Identification and mapping of new genes for resistance to downy mildew in lettuce

KEY MESSAGE: Eleven new major resistance genes for lettuce downy mildew were introgressed from wild Lactuca species and mapped to small regions in the lettuce genome. ABSTRACT: Downy mildew, caused by the oomycete pathogen Bremia lactucae Regel, is the most important disease of lettuce (Lactuca sativa L.). The most effective method to control this disease is by using resistant cultivars expressing dominant resistance genes (Dm genes). In order to counter changes in pathogen virulence, multiple resistance genes have been introgressed from wild species by repeated backcrosses to cultivated lettuce, resulting in numerous near-isogenic lines (NILs) only differing for small chromosome regions that are associated with resistance. Low-pass, whole genome sequencing of 11 NILs was used to identify the chromosome segments introgressed from the wild donor species. This located the candidate chromosomal positions for resistance genes as well as additional segments. F(2) segregating populations derived from these NILs were used to genetically map the resistance genes to one or two loci in the lettuce reference genome. Precise knowledge of the location of new Dm genes provides the foundation for marker-assisted selection to breed cultivars with multiple genes for resistance to downy mildew. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00122-020-03711-z) contains supplementary material, which is available to authorized users.