High-Density Mapping and Candidate Gene Analysis of Pl(18) and Pl(20) in Sunflower by Whole-Genome Resequencing

Downy mildew (DM) is one of the severe biotic threats to sunflower production worldwide. The inciting pathogen, Plasmopara halstedii, could overwinter in the field for years, creating a persistent threat to sunflower. The dominant genes Pl(18) and Pl(20) conferring resistance to known DM races have been previously mapped to 1.5 and 1.8 cM intervals on sunflower chromosomes 2 and 8, respectively. Utilizing a whole-genome resequencing strategy combined with reference sequence-based chromosome walking and high-density mapping in the present study, Pl(18) was placed in a 0.7 cM interval on chromosome 2. A candidate gene HanXRQChr02g0048181 for Pl(18) was identified from the XRQ reference genome and predicted to encode a protein with typical NLR domains for disease resistance. The Pl(20) gene was placed in a 0.2 cM interval on chromosome 8. The putative gene with the NLR domain for Pl(20), HanXRQChr08g0210051, was identified within the Pl(20) interval. SNP markers closely linked to Pl(18) and Pl(20) were evaluated with 96 diverse sunflower lines, and a total of 13 diagnostic markers for Pl(18) and four for Pl(20) were identified. These markers will facilitate to transfer these new genes to elite sunflower lines and to pyramid these genes with broad-spectrum DM resistance in sunflower breeding.