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For each MAMP variant and each pair-wise combination of the three MAMP variants, we tested a linear regression model that included the presence or absence of each MAMP variant as a factor and the wild-type SGI as the response variable. The effect of the most significant MAMP variant in each combination was compared to a model which included only a term for EF-Tu. The differences between the adjusted R2 values of the two models were computed for each genotype. The distribution of the differences for each genotype is shown in the histogram. We tested the effect of the best-fitting model for each genotype on each MAMP variant. For experiments with multiple variants and MAMP variants, pair-wise comparisons between a pair of variants were then compared to a reference distribution of the differences between a pair of best-fitting models (see figure below). Locus-specific associations were mapped on the A. thaliana genome. For each region associated with a single MAMP or MAMP combination, a scan was performed for all SNPs that displayed an -log10(p-value) above threshold. All associated SNPs within a 500 bp region were consolidated as a single association. We then tested all SNPs within this region for their association with the response to each MAMP variant, with the response modeled as above. SNPs with a -log10(p-value) above threshold were then pooled and mapped. The local-genome association results for each MAMP variant and genotype are provided in the data folder of the repository

We identified variation in the detection of flagellin and elongation factor Tu from natural P. viridiflava strains and tested their ability to induce immune-related symptoms on A. thaliana. Our studies revealed that the strains of P. viridiflava recognize elf18 and flg22 to varying degrees. Interestingly, only strains that do not induce HR can recognize flg22, whereas flg22 variants of HR+ strains are only weakly recognized. We hypothesize that the variation in the perception of flagellin and EF-Tu MAMPs alters the microbial community structure in P. viridiflava strains and vice versa.

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Our bioinformatic analysis suggested two P. syringae strains, A2 and A6, as potential candidates. We tested all 20 strains for the presence of flg22 and elf18 sequences by PCR. We confirmed that all 20 strains harbored an intact *elf18*, 16 out of 20 strains an intact *flg22*, and 13 out of 20 strains the trans-acting factor *elF2K* ( S2 Table ). All strains tested positive for both elf18 and flg22. HR- variants of both MAMPs were used to test SGI in plants expressing the RPS2 gene from A. thaliana ecotype Columbia-0 (Col-0). We included the HR- version of elf18, which does not elicit the HR, to test for the specific contribution of the non-pathogenic host genotype to the phenotypic response. HR- elf18 and HR- flg22 had essentially similar phenotypic responses, strongly suggesting that the genotype is a more important factor than the MAMP variants ( S1 Fig ).

A panel of 113 genotypes of A. thaliana were tested for HR to an HR+ flg22 variant (FLS2-FRKN) in order to determine whether natural variation in the receptor affects the HR response. Unlike HR+ elf18, the HR to FLS2-FRKN was similar to that observed for HR- elf18 in several genotypes ( S3 Table ). We estimated the sensitivity of wild-type plants to the 18 flagellin-derived peptides and measured SGI with the MAMP4 assay. None of the 18 peptides elicited an SGI response. The most similar phenotype to flg22-induced SGI was observed for ESP-1 from P. syringae ( S4 Table ).

Using MAMP4, we estimated SGI induced by flg22 and elf18 in individual genotypes of A. thaliana. The distribution of SGI values among genotypes was not unimodal. In contrast to A. lyrata ( S1 Fig ), A. thaliana genotypes exhibited SGI in response to elf18 and flg22. The majority of genotypes (9 out of 16 tested) responded to both MAMPs ( Fig 4 ). Genotypes that did not exhibit SGI to any of the MAMPs represented a subset of the genotypes that were incapable of inducing the HR ( HR-, Fig 4 ). The 15 (6) genotypes that responded to flg22 (elf18) were omitted from further analyses of their response to the other MAMP class. The same 5 genotypes were affected in SGI by both MAMPs ( Fig 4 ).

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What’s new in MAMP PRO

What's new in MAMP PRO

  • New accessory bar (right click the white bar at the top and select Add to the bar)
  • New presentation of SNP information—presented as a table (click table icon next to SNP and variant position box)
  • Increase in the number of MAMP classes (number of MAMP classes = 101 classes)
  • More options to split the chromosome into bins: Begin, middle and end (for example, N/A for no bin, N/A for no bin)
  • Exact location of SNP (position and physical position)
  • Added MAMP PRO Login feature to site
  • Added permission for anonymous users to download raw data
  • Added option to email a file to the MAMP PRO contact person
  • Added option to choose which response log to use when there are multiple response log files
  • Added function to export information as Comma Separated Values
  • Added function to export information in a variety of file formats

MAMP PRO System Requirements

MAMP PRO System Requirements

  • Mac/Windows: Mac 10.11.6, 10.12.x or Windows 7, 8.1, 10 (32- or 64-bit)

  • Linux: Ubuntu 16.04 LTS 64-bit

  • FreeBSD: FreeBSD 10.3 and higher

  • Sierra: High Sierra 10.13.6 and higher

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