Marker-assisted gene pyramiding and reliability of using SNP markers located in recombination suppressed regions in sunflower (Helianthus annuus L.)

Authors: Qi, Lili; MA, GUOJIA - North Dakota State University

Submitted to: Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/17/2019
Publication Date: 12/20/2019
Citation: Qi, L., Ma, G. 2020. Marker-assisted gene pyramiding and reliability of using SNP markers located in recombination suppressed regions in sunflower (Helianthus annuus L.). Genes. https://doi.org/10.3390/genes11010010.
DOI: https://doi.org/10.3390/genes11010010

Interpretive Summary: Rust and downy mildew (DM) are two of the most devastating diseases in sunflowers. There is a long history for the use of resistant varieties or hybrids to control rust and DM in sunflower production. However, resistance is generally nondurable due to the emergence of new pathotypes that overcome plant resistance. Stacking more than one resistance gene (R gene) in a variety is expected to considerably extend the durability of resistance due to the low probability for a pathogen to overcome multiple resistance genes at the same time. In the present study, we developed three lines by stacking two different rust R genes combined with a DM R gene and two lines stacking only two different rust R genes. Germplasms carrying the two rust and one DM R genes provide resistance to all known races of pathogens causing rust and DM identified in North America. Molecular markers related to both disease R genes have been provided to the sunflower industry, enabling breeders to develop additional hybrids with resistance to multiple pathogens, assuring sustainable sunflower production despite the presence of these two devastating diseases.

Technical Abstract: 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 R4 gene), HA-R2 (R5), HA-R8 (R15), and RHA 397 (R13b), were each crossed with a common line, RHA 464, carrying a rust gene R12 and a DM gene PlArg. 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 F2 populations. Five pyramids with different combinations of rust resistance genes were selected in the homozygous condition by marker-assisted selection, and three of them were combined with a DM resistance gene PlArg: R4/R12/PlArg, R5/R12/PlArg, R13b/R12/PlArg, R15/R12, and R13b/R15. 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 34.51 Mb on chromosome 1, which co-segregate with PlArg, were tested in four populations. Use of those markers, located in a recombination suppressed region in marker selection, is discussed.