Transcriptomic analysis implicates ABA signalling and carbon supply in the differential outgrowth of petunia axillary buds

Shoot branching of flowering plants exhibits phenotypic plasticity and variability. This plasticity is determined by the activity of axillary meristems, which in turn is influenced by endogenous and exogenous cues such as nutrients and light. In many species, not all buds on the main shoot develop into branches despite favorable growing conditions. In petunia, basal buds (buds 1-3) typically do not grow out to form branches, while more apical buds (buds 6 and 7) are competent to grow. The genetic regulation of buds was explored using transcriptome analyses of petunia axillary buds at different positions on the main stem. To suppress or promote bud outgrowth, we grew the plants in media with differing phosphate (P) levels. Using RNA-seq, we found many (>5000) differentially expressed genes between bud 6 or 7, and bud 2. In addition, more genes were differentially expressed when we transferred the plants from low P to high P medium, compared with shifting from high P to low P medium. Buds 6 and 7 had increased transcript abundance of cytokinin and auxin-related genes, whereas the basal non-growing buds (bud 2 and to a lesser extent bud 3) had higher expression of strigolactone, abscisic acid, and dormancy-related genes, suggesting the outgrowth of these basal buds was actively suppressed. Consistent with this, the expression of ABA associated genes decreased significantly in apical buds after stimulating growth by switching the medium from low P to high P. Furthermore, comparisons between our data and transcriptome data from other species suggest that the suppression of outgrowth of bud 2 was correlated with a limited supply of carbon to these axillary buds. Candidate genes that might repress bud outgrowth were identified by co-expression analysis. Overall design: RNA-seq were obtained from two hydroponic experiments: in the 1st expt, plants were grown in high phosphate (250 uM) hydroponic, then were split into two groups. One group was transferred to fresh high P hydroponic whilst the other went into low P; in the 3rd expt: plants were placed in low P at the beginning, then split into two groups, one stayed in low P but the other went into high P. 24 h after medium switching, petunia axillary buds from nodes 2, 3, 6, and 7 (node 1 is the first node after cotyledons) were harvested. 3 replicates of a pool of axillary bud tissues from 6-7 plants. In total, 24 samples for the 1st expt and 24 samples from the 3rd expt.