mRNA-seq of individual genetically identical Caenorhabditis elegans adults

Individual phenotypic differences persist even in genetically identical individuals, although separating genetic and environmental causation is difficult or impossible in most organisms. To understand the basis of individual differences in the absence of genetic differences, we measured two quantitative reproductive traits in genetically identical young adult Caenorhabditis elegans roundworms in a shared environment and performed single-individual mRNA-seq on each worm. We identified hundreds of genes for which expression variation was strongly associated with reproductive traits, some of which depended on prior environmental experience and some of which was random. Multiple small sets of genes together were highly predictive of reproductive traits across individuals. Overall design: In the P0 generation, adult C. elegans hermaphrodites were allowed to lay progeny at day 1 or day 3 of adulthood. F1 progeny were then left at 20C throughout their life or shifted to 25C for 8 hours early in life. It was documented when each F1 worm reached egg-laying onset, and 24 hours after egg-laying onset, each F1 young adult worm was collected for individual worm mRNA-seq. The number of progeny laid in the first 24 hours was also measured for each worm.