Tree Genetics and Molecular Breeding 2025, Vol.15, No.5, 192-201 http://genbreedpublisher.com/index.php/tgmb 200 HämäläT., Guiltinan M., Marden J., Maximova S., dePamphilis C., and Tiffin P., 2019, Gene expression modularity reveals footprints of polygenic adaptation in Theobroma cacao, Molecular Biology and Evolution, 37: 110-123. https://doi.org/10.1093/molbev/msz206 Herrera-Rocha F., Fernández-Niño M., Cala M., Duitama J., and Barrios A., 2023, Omics approaches to understand cocoa processing and chocolate flavor development: a review, Food Research International, 165: 112555. https://doi.org/10.1016/j.foodres.2023.112555 Koyama Y., Tomoda Y., Kato M., and Ashihara H., 2003, Metabolism of purine bases, nucleosides and alkaloids in theobromine-forming Theobroma cacao leaves, Plant Physiology and Biochemistry, 41: 977-984. https://doi.org/10.1016/j.plaphy.2003.07.002 Kuhn D., Figueira A., Lopes U., Motamayor J., Meerow A., Cariaga K., Freeman B., Livingstone D., and Schnell R., 2010, Evaluating Theobroma grandiflorum for comparative genomic studies with Theobroma cacao, Tree Genetics and Genomes, 6: 783-792. https://doi.org/10.1007/s11295-010-0291-0 Llerena W., Samaniego I., Vallejo C., Arreaga A., Zhunio B., Coronel Z., Quiroz J., Angós I., and Carrillo W., 2023, Profile of bioactive components of cocoa (Theobroma cacao L.) by-products from ecuador and evaluation of their antioxidant activity, Foods, 12(13): 2583. https://doi.org/10.3390/foods12132583 Mahmood U., Li X., Fan Y., Chang W., Niu Y., Li J., Qu C., and Lu K., 2022, Multi-omics revolution to promote plant breeding efficiency, Frontiers in Plant Science, 13: 1062952. https://doi.org/10.3389/fpls.2022.1062952 Mladenović K., Root Y., and Ramanathan D., 2018, UHPLC-HRMS analysis of theobromine in Theobroma cacao and its products, Journal of Nutrition and Food Sciences, 8: 737. https://doi.org/10.4172/2155-9600.1000737 Nguyen Q., Cao P., Chu N., Tran L., Le M., Luong H., Le Q., Dong G., and Chu H., 2025, The trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase in cocoa (Theobroma cacao L.): genome-wide identification and expression analysis, HAYATI Journal of Biosciences, 32(4): 940-949. https://doi.org/10.4308/hjb.32.4.940-949 Pereira-Caro G., Borges G., Nagai C., Jackson M., Yokota T., Crozier A., and Ashihara H., 2013, Profiles of phenolic compounds and purine alkaloids during the development of seeds of Theobroma cacao cv. Trinitario, Journal of Agricultural and Food Chemistry, 61(2): 427-434. https://doi.org/10.1021/jf304397m Pérez D., González J., Gómez E., Pérez J., Rodríguez J., and Monan M., 2018, Chemical characterization of metabolites from the husk of Theobroma cacao by GC-MS in Cuba, Journal of Applied Biotechnology, 6(2): 39-48. https://doi.org/10.5296/jab.v6i2.13263 Picard M., Scott-Boyer M., Bodein A., Périn O., and Droit A., 2021, Integration strategies of multi-omics data for machine learning analysis, Computational and Structural Biotechnology Journal, 19: 3735-3746. https://doi.org/10.1016/j.csbj.2021.06.030 Ramos-López O., Martínez J., and Milagro F., 2022, Holistic integration of omics tools for precision nutrition in health and disease, Nutrients, 14(19): 4074. https://doi.org/10.3390/nu14194074 Ruiz-Santiago F., Márquez-Rocha F., García-Alamilla P., Carrera-Lanestosa A., Ramírez-López C., Ocaranza-Sánchez E., and Jiménez-Rodríguez D., 2024, Physicochemical and biochemical changes in cocoa during the fermentation step, Fermentation, 10(8): 405. https://doi.org/10.3390/fermentation10080405 Shankar A., and Sharma K., 2022, Fungal secondary metabolites in food and pharmaceuticals in the era of multi-omics, Applied Microbiology and Biotechnology, 106: 3465-3488. https://doi.org/10.1007/s00253-022-11945-8 Sugimoto N., Miwa S., Hitomi Y., Nakamura H., Tsuchiya H., and Yachie A., 2014, Theobromine, the primary methylxanthine found in Theobroma cacao, prevents malignant glioblastoma proliferation by negatively regulating phosphodiesterase-4, extracellular signal-regulated kinase, Akt/mammalian target of rapamycin kinase, and nuclear factor-kappa B, Nutrition and Cancer, 66: 419-423. https://doi.org/10.1080/01635581.2013.877497 Tineo D., Bustamante D., Calderon M., and Oliva M., 2025, Comparative analyses of chloroplast genomes of Theobroma cacao from northern Peru, PLoS One, 20(3): e0316148. https://doi.org/10.1371/journal.pone.0316148 Wickramasuriya A., and Dunwell J., 2017, Cacao biotechnology: current status and future prospects, Plant Biotechnology Journal, 16: 4-17. https://doi.org/10.1111/pbi.12848 Wörheide M., Krumsiek J., Kastenmüller G., and Arnold M., 2021, Multi-omics integration in biomedical research - a metabolomics-centric review, Analytica Chimica Acta, 1141: 144-162. https://doi.org/10.1016/j.aca.2020.10.038 Wu Y., and Xie L., 2024, AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships, Computational and Structural Biotechnology Journal, 27: 265-277. https://doi.org/10.1016/j.csbj.2024.12.030 Yan J., and Wang X., 2022, Machine learning bridges omics sciences and plant breeding, Trends in Plant Science, 28(2): 199-210. https://doi.org/10.1016/j.tplants.2022.08.018
RkJQdWJsaXNoZXIy MjQ4ODYzNA==