An integrative analysis of variation in Lactuca.

My PhD project is part of the NWO TTW project “LettuceKnow” (P17-19). My project corresponds to project 1.1B on the Lactuca pangenome. Since the original LettuceKnow proposal describes this project only in minor detail, we describe this project here in more detail. Lettuce (Lactuca sativa) is an important leafy vegetable worldwide and its role in new farming techniques provides the potential to increase the importance of lettuce in our diet. Although lettuce is well suited for modern and future farming systems, several aspects of plant resilience and plant architecture need to be understood at a genetic level for lettuce breeders to advance in the adaptation of lettuce plants to the future: transition from short-lived resistance genes to a durable immune response and adaptation to new environments created by novel farming techniques and climate change. To this end, 500 wild and cultivated lettuce accessions are being extensively phenotyped. For each accession, transcriptome sequencing under 9 different treatments is being performed. Since these 500 accessions belong to four distinct Lactuca species (both wild and cultivated), analysis of the data needs to be set up in a way that we can compare all genetic variation across species boundaries. Here, we propose to integrate and analyse genomic, transcriptomic and phenotypic variation within the genus Lactuca in a pangenomic way. Such a pangenomic approach will reduce reference bias, help characterise variation across species and can thus identify novel and relevant genetic variation underlying important traits, by which new lettuce varieties can be bred that show durable immune responses and are adapted to modern farming techniques. In the long term, we aim to catalyse genomics-based precision breeding in lettuce.