Cell death at the Solanum lycopersicum and Capsicum graft junction is due to genetic incompatibility
Graft compatibility is the ability of two plants to form cohesive vascular connections. Tomato and pepper grafts are incompatible but the underlying causes of this phenomenon remain unknown.  We utilzied a broad array of techniques to profile graft compatibility including viability, biophysical stability, and growth. Cell death in the junction was quantified using trypan blue and TUNNEL assays. Transcriptomic analysis of cell death in the junction was preformed using RNA-sequncing. Finally a meta-transcriptomic analysis was conducted with published datasets to further explore the genetic signature of graft incompatibility.We found that all varieties of pepper tested across two species were incompatible with tomato. Tomato and pepper graft incompatibility is characterized by stem instability, reduced growth, and persistent cell death in the graft junction. We showed that tomato and pepper heterografts have prolonger transcriptional activity, with defense processes highly enrched. We identfied a large subset of NLRs and genes involved in programmed cell death which were upregulated in incompatible tissue. We also identified a set of genes with orthologs in both tomato and pepper which are upregulated in incompatible grafts including biosythesis of steroidal glycoalkaloids. Finally we utilized various biological stressors to explore the genetic signature of grafting. We found a significant overlap in the genetic profile of grafting and plant parsitism. We also identified over 1000 genes uniquely upregulated in incompatible grafting including genes in involved in DNA-damage repair. Based on the broad upregulation of NLRs and genes involved with programmed cell death, prolonged cell death in the junction, and DNA damage, we have determined that tomato and pepper graft incompatibility is likely caused by a form of genetic incompatibility which triggers an autoimmune-like response. Overall design: The scion and stock of tomato:tomato, pepper:pepper, tomato:pepper, pepper:tomato,  ungrafted tomato, and ungrafted pepper tissue was collected at 7, 14, and 21 DAG. Total RNA was extracted and sequenced.