Natural variation in seed coat color in lettuce and wild Lactuca species

Seed coat color is a well described trait in lettuce (Lactuca sativa), varying from black to pale white pigmentation. In this study, we delve into seed coat color variation of several species within the Lactuca genus, encompassing L. sativa and 15 wild varieties, offering broader insights into the diversity of this trait. To capture seed coat color quantitatively, we use grey pixel values from publicly available images, enabling us to measure seed coat color as a continuous trait across the genus. Darker seed coats predominate within the Lactuca genus, with L. sativa displaying a distinctive bimodal distribution of black and white seed coats. Lactuca virosa exhibits the darkest seed coat coloration and less variation, while Lactuca saligna and Lactuca serriola display lighter shades and greater variability. To identify the polymorphic loci underlying the observed variation we performed GWAS on seed coat color in both L. sativa and L. serriola. For L. sativa, we confirmed the one known major QTL linked to black and white seed coat color, which we reproduce in two independent, published genotype collections (n=129, n=138). Within the same locus, we identify additional candidate genes associated with seed coat color. For L. serriola, GWAS yielded several minor QTLs linked to seed coat color, harboring candidate genes predicted to be part of the anthocyanin pathway. These findings highlight the phenotypic diversity present within the broader Lactuca genus and provide insights into the genetic mechanisms governing seed coat coloration in both cultivated lettuce and its wild relatives.