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Plants are sessile organisms that are under constant attack from microbes. They rely on both preformed defenses, and their innate immune system to ward of the microbial pathogens. Preformed defences include for example the cell wall and cuticle, which act as physical barriers to microbial colonization. The plant immune system is composed of surveillance systems that perceive several general microbe elicitors, which allow plants to switch from growth and development into a defense mode, rejecting most potentially harmful microbes. The elicitors are essential structures for pathogen survival and are conserved among pathogens. The conserved microbe-specific molecules, referred to as microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs), are recognized by the plant innate immune systems pattern recognition receptors (PRRs). General elicitors like flagellin (Flg), elongation factor Tu (EF-Tu), peptidoglycan (PGN), lipopolysaccharides (LPS), Ax21 (Activator of XA21-mediated immunity in rice), fungal chitin, and -glucans from oomycetes are recognized by plant surface localized PRRs. Several of the MAMPs and their corresponding PRRs have, in recent years, been identified. This review focuses on the current knowledge regarding important MAMPs from bacteria, fungi, and oomycetes, their structure, the plant PRRs that recognizes them, and how they induce MAMP-triggered immunity (MTI) in plants.

Cultivated individuals of A. thaliana can be classified into two major phenotypic classes based on their responses to MAMPs [ 5 ]. HR- individuals display no response to MAMPs in seedling growth inhibition assays and do not activate defense responses. HR+ individuals elicit a rapid and extreme reduction in their growth rate in response to MAMPs, but are also able to activate defense responses. In our flg22 assays, a high percentage of this population was HR-. If not suppressed during assay development, HR+ individuals frequently form primary leaves, indicating that they are not growth inhibited by the assay.

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A first line of defense against pathogen attack for both plants and animals involves the detection of microbe-associated molecular patterns (MAMPs), followed by the induction of a complex immune response. Plants, like animals, encode several receptors that recognize different MAMPs. While these receptors are thought to function largely redundantly, the physiological responses to different MAMPs can differ in detail. Responses to MAMP exposure evolve quantitatively in natural populations of A. thaliana, perhaps in response to environment specific differences in microbial threat. Here, we sought to determine the extent to which the detection of two canonical MAMPs were evolving redundantly or distinctly within natural populations. Our results reveal negligible correlation in plant growth responses between the bacterial MAMPs EF-Tu and flagellin. Further investigation of the genetic bases of differences in seedling growth inhibition and validation of 11 candidate genes reveal substantial differences in the genetic loci that underlie variation in response to these two MAMPs. Our results indicate that natural variation in MAMP recognition is largely MAMP-specific, indicating an ability to differentially tailor responses to EF-Tu and flagellin in A. thaliana populations.

Given the natural distribution and species-specificity of MAMPs, it is perhaps unsurprising that MAMP-mediated natural variation in plant defense might be redundant. Here we demonstrate that natural variation in the detection of two different classes of MAMP, elf18 and flg22, is highly redundant. Unlike redundant detections of MAMPs, however, duplicated detections of flg22 or elf18 do not produce the same phenotype, but still detect the two MAMPs.

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After screening all the genotypes for elf18- and flg22-induced SGI, we next defined MAMP recognition thresholds for each MAMP per species, which were quantified as minimum MAMP concentration at which SGI becomes apparent ( Fig 3a ). Only genotypes that did not respond to any of the control or all MAMP variants were included, i.e. genotypes that responded to a treatment were excluded. The species included in this study had been cultivated in the past by the scientific community and analyzed for their response to MAMPs and flagellin variants [ 8-14, 23-25 ]. The quantification threshold for the elf18-perception system of 4nM was in accordance with the previous estimate of 5nM [ 10 ]. The quantification threshold for the flg22-perception system of 5nM is more than two-fold higher than the previous estimate of 2nM [ 14 ], which was obtained in the genotypes used here. A possible explanation for this difference is that the MAMP quantification thresholds obtained in our assay varied somewhat by the biological replicate. Our estimates of the quantification thresholds are consistent with previous findings that the flagellin variants used here are more active than the previously used flagellin variants [ 10 ] and shows that the perception of all flagellin variants in our screen is diminished. The perception of MAMPs in Arabidopsis varies substantially between MAMP variants. Four of the genotypes exhibit a response to both elf18 and flg22 (genotypes 6, 11, 12 and 13), three genotypes only respond to elf18 (genotypes 1, 2 and 5) and one only to flg22 (genotype 8). We generated 19 genotypes with unique combinations of flagellin and EF-Tu protein variants and tested those for elf18- and flg22-induced SGI. We found that genotypes with an elf18- and flg22-insensitive response, but having the same protein variants were separated into separate clusters by the two tested MAMP variants ( Fig 3b, S2 Table ) and that several genotypes responded differently to different MAMP variants. These findings indicate that the flagellin/EF-Tu recognition threshold is in addition to, but not reduced compared to, the perception threshold for elf18 and flg22. The variation in SGI observed between different genotypes and with different MAMP variants is consistent with an evolved recognition system with specific recognition thresholds that also are based on molecular evolution of recognition components.

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