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Background  Shoot branching is one of the important agronomic traits affecting yields and quality of tea plant ( Camellia sinensis ). Cytokinins (CTKs) play critical roles in regulating shoot branching. However, whether and how differently alternative splicing (AS) variant of CTKs-related genes can influence shoot branching of tea plant is still not fully elucidated.    Results  In this study, five AS variants of CTK biosynthetic gene  adenylate isopentenyltransferase  ( CsA-IPT5 ) with different 3′ untranslated region (3ˊ UTR) and 5ˊ UTR from tea plant were cloned and investigated for their regulatory effects. Transient expression assays showed that there were significant negative correlations between CsA-IPT5 protein expression, mRNA expression of  CsA-IPT5  AS variants and the number of ATTTA motifs, respectively. Shoot branching processes induced by exogenous 6-BA or pruning were studied, where  CsA-IPT5  was demonstrated to regulate protein synthesis of CsA-IPT5, as well as the biosynthesis of  trans -zeatin ( t Z)- and isopentenyladenine (iP)-CTKs, through transcriptionally changing ratios of its five AS variants in these processes. Furthermore, the 3′ UTR AS variant 2 (3AS2) might act as the predominant AS transcript.    Conclusions  Together, our results indicate that 3AS2 of the  CsA-IPT5  gene is potential in regulating shoot branching of tea plant and provides a gene resource for improving the plant-type of woody plants.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03254-5.

A novel adenylate isopentenyltransferase 5 regulates shoot branching via the ATTTA motif in Camellia sinensis