We focus on identifying key genes and genetic changes required to generate perennial fruiting plants suitable for indoor growing environments. This involves understanding the genetic control of plant traits such as size, shape, flowering, and fruit development. Our approach integrates multi-omics techniques to gain an in-depth understanding of traits of interest in selected germplasm. Underpinning this work has been bioinformatics tool development to allow integration and analysis of complex datasets. Current practices in Controlled Environment Agriculture (CEA) are well established for the rapid production of annual crops such as lettuce; our goal is to produce perennial plants that can grow and crop well in artificial environments. Progressing changes to plant form and fruiting might also have utility in new growing systems developed to help adapt to climate challenges.