Effect of knockout of GUN1 or NAC103 on gene expression in roots of the WT or rab8d-2

We analyzed the root transcriptome profiles in WT, gun1-101, nac103-11, rab8d-2, gun1-101 rab8d-2, and nac103-11 rab8d-2. Our analysis showed that, compared to WT, approximately 108 genes were misregulated in gun1-101, while 78 genes were affected in nac103-11. Only two genes were influenced by both gun1-101 and nac103-11. In contrast, in the rab8d-2 background, blocking the function of GUN1 (gun1-101 rab8d-2) or NAC103 (nac103-11 rab8d-2) significantly altered the expression levels of approximately 948 and 267 genes, respectively. Importantly, over 72% (about 193) of the misregulated genes in nac103-11 rab8d-2 overlapped with those in gun1-101 rab8d-2, indicating a convergence of the GUN1- and NAC103-dependent signaling pathways in rab8d-2. Overall design: To evaluate the roles of GUN1 and NAC103 on root development in rab8d-2, a mutant with functional deficiency of plastid EF-Tu, we extracted total RNA from roots of WT, rab8d-2, gun1-101, nac103-11, gun1-101 rab8d-2, and nac103-11 rab8d-2 at the 3-day-old seedling stage.