DOI: 10.5061/dryad.h70rxwdkx
title: Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1

description: Activation of plant pattern-triggered immunity (PTI) relies on the
 recognition of microbe-derived structures, termed patterns, through
 plant-encoded surface-resident pattern recognition receptors (PRRs). We
 show that proteobacterial translation initiation factor 1 (IF1) triggers
 PTI in Arabidopsis thaliana and related Brassicaceae species. Unlike for
 most other immunogenic patterns, IF1 elicitor activity cannot be assigned
 to a small peptide epitope, suggesting that tertiary fold features are
 required for IF1 receptor activation. We have deployed natural variation
 in IF1 sensitivity to identify Arabidopsis leucine-rich repeat (LRR)
 receptor-like protein 32 (RLP32) as IF1 receptor using a restriction
 site-associated DNA sequencing approach. RLP32 confers IF1 sensitivity to
 rlp32 mutants, IF1-insensitive Arabidopsis accessions and IF1-insensitive
 Nicotiana benthamiana, binds IF1 specifically and forms complexes with LRR
 receptor kinases SOBIR1 and BAK1 to mediate signaling. Similar to other
 PRRs, RLP32 confers resistance to Pseudomonas syringae, highlighting an
 unexpectedly complex array of bacterial pattern sensors within a single
 plant species.
description: Restriction site–associated DNA sequencing (RAD-seq) and
 quantitative trait locus mapping using package R/qtl were conducted using
 the F2 mapping population of a <em>Arabidopsis</em> ICE153 x
 ICE73 cross as previously described. Details are found in:
 Fan, L., Chae, E., Gust, A. A. & Nürnberger, T. Isolation
 of novel MAMP-like activities and identification of cognate pattern
 recognition receptors in <em>Arabidopsis thaliana</em> using
 next-generation sequencing (NGS)-based mapping. Curr. Protoc. Plant Biol.
 2, 173-189 (2017).
description: File information 1. Reference and variant
 calling data for each sample of RAD-seq. with file name:
 R-V-data.zip Information of files named with
 “qvqr.f2.XXXX.info” in ‘R-V-data.zip’<br>Each file represents
 individual sample run by RAD-seq.<br>Column explanation.
 Column 1: chromosome number * 100,000,000 + position on the
 chromosome (chromosome is based on Arabidopsis thaliana reference genome
 (TAIR10) <br>Column 2: reference nucleotide call<br>Column 3:
 alternative nucleotide call (sample’s call)<br>Column 4: Quality of
 a predicted feature (ranging from 0 to 40) as in ‘SHORE’
 program<br>Column 5: depth <br>Column 6: Ratio of reads
 supporting a predicted feature to total coverage (excluding quality masked
 bases). Heterozygous SNPs and SNPs from pooled samples are divided into
 ’major concordance’ and ’minor concordance’ as in ‘SHORE’
 program<br>Column 7: Number of repetitive positions in the range of
 the prediction 2. QTL analysis genotype
 matrix Column and row information of the file;
 'ICE153ICE73.0.8p.3.7.S5.GT.headQTLtrim2.csv'
 Column 1: phenotype trait 1: quantitative
 measurements<br>Column 2: phenotype trait 2: binary
 trait<br>Column 3 and on: genotype call on the indicated
 position Row 1: marker name (chromosome*100,000,000 +
 position on the chromosome)<br>Row 2: chromosome number<br>Row
 3: position on the respective chromosome<br>Row 4 and on: genotype
 call of each sample