The genome ofLactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildewBremia lactucae

Abstract

SummaryLactuca salignaL. is a wild relative of cultivated lettuce (Lactuca sativaL.), with which it is partially interfertile. Hybrid progeny suffer from hybrid incompatibilities (HI), resulting in reduced fertility and distorted transmission ratios.Lactuca salignadisplays broad spectrum resistance against lettuce downy mildew caused byBremia lactucaeRegel and is considered a non-host species. This phenomenon of resistance inL. salignais called non-host resistance (NHR). One possible mechanism behind this NHR is through the plant–pathogen interaction triggered by pathogen-recognition receptors, including nucleotide-binding leucin-rich repeats (NLRs) and receptor-like kinases (RLKs). We report a chromosome-level genome assembly ofL. saligna(accession CGN05327), leading to the identification of two large paracentric inversions (>50 Mb) betweenL. salignaandL. sativa. Genome-wide searches delineated the major resistance clusters as regions enriched inNLRs andRLKs. Three of the enriched regions co-locate with previously identified NHR intervals. RNA-seq analysis ofBremiainfected lettuce identified several differentially expressedRLKs in NHR regions. Three tandem wall-associated kinase-encoding genes (WAKs) in the NHR8 interval display particularly high expression changes at an early stage of infection. We proposeRLKs as strong candidate(s) for determinants for the NHR phenotype ofL. saligna.