Phenotypic variation across Lactuca species and genome-wide association analysis in L. sativa and L. serriola

Abstract Crop wild relatives provide valuable insights into trait diversity and the genetic basis of agronomic traits. In the genus Lactuca , domesticated lettuce ( Lactuca sativa ) and its wild progenitor, Lactuca serriola , have been extensively studied, yet broader wild species remain underrepresented. Here, we present a phenotypic dataset of 550 Lactuca accessions, including 20 wild relatives, capturing plant morphology, pigmentation, and pathogen resistance traits derived from images and genetic resource collections. To investigate the genetic basis of these traits, we used a jointly processed SNP set for L. sativa and L. serriola , applying an iterative two-step GWAS approach, enabling the dissection of multiple loci per trait. We identified both known and novel QTLs associated with anthocyanin accumulation, leaf morphology, and pathogen resistance in L. sativa and L. serriola . Importantly, we identified L. serriola -specific QTLs undetected in L. sativa , revealing unique genetic architectures underlying anthocyanin biosynthesis and leaf morphology in the wild progenitor. These findings expand the knowledge of Lactuca beyond cultivated varieties, highlighting the potential of wild species for breeding applications. Our dataset and results provide a foundation for further investigations into the evolutionary and agronomic significance of Lactuca diversity.