Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels

Sterken, M.G.; Gao, Arwen W.; Bos, Jelmi uit de; Creij, J.W. van; Kamble, Rashmi; Snoek, L.B.; Kammenga, J.E.; Houtkooper, Riekelt H.


Metabolic homeostasis is sustained by complex biological networks responding to nutrient availability. Genetic and/or environmental perturbations can lead to metabolic disorders, including obesity and type-2 diabetes. Model organisms are particularly suited to study the interactions between genetic and environmental factors. Thus far, metabolism in C. elegans was often studied at the transcriptional level opposed to the metabolite level. Using a recently developed metabolomics platform, we were able to measure metabolites in C. elegans on a large scale. Here, we aimed to identify the genetic factors controlling metabolism using the nematode Caenorhabditis elegans.
We used a quantitative genetic approach with a C. elegans population consisting of 199 recombinant inbred lines (RILs). We measured fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. We were able to measure the metabolite levels of 56 metabolites. Subsequently, we determined transgression and heritabilities for these metabolites. We found large variation in metabolites levels and for 18 metabolites significant transgression was found, these metabolites were predominantly FAs. The heritability was significant for 51 metabolites and ranged between 32 to 82%. Using a single marker model, we found 36 significant metabolite quantitative trait loci (mQTL). Additionally, a full two-marker screen revealed interacting loci for 6 metabolites. Using introgression lines (ILs) we verified the mQTL for two FA’s, C14:1 and C18:2 mapping to chromosome I and IV respectively. We narrowed down both mQTL to a 1.4 Mbp and a 3.6 Mbp region, respectively. Focussing on the chromosome I mQTL we conducted a prioritized candidate screening, revealing several candidate genes that could affect C14:1 levels across the RILs. By RNAi based knock-down in the N2 strain we could verify that five candidate genes affect C14:1 levels: lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81.
In conclusion, genetic variation affecting metabolite levels in C. elegans proofed to be extensive. Natural variation in C. elegans can play an important role to dissect the mechanisms underlying the complex processes of metabolism in a natural and unbiased manner and allow us to identify factors important for gene-by-environment interactions. Therefore, our study provides the basis to investigate additional interventions, such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis.