Excess salicylic acid mediates graft incompatibility by repressing auxin-dependent vascular reconnection in tomato
Ruiduo Han, Kaiwei Meng, Xiujuan WangiD, Kaili MaoiD, Zefeng Chen, Xiaojian XiaiD, Huijia KangiD, Yanhong ZhouiD, Hannah Rae ThomasiD
Abstract
Graft incompatibility limits the combination of scions and rootstocks, yet the signals that block vascular reconnection remain poorly understood. Using incompatible tomato-pepper (Solanum lycopersicum-Capsicum annuum) grafts, we found that salicylic acid (SA) overaccumulates at the graft junction, predominantly in the rootstock, while incompatible scions exhibit enhanced pattern-triggered immunity. SA-deficient nahG-expressing tomato failed to rescue incompatibility and instead showed severely impaired self-graft healing, indicating that successful tissue reunion requires an optimal, rather than minimal, SA response. Defense-associated genes remained activated in failed grafts regardless of SA accumulation, placing SA downstream of incompatibility determination. Exogenous SA application phenocopied incompatibility, blocking xylem reconnection, inducing cell death, and suppressing auxin signaling. Incompatible grafts similarly displayed reduced auxin accumulation and response at the graft junction. Exogenous auxin partially rescued xylem reconnection in incompatible grafts but failed to activate cambial regulator genes or fully restore compatibility. We propose that graft compatibility depends on SA-auxin homeostasis, where moderate SA supports wound-associated defense and regeneration, whereas excessive SA suppresses the auxin-dependent program required for xylem differentiation. These findings identify SA as a dose-dependent regulator of graft healing in tomato and link excessive immune activation to failed vascular regeneration.
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In-depth summary
Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 2 (7 Aug 2026) · CC BY 4.0
Salicylic acid (SA) overaccumulates in tomato-pepper graft rootstocks alongside suppressed auxin; exogenous SA phenocopies failed xylem reconnection, while SA-deficient nahG tomato self-grafts also fail.
Graft incompatibility limits which scions and rootstocks can be combined, and tomato-pepper heterografts show failed xylem reconnection and a prolonged defense transcriptional signature, but SA's role had not been tested. This work shows that SA acts on graft healing in a dose-dependent way and links excess SA to repression of the auxin program needed for vascular regeneration.
Key results
ShownIn compatible self-grafts, SA rises before reconnection and peaks in stocks at 4 DAG in tomato and 6 DAG in pepper. Incompatible heterografts (scion/stock: tomato/pepper T/P, pepper/tomato P/T) accumulate much more SA, mostly in the rootstock, with strong SlPR1 induction.
At 7 days after grafting (DAG), compatible self-grafts held no more than 36.4 ng/g SA. T/P stocks reached 184.6 ng/g (4.8-fold vs average P/P) and P/T stocks 101.9 ng/g (2.8-fold vs T/T); incompatible scions were similar (ns). pPR1:GUS staining at 4 DAG and SlPR1 RT-qPCR at 7 DAG were higher in heterografts than in tomato self-grafts. · Incompatible rootstocks overaccumulate salicylic…; Figure legends
ShownScions of incompatible T/P grafts are in a primed, hyperactive pattern-triggered immunity (PTI) state and resist bacterial infection better. Grafting alone moderately raises PTI.
After 100 nM flg22 on scion leaves at 7 DAG, cumulative ROS in T/P was 4 times that of T/T, and T/T was 1.7 times ungrafted. T/P also had a small late ROS burst under mock, earlier and stronger MAPK phosphorylation, and the highest resistance to Pst DC3000 among ungrafted, T/T and T/P plants. · Incompatible scions demonstrate increased PTI; Figure legends
ShownLowering SA does not rescue incompatibility: nahG tomato grafted with pepper still failed. nahG self-grafts healed poorly despite low SA, with high cell death and persistent defense gene activation, which places SA downstream of compatibility determination.
With n = 10 grafts at 7 DAG, nahG self-grafts had almost no fully reconnected grafts and cell death similar to T-P heterografts. No disease signs appeared by 14 DAG, but adventitious roots formed. RNA-seq found 726 DEGs unique to the n/n scion and 477 unique to the n/n stock. SlPR1 was significantly higher than in T/T in both nahG self-graft tissues and in pepper-on-nahG stocks. · Loss of SA accumulation cannot rescue…; Figure legends
ShownHigh-dose exogenous SA on compatible tomato self-grafts phenocopies incompatibility. It blocks vascular reconnection, raises cell death and lowers junction auxin, repressing auxin biosynthesis, signaling and transport genes.
