Indirect somatic embryogenesis of Theobroma cacao L. in liquid medium and improvement of embryo-to-plantlet conversion rate

Spatiotemporal transcriptome and metabolome landscapes of cotton somatic embryos

Somatic embryogenesis (SE) is a developmental process related to the regeneration of tissue-cultured plants, which serves as a useful technique for crop breeding and improvement. However, SE in cotton is difficult and elusive due to the lack of precise cellular level information on the reprogramming of gene expression patterns involved in somatic embryogenesis. Here, we investigate the spatial and single-cell expression profiles of key genes and the metabolic patterns of key metabolites by integrated single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics (ST), and spatial metabolomics (SM). To evaluate the results of these analyses, we functionally characterized the potential roles of two representative marker genes, AATP1 and DOX2, in the regulation of cotton somatic embryo development. A publicly available web-based resource database ( https://cotton.cricaas.com.cn/somaticembryo/ ) in this study provides convenience for future studies of the expression patterns of marker genes at specific developmental stages during the process of SE in cotton.

Effects of simulated climate change conditions of increased temperature and [CO2] on the early growth and physiology of the tropical tree crop, Theobroma cacao L

Despite multiple studies of the impact of climate change on temperate tree species, experiments on tropical and economically important tree crops, such as cacao (Theobroma cacao L.), are still limited. Here, we investigated the combined effects of increased temperature and atmospheric carbon dioxide concentration ([CO2]) on the growth, photosynthesis and development of juvenile plants of two contrasting cacao genotypes: SCA 6 and PA 107. The factorial growth chamber experiment combined two [CO2] treatments (410 and 700 p.p.m.) and three day/night temperature regimes (control: 31/22 °C, control + 2.5 °C: 33.5/24.5 °C and control + 5.0 °C: 36/27 °C) at a constant vapour pressure deficit (VPD) of 0.9 kPa. At elevated [CO2], the final dry weight and the total and individual leaf areas increased in both genotypes, while the duration for individual leaf expansion declined in PA 107. For both genotypes, elevated [CO2] also improved light-saturated net photosynthesis (Pn) and intrinsic water-use efficiency (iWUE), whereas leaf transpiration (E) and stomatal conductance (gs) decreased. Under a constant low VPD, increasing temperatures above 31/22 °C enhanced the rates of Pn, E and gs in both genotypes, suggesting that photosynthesis responds positively to higher temperatures than previously reported for cacao. However, dry weight and the total and individual leaf areas declined with increases in temperature, which was more evident in SCA 6 than PA 107, suggesting the latter genotype was more tolerant to elevated temperature. Our results suggest that the combined effect of elevated [CO2] and temperature is likely to improve the early growth of high temperature-tolerant genotypes, while elevated [CO2] appeared to ameliorate the negative effects of increased temperatures on growth parameters of more sensitive material. The evident genotypic variation observed in this study demonstrates the scope to select and breed cacao varieties capable of adapting to future climate change scenarios.

Regeneration of cocoa (Theobroma cacao L.) via somatic embryogenesis: Key aspects in the in vitro conversion stage and in the ex vitro adaptation of plantlets

Adapting plantlets to ex vitro conditions is a decisive step in the micropropagation process via organogenesis or somatic embryogenesis (ES). The percentage of success in this stage determines the quality of the product, an example of which is found in cocoa plantlets regenerated by ES, which require specific conditions to overcome the stress of the new environment. Considering the quality of the in vitro plantlets largely determines the survival and growth in ex vitro conditions, the effect of two culture media between the embryo maturation stage and the initial stage of conversion to plantlet was evaluated (EM2 - MM6 and EM2 – MF medium), achieving with the latter greater stem height, root length and the number of true leaves. In the final stage of the conversion and growth of the plantlet, the effect of five culture media was evaluated (ENR6, MF, ENR8, EDL, PR), achieving better results in stem height, root length, and the number of true leaves on MF medium. In addition, it was found that the transition of the EM2-MF had a significant development in the presence of the desired pivoting root and fibrous roots. Under nursery conditions, the growth and development of the plantlets was tested through the inoculation of beneficial microorganisms to promote survival. The plantlets that met the minimum morphological parameters for acclimation were planted in a substrate of coconut palm and sand (3:1 v/v) previously selected in the laboratory (BS). The effect of Pseudomonas ACC deaminase (PAACd), Trichoderma asperellum (Ta) and arbuscular mycorrhiza forming fungus (AMF) and different concentrations of phosphorus (PC) (0%, 50% and 100%) in the Hoagland nutrient solution (1:10) was evaluated. First, for CCN5, 62.5% of survival was obtained with PAACd + AMF. Second, the largest leaf size and survival were obtained with PAACd + Ta for CNCh12 and CCN51; likewise, for CNCh13, the best result was obtained with PAACd. Keywords: Cacao, Clonal propagation, Mycorrhiza, Pseudomonas, Trichoderma.

