Sunflower rust, which is incited by the fungus Puccinia helianthi Schwein., is the most common disease in Australia, Argentina, South Africa, and North America. Three independent genes, R5, R4, and R13 with two alleles R13a and R13b, were discovered in sunflower and are promising sources of resistance to rust. R5 was previously mapped to linkage group (LG) 2, and R4 and R13 were mapped to LG13 of the sunflower genome using simple sequence repeat (SSR) markers. The objective of this study was to finely map R5, R4, R13a, and R13b using newly developed single nucleotide polymorphism (SNP) markers in four F2 populations previously used for SSR mapping. Of the 67 LG2 SNP markers screened, two SNPs, SFW03654 and NSA_000267, flanked R5 at a genetic distance of 0.6 and 1.2 cM, respectively. This flanking narrowed the genetic interval containing R5 from 5.1 to 1.8 cM in length. A total of 69 LG13 SNP markers were analyzed in the R4, R13a, and R13b populations. In the R4 consensus map, the gene R4 was flanked by seven SNP loci; three co-segregating SNPs are on one side (0.7 cM proximal) and four on the other side (0.6 cM distal). Similarly, SNP markers that are tightly linked to both R13a and R13b were identified. R13a was flanked by SNP markers at genetic distances of 0.4 and 0.2 cM. The SNP SFW00757 co-segregated with R13b, and another three co-segregating SNPs were 2.4 cM proximal to R13b. A total of 368 F2 plants from the cross between a resistant BC3F2 plant carrying R5 with HA-R6 carrying R13a were first screened by SSR markers to identify “double-resistant” lines. Twelve F2 plants were identified to be homozygous for a combination of R5 and R13a, which was further confirmed with additional SNP markers developed in the present study. The double-resistant line developed in this study may provide a source of durable resistance to manage rust in confection sunflower production and will help mitigate selection pressure on each gene by the pathogen.
