High-Density Mapping and Candidate Gene Analysis of Pl18 and Pl20 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 Pl₁₈ and Pl₂₀ 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, Pl₁₈ was placed in a 0.7 cM interval on chromosome 2. A candidate gene HanXRQChr02g0048181 for Pl₁₈ was identified from the XRQ reference genome and predicted to encode a protein with typical NLR domains for disease resistance. The Pl₂₀ gene was placed in a 0.2 cM interval on chromosome 8. The putative gene with the NLR domain for Pl₂₀, HanXRQChr08g0210051, was identified within the Pl₂₀ interval. SNP markers closely linked to Pl₁₈ and Pl₂₀ were evaluated with 96 diverse sunflower lines, and a total of 13 diagnostic markers for Pl₁₈ and four for Pl₂₀ 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.