Plant grafting underpins modern horticulture, enabling growers to combine disease resistance, stress tolerance, and improved productivity. Yet incompatibility between certain crops limits its use. Tomato and pepper are valuable Solanaceae members but fail to form stable grafts, resulting in weakened stems, failed vascular bridges, and persistent junction death. Previous explanations focused on mechanical or metabolic mismatches, but these lacked molecular clarity. The persistence of necrotic tissue and reduced growth hinted at deeper causes. Understanding these mechanisms is essential for developing reliable interspecies grafts and ensuring long-term plant health. Due to these challenges, it is necessary to conduct in-depth research on graft incompatibility mechanisms.
A research team from Cornell University, the John Innes Centre, Stanford University, the University of Delaware, and USDA-ARS has revealed why tomato and pepper grafts fail. Their findings, published (DOI: 10.1093/hr/uhae255) on September 11, 2024, in Horticulture Research, show that graft rejection is not just structural but immunological. Instead of forming vascular bridges, the junction activates an autoimmune-like defense response, triggering programmed cell death. This discovery reframes the understanding of graft compatibility and highlights how interspecies tissue fusion can mimic pathogen attack.
The team conducted reciprocal grafts between tomato (Solanum lycopersicum) and several pepper (Capsicum) varieties, including Cayenne, California Wonder, Doux des Landes, and Habanero. Across all combinations, graft survival was low, stem integrity was poor, and xylem reconnections failed. Trypan blue staining showed that unlike self-grafted plants, which recovered from early junction death, heterografts exhibited persistent nonviable tissue for three weeks. RNA-sequencing revealed that incompatible junctions expressed far more differentially regulated genes than compatible controls, with a pronounced enrichment in defense-related pathways. Hundreds of nucleotide-binding and leucine-rich repeat (NLR) receptors were significantly upregulated, alongside regulators such as EDS1, PAD4, and SAG101, indicating effector-triggered immunity. Hormone signaling through salicylic acid, jasmonic acid, and ethylene was also elevated, while steroidal glycoalkaloid biosynthesis surged in incompatible tissue. Comparative transcriptomics showed strong overlap between graft incompatibility and responses to parasitic plants, suggesting shared molecular machinery. Importantly, over 1,000 genes were uniquely upregulated in incompatible grafts, including DNA repair markers like BRCA1 and BARD1, pointing to immune-induced genotoxic stress. Collectively, these findings indicate that tomato–pepper grafts fail because their immune systems perceive each other as invaders.
“Our study demonstrates that graft incompatibility is not simply a physical failure of tissues to merge, but rather a misdirected immune response,” said Dr. Hannah Rae Thomas, lead author of the study. “The tomato and pepper recognize each other as non-self, activating an autoimmune-like defense that leads to cell death at the graft junction. This is the first time such an immunity-based incompatibility has been identified in a cross-species grafted crop. These insights offer new molecular markers to evaluate compatibility and guide breeding for more successful grafting outcomes.”
These findings reshape how horticulturalists and breeders assess graft potential. By identifying molecular markers—such as NLR overactivation and hormone-driven defense signatures—researchers can begin screening species combinations before committing to large-scale grafting trials. The work also underscores that interspecies grafting may resemble pathogen interactions, offering broader lessons for plant immunity research. In practical terms, this discovery could prevent crop losses by avoiding incompatible pairings, inform the development of new rootstocks, and inspire genetic strategies to dampen inappropriate immune responses. Ultimately, unraveling graft incompatibility may expand the range of viable graft combinations and enhance sustainable crop production.
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References
DOI
10.1093/hr/uhae255
Original Source URL
https://doi.org/10.1093/hr/uhae255
Funding information
H.R.T. was supported by a United States Department of Agriculture National Institute of Food and Agriculture (USDA-NIFA) Predoctoral Fellowship (2020-67011-31882); M.H.F., A.G., S.P., and M.N. were supported by the National Science Foundation (NSF) (CAREER IOS-1942437) and by a U.S.-Israel Binational Science Foundation grant (2019192). Imaging data was acquired through the Cornell Institute of Biotechnology’s Imaging Facility, with NIH (S10OD018516) funding for the shared Zeiss LSM880 confocal/multiphoton microscope. Access to the Instron Universal testing stand was supported by the Delaware Center for Musculoskeletal Research from the National Institute of Health’s National Institute of General Medical Sciences (P20GM139760).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.