Propagation of the Colombian genotype of cacao (Theobroma cacao L.) CNCh-12 by somatic embryogenesis

Cocoa production (Theobroma cacao L.) is essential globally and constitutes one of the leading export products for Colombia. Understanding the limitations faced by this crop in Latin American countries, it is required, among other aspects, to contribute to strengthening the first link in the production chain through efficient propagation methods and genetic improvement. Knowing that somatic embryogenesis is an alternative to conventional propagation and constitutes an obligatory step in a breeding platform, the objective of this work was to establish a somatic embryogenesis protocol until the plantlet acclimatization in the nursery for the regional genotype CNCh-12, a promising material with productivities higher than 2,000 kg/ha. Different protocols were evaluated, from callogenesis induction, through the expression of primary somatic embryos (PSE) followed by maturation and subsequent conversion to plantlet two types of explants (petal and staminode) and culture time (according to the stage). Additionally, the induction of secondary somatic embryos (SSE) was evaluated in two culture media (L and F). For CNCh-12, the petal was found as an appropriate explant, with a minimum time of 15 days in induction for PSE formation, without difference between the culture media F and L (22 average embryos). Embryo maturation was achieved in medium F after 30 days, followed by an additional 30 days for conversion to plantlet (52.83%). The concentration of salts to increase the conversion and development of the embryos was 1/5 of that used in F. The highest number of SSE was in the L medium. Finally, the ex-vitro adaptation was achieved when the plants were planted in 50:50 sand-coconut fiber and moistened weekly with Hoagland's solution (1:10). Keywords: Cacao, petals, in vitro propagation, plant growth regulators, somatic embryogenesis.

Cost Analysis of Cacao (Theobroma cacao L.) Plant Propagation through the Somatic Embryogenesis Method

In vitro cacao (Theobroma cacao L.) production via somatic embryogenesis (SE) is being implemented to mass propagate clonal plant material with the donor material’s prominent characteristics. Though it is an advanced technology, it is con-sidered expensive compared to other propagation techniques. This work focused on identifying the critical financial feasi-bility factors for the SE productive process. The process's costs were estimated, identifying factors influencing each la-boratory's standardized ES process. A Monte Carlo Simulation (MCS) was performed to evaluate different variables upon increasing productive scale in a biofactory (commercial-scale production). The projected lot volume was 100,000 plantlets in solid media, considering the process flow from in vitro introduction to acclimation. A biofactory operational model was projected, establishing time and operator movements and identifying direct and indirect costs. Costs were defined by the standardized or integral method, with estimated and budgeted calculations to set the cost per plantlet. The identified cost components were culture medium (CM), indirect manufacturing costs (IMC), labor (direct and indirect) and operating expenses. Labor had the most significant share of the costs, at 53%, followed by operating expenses, at 30%, CM, at 12%, and IMC, at 5%. The MCS helped define that the variables with the highest impact on unit price were the embryos’ response in the germination-acclimation stage and the proliferation coefficient during the maturation stage. This projection yielded a figure of US $0.73 per plantlet. However, strategies to reduce this cost have been proposed. These strategies are mainly conducive to optimizing labor and implementing practices that increase multiplication. Keywords. Plant Tissue culture, Cost analysis, Large-scale production, Biofactory, Monte Carlo Simulation (MCS)

Theobroma cacao: Somatic Embryogenesis

A two-step process combining direct and indirect somatic embryogenesis, on solid and liquid medium, respectively is described for Theobroma cacao L. Staminodes and petals from unopened bud flowers are used to induce primary direct embryos. Then, these primary embryos are cut to produce embryogenic calli which will develop secondary embryos. This step of indirect SE allows us to produce large quantities of embryos and to do mass propagation using liquid culture medium. Despite a very strong clone dependency and high batch-to-batch variability, about 80% of T. cacao cultivars respond to somatic embryogenesis and can be propagated by this method.

Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.)

Transcriptome analysis of maize embryogenic callus and somatic embryos reveals associated genes reprogramming, hormone signaling pathways and transcriptional regulation involved in somatic embryogenesis in maize. Somatic embryos are widely utilized in propagation and genetic engineering of crop plants. In our laboratory, an elite maize inbred line Y423 that could generate intact somatic embryos was obtained and applied to genetic transformation. To enhance our understanding of regulatory mechanisms during maize somatic embryogenesis, we used RNA-based sequencing (RNA-seq) to characterize the transcriptome of immature embryo (IE), embryogenic callus (EC) and somatic embryo (SE) from maize inbred line Y423. The number of differentially expressed genes (DEGs) in three pairwise comparisons (IE-vs-EC, IE-vs-SE and EC-vs-SE) was 5767, 7084 and 1065, respectively. The expression patterns of DEGs were separated into eight major clusters. Somatic embryogenesis associated genes were mainly grouped into cluster A or B with an expression trend toward up-regulation during dedifferentiation. GO annotation and KEGG pathway analysis revealed that DEGs were implicated in plant hormone signal transduction, stress response and metabolic process. Among the differentially expressed transcription factors, the most frequently represented families were associated with the common stress response or related to cell differentiation, embryogenic patterning and embryonic maturation processes. Genes include hormone response/transduction and stress response, as well as several transcription factors were discussed in this study, which may be potential candidates for further analyses regarding their roles in somatic embryogenesis. Furthermore, the temporal expression patterns of candidate genes were analyzed to reveal their roles in somatic embryogenesis. This transcriptomic data provide insights into future functional studies, which will facilitate further dissections of the molecular mechanisms that control maize somatic embryogenesis.

Introducing a hybrid artificial intelligence method for high-throughput modeling and optimizing plant tissue culture processes: the establishment of a new embryogenesis medium for chrysanthemum, as a case study

Data-driven models in a combination of optimization algorithms could be beneficial methods for predicting and optimizing in vitro culture processes. This study was aimed at modeling and optimizing a new embryogenesis medium for chrysanthemum. Three individual data-driven models, including multi-layer perceptron (MLP), adaptive neuro-fuzzy inference system (ANFIS), and support vector regression (SVR), were developed for callogenesis rate (CR), embryogenesis rate (ER), and somatic embryo number (SEN). Consequently, the best obtained results were used in the fusion process by a bagging method. For medium reformulation, effects of eight ionic macronutrients on CR, ER, and SEN and effects of four vitamins on SEN were evaluated using data fusion (DF)-non-dominated sorting genetic algorithm-II (NSGA-II) and DF-genetic algorithm (GA), respectively. Results showed that DF models with the highest R² had superb performance in comparison with all other individual models. According to DF-NSGAII, the highest ER and SEN can be obtained from the medium containing 14.27 mM NH₄⁺, 38.92 mM NO₃^-, 22.79 mM K⁺, 5.08 mM Cl^-, 3.34 mM Ca²⁺, 1.67 mM Mg²⁺, 2.17 mM SO₄^2-, and 1.44 mM H₂PO₄^-. Based on the DF-GA model, the maximum SEN can be obtained from a medium containing 0.61 μM thiamine, 5.93 μM nicotinic acid, 0.25 μM biotin, and 0.26 μM riboflavin. The efficiency of the established-optimized medium was experimentally compared to Murashige and Skoog medium (MS) for embryogenesis of five chrysanthemum cultivars, and results indicated the efficiency of optimized medium over MS medium.Key points• MLP, SVR, and ANFIS were fused by a bagging method to develop a data fusion model.• NSGA-II and GA were linked to the data fusion model for establishing and optimizing a new embryogenesis medium.• The new culture medium (HNT) had better efficiency than MS medium.

