this method can be used to distinguish between different worm strains, e.g.
lin-15A, and
lin-15B; and detect synthetic interactions e.g. lin-15AB. We have also tested whether the lack of RNAi sensitivity observed in CB4856 (Hawaii) compared to N2 (Bristol) could be detected. This effect has been largely attributed to polymorphisms in
ppw-1. We have used a panel of 12 RNAi feeding clones, and found that Hawaii is rather resilient to most RNAi clones, but not so to
sumo-1. Therefore, we can distinguish Bristol from Hawaii using this assay. Then, using 50 Recombinant Inbred Lines (RILs) between Hawaii and Bristol, we tested which of these are sensitive to RNAi and performed QTL analysis. We have found that even though most can fall into one or the other category a number of RILs are hypersensitive or nearly totally resistant to RNAi. Interestingly, we have found a RIL that phenotypically behaves as Hawaii (i.e. is RNAi insensitive), but is genotypically Bristol for ppw -1. Therefore, we have established a new method that significantly improves the throughput of RNAi in liquid, since reading a 96-well plate takes seconds. Additionally, we demonstrate that RNAi sensitivity is a complex trait that can be quantified using our food consumption assay.