Genome-wide characterization of the NLR gene family in tomato (Solanum lycopersicum) and their relatedness to disease resistance

Abstract

Nucleotide-binding leucine-rich-repeat receptors (NLR), the largest group of genes associated with plant disease resistance (R), have attracted attention due to their crucial role in protecting plants from pathogens. Genome-wide studies of NLRs have revealed conserved domains in the annotated tomato genome. The 321 NLR genes identified in the tomato genome have been randomly mapped to 12 chromosomes. Phylogenetic analysis and classification of NLRs have revealed that 211 genes share full-length domains categorized into three major clades (CNL, TNL, and RNL); the remaining 110 NLRs share partial domains and are classified in CN, TN, and N according to their motifs and gene structures. The cis-regulatory elements of NLRs exhibit the maximum number of these elements and are involved in response to biotic and abiotic stresses, pathogen recognition, and resistance. Analysis of the phylogenetic relationship between tomato NLRs and orthologs in other species has shown conservation among Solanaceae members and variation with A. thaliana. Synteny and Ka/Ks analyses of Solanum lycopersicum and Solanum tuberosum orthologs have underscored the importance of NLR conservation and diversification from ancestral species millions of years ago. RNA-seq data and qPCR analysis of early and late blight diseases in tomatoes revealed consistent NLR expression patterns, including upregulation in infected compared to control plants (with some exceptions), suggesting the role of NLRs as key regulators in early blight resistance. Moreover, the expression levels of NLRs associated with late blight resistance (Solyc04g007060 [NRC4] and Solyc10g008240 [RIB12]) suggested that they regulate S. lycopersicum resistance to P. infestans. These findings provide important fundamental knowledge for understanding NLR evolution and diversity and will empower the broader characterization of disease resistance genes for pyramiding through speed cloning to develop disease-tolerant varieties.

Graft incompatibility between pepper and tomato can be attributed to genetic incompatibility between diverged immune systems

“…To further explore how defense processes might be involved in the incompatible response, we targeted NLRs and downstream molecular signaling involved in defense for deeper analysis. Using a collection of 320 previously annotated tomato NLRs (Bashir et al ., 2022), we identified 97 defense-related receptors that were significantly upregulated in incompatible grafts (Fig. 6c, Table S12).…”

TIR-NBS-LRR genes play a role in plant defense against biotic stress in Solanum lycopersicum

“…There was very high discrepancy and fluctuation among the reported literature studies for the number of TNLs present in tomatoes. For example, Qian et al (2017), Andolfo et al (2013Andolfo et al ( , 2014 and Bashir et al (2022) reported different numbers for full length TNLs in tomatoes with the maximum count reaching twenty-six. This discrepancy perhaps arose due to the nature of the work being carried out with more emphasis on the in-silico genome wide identification of all the NBS-LRRs and less focus was placed on the TNLs.…”

“…However, elaboration upon role of TNL members under biotic stress was almost negligible in such reports. A recent report on genome wide identification of NLRs (NBS-LRR receptors) identified the TNL repertoire, yet, an expression analysis was lacking for these genes (TNLs) for early blight disease as well as for other biotic stresses (Bashir et al 2022). Thus, in the present work, after identifying the TNL gene family members, they were assessed by protein-protein interaction prediction and expression analysis using RNA-Seq data for the spatio-temporal expression and biotic stresses.…”

NLR- and mlo-Based Resistance Mechanisms against Powdery Mildew in Cannabis sativa

“…They represent the major class of intracellular innate immune receptors and the most represented group of resistance genes. To date, several NBS–LRR resistance genes and quantitative trait loci (QTLs) for plant resistance to pathogens were mapped in plants, some of which were also cloned [ 24 , 25 ], and, in many cases, a co-localization between QTLs and genes was highlighted. This made it possible to identify candidate genes and to develop molecular markers for plant resistance [ 24 , 25 ].…”

“…To date, several NBS–LRR resistance genes and quantitative trait loci (QTLs) for plant resistance to pathogens were mapped in plants, some of which were also cloned [ 24 , 25 ], and, in many cases, a co-localization between QTLs and genes was highlighted. This made it possible to identify candidate genes and to develop molecular markers for plant resistance [ 24 , 25 ]. In cannabis, the involvement of NLRs in gene-for-gene interaction with PM has been recently demonstrated [ 18 ].…”