Map saturation and SNP marker development for the rust resistance genes (R 4 , R 5 , R 13a , and R 13b ) in sunflower (Helianthus annuus L.)

Abstract

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, R 5 , R 4 , and R 13 with two alleles R 13a and R 13b , were discovered in sunflower and are promising sources of resistance to rust. R 5 was previously mapped to linkage group (LG) 2, and R 4 and R 13 were mapped to LG13 of the sunflower genome using simple sequence repeat (SSR) markers. The objective of this study was to finely map R 5 , R 4 , R 13a , and R 13b 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 R 5 at a genetic distance of 0.6 and 1.2 cM, respectively. This flanking narrowed the genetic interval containing R 5 from 5.1 to 1.8 cM in length. A total of 69 LG13 SNP markers were analyzed in the R 4 , R 13a , and R 13b populations. In the R 4 consensus map, the gene R 4 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 R 13a and R 13b were identified. R 13a was flanked by SNP markers at genetic distances of 0.4 and 0.2 cM. The SNP SFW00757 co-segregated with R 13b , and another three co-segregating SNPs were 2.4 cM proximal to R 13b . A total of 368 F2 plants from the cross between a resistant BC3F2 plant carrying R 5 with HA-R6 carrying R 13a were first screened by SSR markers to identify “double-resistant” lines. Twelve F2 plants were identified to be homozygous for a combination of R 5 and R 13a , 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.