Final Report Summary - TFMORPHOGENCOMPET (The basis of morphogenetic competence in tomato development: a role for Trifoliate) Final Publishable Summary Report:Background:Aerial architecture of land plants is mainly determined by two morphological structures: branches and leaves. Branches are lateral axes of growth established via the activity of axillary meristems (AMs) localised in the leaf axils. Each AM develops into an axillary bud that can establish a new axis of growth supporting the development of lateral organs, e.g. leaves and flowers. Leaves are initiated from shoot apical meristems and can be more or less complex, depending on the species (Figure 1). Transcription factors promoting the formation of either axillary meristems (AMs) or compound leaves are quite well described. Yet, there is still much to be learned about the establishment and maintenance of pools of morphogenetic competent cells that are the ultimate source for the formation of specialised morphological structures, such as an AM or a leaflet.Objectives:The TFMORPHOGENCOMPET project aims at combining RNA-sequencing data with molecular biology, genetics and plant physiology to ascertain the role of one transcription factor, Trifoliate (Tf), as a major regulator of tomato axillary meristem initiation and leaflet development. This combination will permit to establish if AM and compound leaf development in tomato is directed by a common molecular pathway. Moreover, it will expand our knowledge on i) which and ii) how new regulators (directly) targeted by the Trifoliate (Tf) gene control the progression during the development of AM and compound leaf primordia. The deep sequencing approaches will provide unprecedented detailed information on the genes/loci (directly) targeted by Tf at specific developmental stages. The dedicated, functional follow-up study will provide insight in the Tf-controlled molecular mechanism regulating the establishment and maintenance of pools of morphogenetic competent cells that are necessary to allow the formation of both AMs and leaflets in tomato.Results:Using next-generation DNA sequencing technology, the TFMORPHOGENCOMPET project has revealed that an important number of genes are commonly expressed between two important developmental stages of tomato leaf development. It also revealed that Tf is regulating the expressions of different subsets of genes with few common targets between both stages. Unfortunately, no differentially expressed genes have been found between the leaf axil of the studied mutant and the one of the wild-type tomato plant. These main results revealed that Tf (1) plays a role in the patterning of tomato leaf, (2) doesn’t seem implicated in the initiation and/or development of the axillary meristems in tomato. For the latter, one possible explanation would be that Tf is required in later stages of axillary meristems development than the ones expected.Nonetheless, two candidate genes are now under investigation regarding their potential function in compound leaf development of tomato plants. By combining molecular and physiologic approaches, we will learn more about their function within the compound leaf development but also their potential interactions with already known regulators of tomato leaf development. At the moment, tomato mutant for these two genes are being generated using the novel genome-editing CRISPR-Cas9 approach. This approach is likely to be considered as a non-transgenic one, as no residual vector is left into the plant after several generations. On top, a comparative approach in Arabidopsis thaliana is already under study, and thus, will give an evolutionary context to the function of these two candidate genes.In crop production, a reduction in shoot branching is a highly desirable trait, because axillary branches lead to a reduction in yield of the main stem. Thus it is important to conceive, and ultimately control, the underlying mechanism of axillary meristem formation. As Tf was first identify as a tomato regulator of axillary meristem formation, this project was aiming, in long term, to improve agricultural practice and support plant breeding companies that demand plants with a specific architecture i.e. plant with one main stem as well as with highest possible crop yield. Unfortunately, and as describe above, no differentially expressed gene were found in that particular tissue between the wild-type and the mutant plants. However, RNA in situ hybridisations of the two selected genes, revealed they are both present in the axillary meristem in formation. Therefore, the knowledge obtained in this project could still potentially be of great value to European plant breeding companies to modify lateral growth, and to some extent final plant architecture.