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Abstract Graft compatibility is the capacity of two plants to form cohesive vascular connections. Tomato and pepper are incompatible graft partners; however, the underlying cause of graft rejection between these two species remains unknown. We diagnosed graft incompatibility between tomato and diverse pepper varieties based on weakened biophysical stability, decreased growth, and persistent cell death using viability stains. Transcriptomic analysis of the junction was performed using RNA sequencing, and molecular signatures for incompatible graft response were characterized based on meta-transcriptomic comparisons with other biotic processes. We show that tomato is broadly incompatible with diverse pepper cultivars. These incompatible graft partners activate prolonged transcriptional changes that are highly enriched for defense processes. Amongst these processes was broad nucleotide-binding and leucine-rich repeat receptors (NLR) upregulation and genetic signatures indicative of an immune response. Using transcriptomic datasets for a variety of biotic stress treatments, we identified a significant overlap in the genetic profile of incompatible grafting and plant parasitism. In addition, we found over 1000 genes that are uniquely upregulated in incompatible grafts. Based on NLR overactivity, DNA damage, and prolonged cell death, we hypothesize that tomato and pepper graft incompatibility is characterized by an immune response that triggers cell death which interferes with junction formation. 

SUMMARY Stalk mechanical properties impact plant stability and interactions with pathogenic microorganisms. The evaluation of stalk mechanics has focused primarily on the end‐of‐season outcomes and defined differences among inbred and hybrid maize genotypes. However, there is a gap in understanding how these different end‐of‐season outcomes are achieved. This study measured stalk flexural stiffness in maize inbred genotypes across multiple environments and in maize commercial hybrid genotypes under different disease states. Under all conditions, stalk flexural stiffness followed a biphasic trajectory, characterized by a linear increase phase and a sustained phase. Within a genotype, the environment or disease state altered the rate of increase in the linear phase but did not impact the timing of transition to the sustained phase. Whereas between genotypes, the timing of transition between phases varied. Destructive 3‐point bend tests of inbred stalks showed that the trajectory of stalk mechanics is defined by the bending modulus, not the geometry. Together, these results define a biphasic trajectory of maize stalk mechanics that can be modulated by internal and external factors. This work provides a foundation for breeding programs to make informed decisions when selecting for optimized stalk mechanical trajectories, which are necessary for enhancing resilience to environmental stresses.