Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata

Abstract

High levels of phenotypic variation in resistance appears to be nearly ubiquitous across natural host populations. Molecular processes contributing to this variation in nature are still poorly known, although theory predicts resistance to evolve at specific loci driven by pathogen-imposed selection. Nucleotide-binding leucine-rich repeat (NLR) genes play an important role in pathogen recognition, downstream defense responses and defense signaling. Identifying the natural variation in NLRs has the potential to increase our understanding of how NLR diversity is generated and maintained, and how to manage disease resistance. Here, we sequenced the transcriptomes of five different Plantago lanceolata genotypes when inoculated by the same strain of obligate fungal pathogen Podosphaera plantaginis. A de novo transcriptome assembly of RNA-sequencing data yielded 24,332 gene models with N50 value of 1,329 base pairs and gene space completeness of 66.5%. The gene expression data showed highly varying responses where each plant genotype demonstrated a unique expression profile in response to the pathogen, regardless of the resistance phenotype. Analysis on the conserved NB-ARC domain demonstrated a diverse NLR repertoire in P. lanceolata consistent with the high phenotypic resistance diversity in this species. We find evidence of selection generating diversity at some of the NLR loci. Jointly, our results demonstrate that phenotypic resistance diversity results from a crosstalk between different defense mechanisms. In conclusion, characterizing the architecture of resistance in natural host populations may shed unprecedented light on the potential of evolution to generate variation.

Time Course RNA-seq Reveals Soybean Responses against Root-Lesion Nematode and Resistance Players

“…Different plant genotypes can respond differently to pathogen infection at the genome and transcriptome levels, with genomic polymorphisms and differential gene expression and splicing [ 40 , 41 , 42 ]. This study used RNA-seq data from susceptible and moderately resistant to RLN soybean genotypes infected at different time-points to investigate general responses against the nematode infection, such as differences in gene modulations between genotypes.…”

“…Activation of GO categories related to oxidoreduction reactions and calcium binding in BRS and TMG at 1 dpi suggests pathogen perception and immune response induction in moderately resistant and susceptible genotypes. [ 42 , 50 , 51 ]. Reactivation of oxidative burst genes in BRS at 8 dpi may be due to RLN biology.…”

Patterns of presence-absence variation of NLRs across populations ofSolanum chilenseare clade-dependent and mainly shaped by past demographic history

“…The NB-ARC domain has a high conservation across the plant kingdom (Shao et al ., 2016) and can be confidently resolved (Barragan & Weigel, 2021). This approach has been used successfully in previous NLR studies (Lee & Chae, 2020; Safdari et al ., 2021). A total of 177 NB-ARC loci were identified, of which seven were eliminated because they represented duplicated or overlapping loci (Dataset S2).…”

“…The NB-ARC domain has a high conservation across the plant kingdom 39 and can be confidently resolved 1 . This approach has been successfully used to study the PAV of NLRs in A. thaliana accessions 25 and de novo transcriptome analyses of NLR 40 . This comparison allowed us to identify additional NLRs, but in similar proportions to annotations carried out on the previous genome assembly (Table S1), with a total of 123 (72%) NB-ARCs belonging to the CNL clade, whereas 27 and 20 genes belong to the TNL and RNL clades.…”

Demographic and genetic impacts of powdery mildew in a young oak cohort

“…Studies on the impact of pathogens on plant populations have been extensively performed in an agricultural context, in relation to yield losses (e.g., Savary et al 2019). Studies in natural systems are fewer, and mainly focused on some model systems (Burdon & Thrall 2014), e.g., flax rust (Thrall et al 2012), Arabidopsis pathogens (Creissen et al 2016), anther smut of Silene (Bernasconi et al 2009), Plantago powdery mildew (Laine 2004;Safdari et al 2021). In this study, we aimed to characterize the impacts of powdery mildew on fitness-related traits and genetic diversity during the early life-stages of an oak cohort.…”