An innovative automated active compound screening system allows high-throughput optimization of somatic embryogenesis in Coffea arabica

Somatic embryogenesis (SE) faces many challenges in fulfilling the growing demand for elite materials. A high-throughput approach is required to accelerate the optimization of SE protocols by multiplying experimental conditions within a limited time period. For the first time in plant micropropagation, we have developed a miniaturized and automated screening system to meet high-throughput standards. Coffea arabica embryo regeneration, classically achieved in 250-ml Erlenmeyer flasks, was successfully miniaturized in 24-well plates, allowing a volume downscaling factor of 100 and a space saving of 53 cm²/well. Cell clusters were ground and filtered to fit the automated pipetting platform, leading to fast, reproducible and uniform cluster distribution (23.0 ± 5.5 cell clusters/well) and successful regeneration (6.5 ± 2.2 embryos/well). Pilot screening of active compounds on SE was carried out. Compounds belonging to the histone deacetylase inhibitor family were tested for embryo regeneration efficiency. Cells treated with 1 µM Trichostatin A showed a marked 3-fold increase in the number of regenerated embryos. When re-tested in 250-ml flasks, the same enhancement was obtained, thereby validating the miniaturized and automated screening method. These results showed that our screening system is reliable and well suited to screening hundreds of compounds, offering unprecedented perspectives in plant micropropagation.

Unravelling the Metabolic and Hormonal Machinery During Key Steps of Somatic Embryogenesis: A Case Study in Coffee

Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial-and-error approach. Using coffee as a model plant, we report here the first global analysis of metabolome and hormone dynamics aiming to unravel mechanisms regulating cell fate and totipotency. Sampling from leaf explant dedifferentiation until embryo development covered 15 key stages. An in-depth statistical analysis performed on 104 metabolites revealed that massive re-configuration of metabolic pathways induced SE. During initial dedifferentiation, a sharp decrease in phenolic compounds and caffeine levels was also observed while auxins, cytokinins and ethylene levels were at their highest. Totipotency reached its highest expression during the callus stages when a shut-off in hormonal and metabolic pathways related to sugar and energetic substance hydrolysis was evidenced. Abscisic acid, leucine, maltotriose, myo-inositol, proline, tricarboxylic acid cycle metabolites and zeatin appeared as key metabolic markers of the embryogenic capacity. Combining metabolomics with multiphoton microscopy led to the identification of chlorogenic acids as markers of embryo redifferentiation. The present analysis shows that metabolite fingerprints are signatures of cell fate and represent a starting point for optimizing SE protocols in a rational way.

Morpho-histological development of the somatic embryos of Typha domingensis

Background

Sustainable methods of propagation of Typha domingensis through somatic embryogenesis can help mitigate its current condition of ecological marginalization and overexploitation. This study examined whether differentiation up to coleoptilar embryos could be obtained in an embryogenic line proliferated with light and high auxin concentration.

Methods

Murashige and Skoog medium at half ionic strength and containing 3% sucrose and 0.1% ascorbic acid was used for the three embryogenic phases. Induction started with aseptic 9-day-old germinated seeds cultured in 0.5 mg L⁻¹ 2,4-dichlorophenoxyacetic (2,4-D). Proliferation of the embryogenic callus was evaluated at 2,4-D concentrations ranging from 0 to 2 mg L⁻¹ in cultures maintained in the dark. The dominant embryogenic products obtained in each treatment were used as embryogenic lines in the third phase. Thus, maturation of the somatic embryos (SEs) was analyzed using four embryogenic lines and under light vs. dark conditions. Embryogenic differentiation was also monitored histologically.

Results

Proliferation of the nine morphogenetic products was greater in the presence of 2,4-D, regardless of the concentration, than in the absence of auxin. Among the products, a yellow callus was invariably associated with the presence of an oblong SE and suspended cells in the 2,4-D treatments, and a brown callus with scutellar somatic embryos (scSEs) in the treatment without 2,4-D. During the maturation phase, especially the embryogenic line but also the light condition resulted in significant differences, with the highest averages of the nine morphogenetic products obtained under light conditions and the maximum concentration of auxin (YC3 embryogenic line). Only this line achieved scSE growth, under both light and dark conditions. Structurally complete coleoptilar somatic embryos (colSEs) could be anatomically confirmed only during the maturation phase.

Discussion

In the embryogenic line cultured with the highest auxin concentration, light exposure favored the transdifferentiation from embryogenic callus to scSE or colSE, although growth was asynchronous with respect to the three embryogenic phases. The differentiation and cellular organization of the embryos were compatible with all stages of embryogenic development in other monocotyledons. The growth of colSEs under light conditions in the YC3 embryogenic line and the structurally complete anatomic description of colSEs demonstrated that differentiation up to coleoptilar embryos could be obtained. The diversity of embryogenic products obtained in the YC3 embryogenic line opens up the opportunity to synchronize histological descriptions with the molecules associated with the somatic embryogenesis of Typha spp.