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

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 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.

Genetic Insight into Disease Resistance Gene Clusters by Using Sequencing-Based Fine Mapping in Sunflower (Helianthus annuus L.)

“…Resistance genes could be ineffective during coevolution with pathogens in which some pathogens can quickly change their genomic components by mutation or recombination when selective pressure is favored [ 82 ]. R gene pyramiding is a commonly accepted, effective method to create durable resistance in crops [ 83 , 84 ]. It is more feasible to combine R 13a , R 13b , R 16 , and Pl 33 with disease resistance genes from other chromosomes or from the same chromosomes but at distal locations due to the increased possibility of linkage.…”

Molecular Breeding Strategy and Challenges Towards Improvement of Downy Mildew Resistance in Cauliflower (Brassica oleracea var. botrytis L.)

“…Similarly, in apple, pyramiding of three resistance QTLs to scab resulted in durable resistance which acted at different stages of fungal infection cycle ( Laloi et al, 2017 ). Marker-assisted gene pyramiding by combining two or more downy mildew resistance genes was performed in several crops such as in grape vine ( Schwander et al, 2012 ; Nascimento-Gavioli et al, 2017 ; Saifert et al, 2018 ) and sunflower ( Qi et al, 2017 ; Qi and Ma, 2019 ). Pyramiding of QTLs with different specificities/broad-spectrum QTLs, and QTLs associated with different resistance mechanism are expected to increase the durability by showing stable levels of resistance in multiple environments.…”

Registration of HA‐DM12, HA‐DM13, and HA‐DM14 oilseed sunflower germplasms with resistance to sunflower downy mildew and rust

“…Gene pyramiding has been successfully used in crops to develop cultivars with multiple and long‐lasting resistance in rice ( Oryza L.), wheat ( Triticum aestivum L.), barley ( Hordeum L.), soybean [ Glycine max (L.) Merr. ], and sunflower (for review see Malav et al., 2016; Qi & Ma, 2020). However, phenotype‐based gene pyramiding is very time consuming and is often impossible due to the lack of pathogen isolates with specific virulent genes.…”