Abstract Background Resistance and growth are opposing characteristics in plants. SA INSENSITIVITY OF npr1 - 5 ( SSI2 ) encodes a stearoyl-ACP desaturase (S-ACP DES) that has previously been reported to simultaneously enhance resistance and repress growth. Results Here, we characterize ssi2 - 2 , a novel mutant allele of SSI2 that has two amino acid substitutions. Compared with wild-type and two other mutants of SSI2 , ssi2 - 2 showed intermediate phenotypes in growth size, punctate necrosis, resistance to the bacterial pathogen Pst DC3000, salicylic acid (SA) content, pathogenesis-related ( PR ) gene levels and 18:1 content. These results indicate that ssi2 - 2 is a weak mutant of SSI2 . Additionally, by using ssi2 - 2 as an intermediate control, a number of differentially expressed genes were identified in transcriptome profiling analysis. These results suggest that constitutive expression of defense-related genes and repression of IAA signaling-associated genes is present in all SSI2 mutants. Conclusions Taken together, our results suggest that the weak ssi2 - 2 mutant maintains a better balance between plant immunity and vegetative growth than other mutants, consequently providing a basis to genetically engineer disease resistance in crop plants.