Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species.

Camu camu is a typical Amazon native fruit shrub that possesses a diploid genome, moderate genetic diversity, and population structure. The fruits accumulate several essential nutrients and synthesize L-ascorbic acid (vitamin C) in great quantities and an array of diverse secondary metabolites with corroborated in vitro and in vivo health-promoting activities. These beneficial effects include antioxidative and antiinflammatory activities, antiobesity, hypolipidemic, antihypertensive and antidiabetic effects, DNA damage and cancer protection effects, and other bioactivities. Many health-promoting phytochemicals are biosynthesized in several metabolic pathways of camu camu. Their reconstruction from the fruit transcriptome database was accomplished by our research group. These include basic metabolic pathways such as glycolysis and pentose phosphate pathway, vitamin C biosynthesis pathways, and pathways involved in secondary metabolites production. Due to their agronomic potential and fruits growing demand, recently, based on an ideotype, programs were initiated for their domestication and genetic improvement, but so far with very negligible achievements. Consequently, we propose new strategies to accelerate the processes of domestication and genetic improvement based on state of the art technologies for multiomic data analysis and innovative molecular tools.

The Amazonian shrub Myrciaria dubia (camu-camu) produces vitamin C-rich fruits of growing commercial interest. However, sustainable utilization requires assessment and protection of the genetic diversity of the available germplasm. This study aimed to develop and apply microsatellite markers to assess genetic diversity and construct a core collection of M. dubia germplasm from the Peruvian Amazon. Sixteen polymorphic microsatellite loci were developed using an enrichment approach. The evaluation of 336 genotypes from 43 accessions of the germplasm bank, originating from eight river basins, was conducted using these newly developed markers. Genetic diversity parameters, including observed and expected heterozygosity, were calculated. Analysis of molecular variance (AMOVA) was performed to assess the distribution of genetic variation within and among accessions and river basins. Bayesian clustering analysis was employed to infer population structure. A core collection was constructed to maximize allelic richness. High genetic diversity was observed, with heterozygosity values ranging from 0.468 to 0.644 (observed) and 0.684 to 0.817 (expected) at the river basin level. AMOVA indicated significant genetic variation within (73–86%) compared to among (14–27%) accessions and river basins. Bayesian clustering detected ten genetic clusters, with several degrees of admixture among river basins, except for the genetically homogeneous Putumayo River basin. A core collection comprising 84 plant genotypes (25% of the full collection) was established, representing 90.82% of the overall allelic diversity. These results have important implications for M. dubia conservation strategies and breeding programs, in demonstrating a need for genetic connectivity between populations but preserving unique genetic resources in isolated basins. These results validate the expected levels of diversity and population subdivision in a crop and stress the need to secure genetically diverse germplasms, underscoring the importance of thorough genetic characterization for ex situ germplasm management.

Introduction: The ex situ conservation and characterization of native Theobroma cacao L. genetic resources are critical for sustainable cacao production and breeding programs in the face of climate change and escalating disease pressures. This study aimed to establish and characterize a novel germplasm bank from the Loreto region of the Peruvian Amazon, a key center of cacao diversity.Methods: We collected 140 native cacao accessions across 15 river basins in eight provinces of the Loreto region. Accessions were propagated using optimized grafting techniques with IMC 67 rootstock. Phenotypic evaluation was conducted on 402 plants using 36 standardized descriptors (25 quantitative and 11 qualitative). Data analysis included multivariate analysis using Uniform Manifold Approximation and Projection (UMAP) and Shannon-Weaver diversity indices to assess morphological diversity patterns.Results: Grafting achieved 100% survival rate, establishing a comprehensive germplasm bank. Phenotypic characterization revealed exceptional morphological diversity, with quantitative traits exhibiting substantial variation, particularly in fruit characteristics (CV = 15.82–50.82%) and pod index (CV = 144.82%). Multivariate analysis identified five distinct phenotypic groups, with reproductive traits showing stronger differentiation than vegetative traits. Shannon-Weaver diversity indices highlighted high overall phenotypic diversity (H' ≈ 0.7), with seed longitudinal shape and fruit apex form displaying the highest trait-specific diversity (H' > 1.0).Conclusion: This comprehensive characterization establishes a foundation for future multiomics studies and advanced breeding strategies. The documented diversity offers opportunities to leverage CRISPR-Cas-based editing and omics technologies to develop climate-resilient, high-yielding cacao varieties with superior quality traits, contributing significantly to global cacao conservation and improvement programs.

Cacao is an economically important crop that is currently planted in Asia, Africa, and America. Cuttings is a technique of vegetative propagation suitable for the conservation of selected desirable characteristics in cacao trees. The objective of this study was to evaluate the rooting of cacao cuttings in mini-tunnels with different doses of indole-3-butyric acid (IBA) to obtain a simple and viable vegetative propagation protocol. The experiment was carried out under a completely randomized design (CRD). Cuttings 5 to 7cm long were collected from the middle area of cacao tree crowns and treated with doses of 0, 1000, 2000, and 3000ppm of IBA; then they were placed in Jiffy© pellets and set to root in plastic-covered mini-tunnels with fog irrigation. The results indicate that treatments with 0 and 1000ppm of IBA produced the highest values in survival (100, both treatments) and rooting percentage (87.7 and 90.0, respectively) as well as number and length of roots (4.3 roots-4.21cm in length and 4.5 roots-5.32cm in length, respectively); likewise, cuttings treated with 0ppm rooted after 2440 days, followed by doses of 1000ppm (2446 days). All rooted cuttings without IBA (0ppm) achieved 100 acclimatization in nursery. In general, the best results were obtained without IBA application (Control 0ppm) in all the parameters evaluated, similar to those obtained with the application of 1000ppm IBA; these results indicate the success and efficiency of the vegetative propagation protocol proposed in this study.

Myrciaria dubia (Kunth) McVaugh (camu‐camu) is a shrub native to the Amazon region that produces fruits with a high content of vitamin C and various bioactive compounds, making it a functional food with antioxidant, anti‐inflammatory, and antimicrobial properties. However, it is unknown which microorganisms are associated with its root system and can influence its growth and productivity. Arbuscular mycorrhizal fungi (AMF) are associated with most plants and are essential for their establishment, survival, and productivity since they facilitate their nutrition, increase water absorption, and improve soil structure. Although the AMF association is already known in some species of Myrciaria, no report is available on its association in M. dubia. This study presents, for the first time, the symbiotic association between AMF and M. dubia from the INIA San Roque experimental station located in the Amazon region, Peru. For the morphological and molecular analyses of the AMF, samples of rhizospheric soil and roots from two native accessions of the National Germplasm Bank of M. dubia were collected. Eighteen AMF morphospecies were identified in rhizospheric soil, belonging to nine genera Acaulospora, Ambispora, Entrophospora, Diversispora, Gigaspora, Glomus, Paraglomus, Funneliformis, and Sclerocystis, being the first one the most frequent. The roots of M. dubia showed high colonization by AMF (mean = 91%), and characteristic structures of arbuscular mycorrhizae, such as vesicles, hyphae, and arbuscules, could be observed. Likewise, the molecular analysis detected the presence of genetic material (rDNA) corresponding to AMF in the roots of both accessions. Our results evidenced the symbiotic association between AMF and M. dubia, which encourages further investigation of the functional potential of these microorganisms in this economically crucial agricultural plant in Peru.