The SlERF4-9-SlCDF1/3-SlAEC2/SlPIN5 module regulates tomato root morphogenesis

AP2/ERF transcription factors regulate plants' growth, development, and stress responses. In this study, the seed germination rate and seedling growth were reduced in the tomato <i>slerf4-9</i> mutant. The fresh weight, drought weight, number of primary lateral roots (LRs), average root diameter, and number of root tips were also decreased in the mutant. The findings suggest that SlERF4-9 plays a significant role in root growth and development. The results of RNA-seq analysis of young roots indicated that the mutation of <i>SlERF4-9</i> did not affect the expression of genes related to auxin biosynthesis or signal transduction, but it did reduce the expression of the auxin efflux carrier genes <i>SlAEC2</i> and <i>SlPIN5</i>. Moreover, the mutation of <i>SlERF4-9</i> affected the distribution of auxin in the roots of DR5 × WT and DR5 × <i>slerf4-9</i> hybrid tomato seedlings. However, the promoters of <i>SlAEC2</i> and <i>SlPIN5</i> do not possess the GCC-box or DRE elements, suggesting that SlERF4-9 does not directly regulate their transcription. In addition, the expression levels of the two Cycling DOF Factors (CDFs) <i>SlCDF1</i> and <i>SlCDF3</i> decreased in the roots of the <i>slerf4-9</i> mutant. Moreover, the GCC-box was present in the promoters of <i>SlCDF1</i> and <i>SlCDF3</i>. Therefore, exploring the regulatory relationships between <i>SlERF4-9</i>, <i>SlCDF1</i>/<i>3</i>, and <i>SlAEC2/SlPIN5</i> will further our understanding of the molecular mechanisms of tomato root growth and development.