Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map

Abstract Molluscs are a highly speciose phylum that exhibit an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail, Cepaea nemoralis, for which classical genetic studies have identified around nine loci that control shell colour variation, several of which are physically linked and inherited together as a ‘supergene’. As a first step towards characterising and identifying the loci underlying the polymorphism, we used whole genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then used trait mapping to identify 95% confidence intervals for the chromosomal regions that contain the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The final linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as identification of candidate loci within the supergene and the mid-banding phenotype.