Of 0.02, 0.05 and 0.1 mM SA, only 0.1 mM disrupted healing: 16.7% of grafts failed to adhere and 50% showed nonvascular adhesion only, with more trypan blue cell death. Auxin and YUC3, IAA9, SAUR32 and PIN1 expression fell as SA rose. WGCNA module ME1 (P = 9.6e-05), up only in compatible stocks, was topped by response to auxin. · Increased SA represses graft healing; SA inhibits auxin accumulation in the graft…; Figure legends
SuggestedIncompatible grafts accumulate less auxin at the junction. Exogenous auxin (IAA) only partly restores vascular differentiation and does not activate cambial regulators, so auxin alone cannot restore compatibility.
pDR5:GUS signal appeared at 2 DAG in tomato self-grafts, only weakly at 4 DAG in tomato/pepper, and was absent from pepper/tomato reporter stocks. Auxin was significantly lower in T/P and P/T stocks. With 100 μM IAA, heterografts formed new but non-cohesive vascular tissue, auxin genes changed non-significantly, and cambial regulators (WOX4, PXY) did not rise. · Incompatible grafts have reduced auxin…; Exogenous auxin has limited, but significant…; Immune activation suppressed the necessary auxin…; Figure legends
Methods, data and reproducibility
Tomato and pepper self-grafts and reciprocal heterografts (wild type, SA-deficient nahG, and PR1 or DR5 GUS reporter lines) were profiled by UPLC-MS/MS hormone quantification, PTI assays, propidium iodide and trypan blue histology, RT-qPCR and graft-junction RNA-seq, plus an exogenous SA dose series (0.02, 0.05, 0.1 mM) and a single 100 μM IAA treatment.
- Tomato and pepper self-grafts plus reciprocal tomato-pepper heterografts (tomato cv. Money Maker, Alisa Craig; pepper cv. Xiangla No.7), splice-grafted at 3 weeks · Solanum lycopersicum; Capsicum annuum · n = n = 10 grafts for phenotyping and histology
- 35S:nahG SA-deficient tomato (cv. Money Maker) in self-grafts and reciprocal heterografts with pepper · Solanum lycopersicum; Capsicum annuum · n = n = 10
- pPR1:GUS reporter (2048b promoter of Solyc01g106620) and pDR5:GUS auxin reporter tomato lines (cv. Alisa Craig), self-grafted or grafted to wild-type pepper · Solanum lycopersicum (grafted with Capsicum annuum)
- Graft-junction RNA-seq at 7 DAG (NovaSeq X Plus, paired-end 150bp) of scions and stocks from WT, nahG and pepper self- and heterograft combinations · Solanum lycopersicum; Capsicum annuum · n = 3 biological replicates per graft combination
- UPLC-MS/MS quantification of SA and auxin in scion and stock tissue over days after grafting and under SA treatments · Solanum lycopersicum; Capsicum annuum · n = at least three independent biological replicates
- Compatible tomato self-grafts treated with SA (0.02, 0.05, 0.1 mM), and self- and heterografts treated with 100 μM IAA · Solanum lycopersicum; Capsicum annuum · n = at least ten biological replicates for imaging
- Spray inoculation of scion leaves from ungrafted, T/T and T/P plants at 7 DAG with Pseudomonas syringae pv. tomato DC3000 (10^7 CFU mL⁻¹) · Pseudomonas syringae pv. tomato; Solanum lycopersicum
- Methods & tools
- UPLC-MS/MS with D4-SA and D5-IAA internal standards, GUS reporters (pPR1:GUS, pDR5:GUS), flg22 ROS burst and MAPK phosphorylation assays, Trypan blue light microscopy and propidium iodide confocal imaging, fastp, HISAT2 (ITAG4 tomato, CM334 pepper genomes), StringTie, DESeq2 (pairwise and likelihood ratio test), topGO, WGCNA, Fiji, GraphPad Prism version 9
- Reagents & environment
- GraphPad Prism version 9; R with Tidyverse, dplyr, DESeq2, ggplot2, UpSetR, pheatmap, topGO, WGCNA; TBtools. Reads mapped to ITAG4 tomato and CM334 pepper genomes. No other software versions stated.
- Reproducibility gaps
- The RNA-seq data are stated to be deposited in NCBI GEO, but no accession is printed. No code repository is given, and supplemental data are only attached to the preprint. The ROS assay luminol and peroxidase concentrations are left as placeholders ('X').
Limitations (5)
- The nahG transgene may have off-target effects beyond lowering SA: a cited Arabidopsis study found nahG induced 5 times as many differentially expressed immune genes as sid2. The authors urge caution with nahG grafts and suggest SA biosynthesis mutants instead. · stated by the authors
- The authors note that non-sterile bench grafting could have predisposed nahG plants to graft-transmissible disease; extending healing to 14 DAG revealed no obvious disease signs, though nahG self-grafts still performed poorly. · stated by the authors
- Exogenous IAA (100 μM) had inconsistent, mostly non-significant effects in incompatible grafts. It did not activate cambial regulators such as WOX4 and PXY or fully restore xylem reconnection. · stated by the authors
- The causal SA-to-auxin link in heterografts is inferred mainly from SA applied to compatible tomato self-grafts and from correlative transcriptomics. SA was never lowered genetically inside heterografts except with the confounded nahG line. · noted in this summary
- The control and timing descriptions are inconsistent. Methods say SA was dissolved in 100% ethanol with solvent-only mocks, but Results and legends call the mock water. Auxin was compared across grafts at 4 DAG, whereas SA was compared at 7 DAG. · noted in this summary
Who should read:Read this if you study graft compatibility, vascular regeneration, or salicylic acid-auxin crosstalk in Solanaceous crops and want hormone, reporter and transcriptome evidence from tomato-pepper grafts.
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