Next-gen genetical genomics; RNA-sequencing of a new multi-parent recombinant inbred line population of Caenorhabditis elegans

The combination of recent advances in cost-effective RNA sequencing and a new freshly isolated C. elegans strains from the wild brings forth the next-generation of quantitative genetic approaches. We used RNA-sequencing to measure variation in gene expression and genotype in a panel of 200 recombinant inbred lines derived from a collaborative cross between four wild isolates: JU1511, JU1926, JU1931 and JU1941. The RNA-seq data provided information on two levels. Firstly, by extracting the SNP variation from the RNA-seq data we could create a genetic map. Secondly, by extracting the gene expression variation from the same RNA-seq data we could use expression QTL mapping to the find the regulatory loci causal for the variation in gene expression between the RILs. We found that the crossing design resulted in an increased number of recombination events in the RILs, compared to a standard two parental CB4856 and N2 cross. This increased number of recombination events, genetic markers and local association mapping due to four types of parental types of genetic variation resulted in an increased resolution of eQTLs. Moreover we obtained insights into the divergent regulatory loci and their targets between natural isolates of C. elegans. Here we present several features and promises of the new multi parental recombinant inbred line population.