Genetic basis of a seasonal life-history polyphenism

Seasonal polyphenisms are common across the animal and plant kingdom yet we understand the explicit interactions between genetics and environment for only a few taxa. Are the genomic regions and their variants associated with the trait the same or different across environments? Is the response to selection shared or different across different "background" selection environments? Offspring type in the sacoglossan sea slug Alderia willowi is a seasonally modulated interaction between genotype and phenotype that results in offspring of wildly different developmental trajectories. In a genome-wide association test I found 41 SNPs associated with offspring type. In an evolve and resequence experiment I found thousands of loci changed in frequency following selection. These loci were partially shared (37%) between low and high salinity. Of the 41 candidate SNPs identified in the GWAS only seven also showed significant allele frequency change across replicates in the selection experiments with four in high salinity, two in low and one in both. This reveals a broad pattern of allele frequency change that is largely unique to the environment in which selection for the same phenotype occurs. The results presented in this paper showcase the ability of phenotypic plasticity to move the phenotype independent of the genotype and thus maintain the polyphenism that is so striking in this species.