Artificial intelligence (AI) and machine learning (ML) tools are poised to solve some of the stickiest research challenges in in vitro plant science: standardizing the subjective, clarifying the complex, and making plant growth predictable. The complexity of in vitro plant systems, marked by high dimensionality and variable interactivity, limits the efficacy of traditional experimentation and slows research progress. Emerging AI/ML tools may improve research decision-making by advancing standardized data collection, interpretation and design of genomic sequences, and predictive experimental design. This work discusses key concepts in AI/ML for plant scientists, and reviews recent implementations in in vitro workflows. The application of AI/ML tools in media optimization is examined in depth, highlighting lab-specific, single-use models developed for this purpose. Finally, this work introduces a new architecture for easy-to-adopt ML media prediction across labs and experimental objectives termed MERISTEM: Multi-context Evaluation and Representation via Ingredient SeT EMbeddings. MERISTEM chains two features: (1) a recipe encoder (Set Transformer) facilitating learning across recipes of varying composition, and (2) a multi-head neural network (multi-layer perceptron) supporting prediction of multiple outcomes. A proof-of-concept MERISTEM model was trained on data aggregated from eight studies on shoot induction across multiple species. Using a Non-dominated Sorting Genetic Algorithm II for multi-objective optimization, the proof-of-concept model makes biologically meaningful recommendations for media recipes even when prior data about a predicted ingredient is unavailable. This approach represents an important step toward a unified tool for media design, enabling researchers to identify optimal media recipes for multiple use cases and any combination of ingredients without the need for prior experimental screens.
Gymnanthemum amygdalinum (Delile) Sch. Bip. (bitter leaf) is a medicinally important perennial shrub with broad therapeutic applications which has been used in ancient medicine systems. This plant is rich in diverse bioactive compounds, its ethno-pharmacological importance is supported by its antioxidant, anti-inflammatory, antidiabetic, antibacterial and anticancer effects. The species is a rich reservoir of bioactive compounds. Escalating medicinal demand, overharvesting pressures and constraints associated with conventional propagation methods underscore the urgent need for its conservation through robust in vitro approaches. This research optimizes a very efficient micropropagation process using nodal explants and evaluates the genetic homogeneity of regenerated plantlets with Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) molecular markers. Murashige and Skoog (MS) medium supplemented with 1.5 mg L−1 6-benzylaminopurine (BAP) resulted in the maximum shoot bud induction (92.72
Idesia polycarpa is an economically significant woody plant in China with multiple applications due to its high oil content and strong adaptability. However, its conventional propagation is inefficient. For the micropropagation and genetic improvement of this species, establishing an effective regeneration protocol is critically important. Currently, an effective in vitro regeneration procedure for I. polycarpa was successfully obtained with hypocotyls as explants and through the optimization of culture-related factors. Hypocotyls 1 cm in length from 25 d seedlings were first incubated on MS basal medium containing 1.0 mg L⁻1 TDZ and 0.5 mg L⁻1 IBA for callus formation, with compact callus obtained following 30 d of culture. Subsequently, callus (with 1 cm diameter) was moved to MS medium added with 2.0 mg L⁻1 TDZ alongside 0.05 mg L⁻1 IBA for differentiation. 40 d later, 1 to 5 adventitious buds were observed from each callus, with a 64.82
Induction and development of healthy roots is necessary for both micropropagation and the successful rescue of in vitro genetically transformed or edited plants. Pear (Pyrus) genotypes are known to be recalcitrant to rooting treatments, and responses are highly genotype-dependent. Floral foam has been used successfully in some species to improve rooting, or de novo root regeneration (DNRR). In this study, the use of floral foam was assessed for effects on DNRR efficiency and root qualities, for five genetically diverse Pyrus genotypes. DNRR efficiency was compared between floral foam, agar, and covered agar containing the same rooting hormone composition to assess the role of darkening of the root zone during rooting. The effect of floral foam was genotype-dependent, and increased DNRR efficiencies in most genotypes. In the case of P. communis 'Tsarigradka', the delivery method of auxin (dipping in a high concentration solution, rather than receiving a low concentration dissolved in the medium) in combination with floral foam was necessary to increase DNRR efficiency. Rooting in agar with the root zone covered to impose darkness did not show improvements over uncovered agar, suggesting that darkening of the root zone is not sufficient to explain improvements from using floral foam. Together, these results suggest that use of floral foam can be an effective strategy for rooting plants produced from in vitro methods.
Grape is an ancient cultivated crop that is highly prized for its fresh fruit and value-added products. Grapevine cultivation is limited by several diseases, which severely impact yield and productivity. Disease management is achieved using intensive pesticide spray schedules, which can adversely affect consumer health and the ecosystem. Disease-resistant grapevine cultivars that can be successfully cultivated with minimal pesticide use has long been desired by both growers and consumers. Grapevine improvement using conventional breeding approaches is difficult and time consuming, which constrains the development of new cultivars with disease resistance and enhanced quality traits. Grapevine biotechnology can be effectively used to complement conventional breeding techniques and speed up the development of new cultivars with improved traits. Rapid strides have been made in grapevine biotechnology since the first report on somatic embryogenesis in Vitis fifty years ago. Several in vitro culture protocols have been optimized and are routinely applied for grapevine genetic improvement and disease-free plant production. The use of embryogenic cultures as target tissues has enabled the development of highly efficient and reproducible genetic transformation protocols. Concerted efforts in whole genome sequencing now make it possible to identify Vitis genes and genetic elements conferring disease resistance, abiotic stress tolerance and quality traits. These advances should enable precision breeding and genome editing for improvement of traits of interest in existing commercial wine and table grape cultivars without altering existing desirable characteristics. The current review describes the discovery and optimization of in vitro protocols including micropropagation, embryo rescue and somatic embryogenesis for grapevine regeneration. The application of these protocols for grapevine genetic improvement via precision breeding and genome editing technologies is also discussed.
