Exploring leaf variegation in Arabidopsis yellow variegated2 by single-cell RNA sequencing

Deficiency in the chloroplast metalloprotease FtsH2 causes the Arabidopsis leaf-variegated mutant yellow variegated2 (var2) to develop leaves with irregular green sectors and white sectors. This raises an intriguing question: why do genetically identical cells exhibit such dramatic phenotypic differences? The phenomenon highlights the probabilistic fates of chloroplasts in var2. Previous studies proposed that patchy expression of FtsH8-a functionally redundant gene of FtsH2-explains this variegation. Here, we employed single-cell RNA sequencing (scRNA-seq) to investigate leaf variegation for the first time. We demonstrated the patchy expression of FtsH8 at the single-cell level, which supports the threshold model. Our pseudotime analysis suggests that white sector formation in developing var2 leaves enables cells to reduce reactive oxygen species (ROS) via suppression of photosynthetic genes. Supporting this, treatment with a ROS scavenger markedly reduced the proportion of white sectors. Furthermore, we showed that suppression of photosynthetic genes in var2 is a trade-off that ensures proper progression of the cell cycle. Taken together, our study offers new insights into the mechanisms underlying leaf variegation.