Abstract
SummaryOver the last 40 years, new sunflower downy mildew isolates (Plasmopara halstedii) have overcome major gene resistances in sunflower, requiring the identification of additional and possibly more durable broad‐spectrum resistances. Here, 354 RXLR effectors defined in silico from our new genomic data were classified in a network of 40 connected components sharing conserved protein domains. Among 205 RXLR effector genes encoding conserved proteins in 17 P. halstedii pathotypes of varying virulence, we selected 30 effectors that were expressed during plant infection as potentially essential genes to target broad‐spectrum resistance in sunflower. The transient expression of the 30 core effectors in sunflower and in Nicotiana benthamiana leaves revealed a wide diversity of targeted subcellular compartments, including organelles not so far shown to be targeted by oomycete effectors such as chloroplasts and processing bodies. More than half of the 30 core effectors were able to suppress pattern‐triggered immunity in N. benthamiana, and five of these induced hypersensitive responses (HR) in sunflower broad‐spectrum resistant lines. HR triggered by PhRXLRC01 co‐segregated with Pl22 resistance in F3 populations and both traits localized in 1.7 Mb on chromosome 13 of the sunflower genome. Pl22 resistance was physically mapped on the sunflower genome recently sequenced, unlike all the other downy mildew resistances published so far. PhRXLRC01 and Pl22 are proposed as an avirulence/resistance gene couple not previously described in sunflower. Core effector recognition is a successful strategy to accelerate broad‐spectrum resistance gene identification in complex crop genomes such as sunflower.
Highlights
Downy mildew caused by Plasmopara halstedii is a major disease affecting sunflower (Helianthus annuus L.), the fourth most important oil crop in the world after oil palm, soybean and rapeseed
Metrics comparisons with the published P. halstedii assembly suggest that our assembly is less fragmented, as it is composed of less scaffolds (745 versus 3162), less contigs (3051 versus 7857) with a larger N50 for our genomic contigs (56.4 kb versus 16.2 kb)
Its completeness was assessed using BUSCO 3.0.2 (Waterhouse et al, 2018). This indicated the presence of 87.2% of the conserved genes from the Stramenopiles and Alveolata database at the genome level, and 88.9% at the proteome level, similar to the earlier published proteome (Table S2)
Summary
Downy mildew caused by Plasmopara halstedii is a major disease affecting sunflower (Helianthus annuus L.), the fourth most important oil crop in the world after oil palm, soybean and rapeseed. P. halstedii is an obligate biotrophic oomycete, requiring a living Helianthus host to complete its life cycle and still has not been successfully cultured in vitro. It belongs to the Peronosporales, a devastating oomycetes order including the hemibiotroph genus Phytophthora, which causes late blight, and obligate biotrophs, which cause downy mildews (Fawke et al, 2015). P. halstedii infects sunflower seedlings through the roots, leading eventually to plant death It colonizes the hypocotyl, cotyledons and leaves where sporulation and disease symptoms are observed, seriously affecting yield (Gascuel et al, 2015). More than 20 Pl genes conferring resistance to at least one pathotype of P. halstedii have been
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