Title: Predation effects on fitness and gene expression: genotype-phenotype mapping in Daphnia.
Fitness is determined by complex interactions between genotype and environment and might differ substantially among individuals of the same species. While genome-wide sequencing has become easier, a common
challenge in identifying the genotypic basis of fitness variation in empirical studies is obtaining fitness measurements in replicated
conditions. The ecological model organism Daphnia is well suited for this aim, since its clonal reproduction mode allows for a repeated testing of given genotypes in different environments. To identify the
molecular basis of response to predation, we exposed 24 different clonal lines from 4 different populations to fish kairomones in a highly replicated setup and measured life history traits; the same traits were measured in the absence of stress. All these clonal lines were genotyped through RNAseq, providing genome-wide SNP data. A genome wide
association approach revealed a few genes correlating with fitness in stressful and stress free conditions. A GxE analysis allowed inferring a limited set of genes where the observed fitness variation results from
the interplay of both drivers. Furthermore, transcripts differentially expressed under predation were identified with an RNAseq experiment on two clonal lines with contrasting life histories. A co expression
network approach allowed identifying modules highly correlated with treatment and fitness-associated traits. With this combination of approaches, we were able to narrow down to key genes correlated with
fitness in D. galeata in contrasting environments, through changes at either the regulatory or the sequence level.