Transcriptome analysis revealed the interaction among strigolactones, auxin, and cytokinin in controlling the shoot branching of rice.

KEY MESSAGE: Strigolactones inhibit bud growth by negatively regulating the auxin transport without changing the auxin biosynthesis and suppressing the expression of A-ARR in buds. Strigolactones (SLs) are important phytohormones associated with regulation of shoot branching in rice. Rice shoot branching is persuasively mediated by plant hormones like auxin, cytokinins (CKs) and SLs. The interactions among these hormones were diversely investigated by many researchers but remained a subject of debate. In the present study, the removal of panicle and application of subsequent synthetic SLs were used to regulate rice bud growth on node 2 (the second node from panicle) at full heading stage. The bud growth was significantly induced after panicle removal but GR24 (synthetic SLs) application inhibited it, along with variations in endogenous hormone contents in bud. RNA samples from buds were subjected to RNA sequencing through Illumina HiSeq 2000 (RNA-seq). Comparison of transcript expression levels among three treatments, viz. (1) intact (Co), (2) removed panicle (RP) and (3) RP combined with synthetic SL GR24 (GR) revealed the involvement of numerous genes associated with hormone signal transduction. GR24 supply minimized the RP-induced enhancement of auxin early response genes, independent of ARF. CK signal transduction was also induced by RP, but type-A ARR were the only genes responding to GR without any other CK signal associated genes. Additionally, RP and GR can also modulate auxin transport and CK degradation by regulating the genes' expression involved in the biosynthesis of flavonoid, phenylpropanoid and benzoxazinoid. Contemplating the results obtained so far, it is possible to open new vistas of research to reveal the interactions among SLs, auxin and CK in controlling the shoot branching of rice.