RNA-seq analysis of axillary buds of tomato WT, 156OE and rSBP15OE plants

Shoot branching (SB) is an undesired trait in many crops, including tomato, as it may redirect assimilates away from developing flowers and fruits. Better understanding of the molecular mechanisms underlying bud arrest could help to generate plants with improved architecture and reduced lateral SB. We have previously shown that overexpression of the microRNA156 (miR156) in tomato increases the number of side branches; here, we have characterized in detail how the miR156/SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL/SBP) hub modulates axillary bud (AB) development by connecting multiple phytohormones with known SB-associated genes. We have demonstrated that miR156-targeted SlSBPs modulate SB by regulating the action of distinct hormones, such as gibberellin, auxin and abscisic acid (ABA). Our results showed that plants overexpressing a miR156-resistant version of SlSBP15 (rSBP15) displayed arrest ABs throughout development. To unravel the underlying molecular mechanisms within buds, we conducted NGS-based transcriptomics analyses (RNA-Seq) to compare the transcriptome in the ABs from 25-dpg WT (MT), 156-OE, and rSBP15 plants.