Marker-Assisted Gene Pyramiding and the Reliability of Using SNP Markers Located in the Recombination Suppressed Regions of Sunflower (Helianthus annuus L.)

Rust caused by the fungus Puccinia helianthi and downy mildew (DM) caused by the obligate pathogen Plasmopara halstedii are two of the most globally important sunflower diseases. Resistance to rust and DM is controlled by race-specific single dominant genes. The present study aimed at pyramiding rust resistance genes combined with a DM resistance gene, using molecular markers. Four rust resistant lines, HA-R3 (carrying the R(4) gene), HA-R2 (R(5)), HA-R8 (R(15)), and RHA 397 (R(13b)), were each crossed with a common line, RHA 464, carrying a rust gene R(12) and a DM gene Pl(Arg). An additional cross was made between HA-R8 and RHA 397. Co-dominant simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers linked to the target genes were used to discriminate between homozygotes and heterozygotes in F(2) populations. Five pyramids with different combinations of rust resistance genes were selected in the homozygous condition through marker-assisted selection, and three of them were combined with a DM resistance gene Pl(Arg): R(4)/R(12)/Pl(Arg), R(5)/R(12)/Pl(Arg), R(13b)/R(12)/Pl(Arg), R(15)/R(12), and R(13b)/R(15). The pyramiding lines with the stacking of two rust and one DM genes were resistant to all known races of North American sunflower rust and all known races of the pathogen causing DM, potentially providing multiple and durable resistance to both rust and DM. A cluster of 12 SNP markers spanning a region of 34.5 Mb on chromosome 1, which co-segregate with Pl(Arg), were tested in four populations. Use of those markers, located in a recombination suppressed region in marker selection, is discussed.