Global expression patterns of R-genes in tomato and potato

Original Publication

von Dahlen JK, Schulz K, Nicolai J and Rose LE (2023) Global expression patterns of R-genes in tomato and potato. Front. Plant Sci. 14:1216795. doi: 10.3389/fpls.2023.1216795

Abstract

The study explores how resistance genes (R-genes) in tomato and potato plants respond to pathogen infection by analyzing the expression of 940 R-genes across 315 transcriptome libraries. Results show that most R-genes are expressed at low levels, with a subset showing moderate to high expression across various conditions, regardless of infection. This subset includes NRCs (NLR required for cell death). About 10% of R-genes were differentially expressed during infection, with both up- and down-regulation patterns. Tissue-specific expression emerged as a key factor influencing R-gene activity. The findings challenge the belief that R-gene expression is primarily induced by pathogen attack, suggesting instead that a core set of R-genes is constitutively active, providing plants with a constant state of readiness for defense.

License

Copyright © 2023 von Dahlen, Schulz, Nicolai and Rose. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Data availability

Publicly available datasets were analyzed in this study. A total of 315 transcriptome datasets of tomato (Zouari et al., 2014; Du et al., 2015; Barad et al., 2017; Sarkar et al., 2017; Sugimura and Saito, 2017; Xue et al., 2017; Yang et al., 2017; Zheng et al., 2017; Chen et al., 2018; Shukla et al., 2018; Fawke et al., 2019; Pesti et al., 2019; Wang et al., 2019b) and potato (Goyer et al., 2015; Zuluaga et al., 2015; Dees et al., 2016; Gao and Bradeen, 2016; Kochetov et al., 2017; Levy et al., 2017; Li et al., 2017; Lysøe et al., 2017; Hao et al., 2018; Kumar et al., 2018) were obtained from the Sequence Read Archive (Figure S1).