Genetic basis of thermal plasticity variation in Drosophila melanogaster body size

Body size is a quantitative trait that is closely associated to fitness and under the control of both genetic and environmental factors. While developmental plasticity for this and other traits is heritable and under selection, little is known about the genetic basis for variation in plasticity that can provide the raw material for its evolution. We quantified genetic variation for body size plasticity in Drosophila melanogaster by measuring thorax and abdomen length of females reared at two temperatures from a panel representing naturally segregating alleles, the Drosophila Genetic Reference Panel (DGRP). We found variation between genotypes for the levels and direction of thermal plasticity in size of both body parts. We then used a Genome-Wide Association Study (GWAS) approach to unravel the genetic basis of inter-genotype variation in body size plasticity, and used different approaches to validate selected QTLs and to explore potential pleiotropic effects. We found mostly \"private QTLs\", with little overlap between the candidate loci underlying variation in plasticity for thorax versus abdomen size, for different properties of the plastic response, and for size versus size plasticity. We also found that the putative functions of plasticity QTLs were diverse and that alleles for higher plasticity were found at lower frequencies in the target population. Importantly, a number of our plasticity QTLs have been targets of selection in other populations. Our data sheds light onto the genetic basis of inter-genotype variation in size plasticity that is necessary for its evolution.\n\nSignificance StatementThe environmental conditions under which development takes place can affect developmental outcomes and lead to the production of phenotypes adjusted to the environment adults will live in. This developmental plasticity, which can help organisms cope with environmental heterogeneity, is heritable and under selection. Plasticity can itself evolve, a process that will be partly dependent on the available genetic variation for this trait. Using a wild-derived D. melanogaster panel, we identified DNA sequence variants associated to variation in thermal plasticity for body size. We found that these variants correspond to a diverse set of gene functions. Furthermore, their effects differ between body parts and properties of the thermal response, which can, therefore, evolve independently. Our results shed new light onto a number of key questions about the long discussed genes for plasticity.