Tree Genetics and Molecular Breeding 2025, Vol.15, No.5, 192-201 http://genbreedpublisher.com/index.php/tgmb 192 Feature Review Open Access Metabolomic and Genomic Analysis of Theobromine Biosynthesis in Theobroma cacao Xingzhu Feng, Shaomin Yang, Jianli Zhong Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: jianli.zhong@hibio.org Tree Genetics and Molecular Breeding, 2025, Vol.15, No.5 doi: 10.5376/tgmb.2025.15.0023 Received: 01 Sep., 2025 Accepted: 07 Oct., 2025 Published: 14 Oct., 2025 Copyright © 2025 Feng et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Feng X.Z., Yang S.M., and Zhong J.L., 2025, Metabolomic and genomic analysis of theobromine biosynthesis in Theobroma cacao, Tree Genetics and Molecular Breeding, 15(5): 192-201 (doi: 10.5376/tgmb.2025.15.0023) Abstract This study combined metabolomics and genomics data to analyze the biosynthesis of theobromine in Theobroma cacao. The results show that theobromine is mainly synthesized in the young peels and cotyledons, and gradually accumulates in the seeds as the tissues mature. Metabolic pathway analysis revealed that the synthesis of theobromine is related to the transformation of purine nucleotides such as AMP and GMP, with key intermediates including 7-methylxanthosine and 3-methylxanthine. Genomic research has found that during the domestication process, genes related to theobromine metabolism were significantly selected, thereby affecting the theobromine content in different varieties. Multi-omics data also indicate that post-processing steps such as fermentation can lead to a decrease in theobromine levels. This study aims to provide molecular targets and theoretical references for improving cocoa quality and developing functional components. Keywords Theobroma cacao; Theobromine; Metabolomics; Genomics; Biosynthetic pathway 1 Introduction Theobroma cacao is an important cash crop in tropical regions. Its seeds-cocoa beans-are the main raw materials for chocolate and a variety of foods, beverages and cosmetics. The cocoa industry has brought income to millions of smallholder farmers in West Africa, Central and South America, and Asia, and holds an important position in global agricultural trade, with an annual output of several million tons and a value of approximately 12 billion US dollars (González et al., 2019). Furthermore, cocoa bean by-products such as bean shells and peels are also rich in bioactive substances and are regarded as new resources for sustainable agriculture and the development of the bioeconomy. Theobromine is the most abundant methylxanthine alkaloid in cocoa beans. It not only endows chocolate with a unique bitterness and flavor, but also has multiple physiological functions. Studies have shown that theobromine has health benefits such as antioxidation, anti-inflammation and cardiovascular protection (Sugimoto et al., 2014). Theobromine also plays an important role in the growth process of Theobroma cacao itself, which can help the plant resist pathogens and environmental stress (Pereira-Caro et al., 2013; Cornejo et al., 2018). Its content and distribution are affected by variety, developmental stage and processing procedure, and thereby determine the quality and functional characteristics of cocoa products (Zheng et al., 2004; Cortez et al., 2023; Ruiz-Santiago et al., 2024). This study combines metabolomics and genomics to elucidate the biosynthetic pathways and regulatory mechanisms of theobromine, reveal its accumulation changes at different tissues and developmental stages, analyze related metabolic pathways and key enzyme genes, and explore the selection pressure and genetic variation of these genes in the domestication and variety improvement of Theobroma cacao. This study aims to provide theoretical basis and molecular tools for improving cocoa quality, developing functional foods, and promoting the sustainable utilization of cocoa resources. 2 Biochemical Pathway of Theobromine Biosynthesis 2.1 Overview of purine alkaloid biosynthesis Theobromine and caffeine both belong to purine alkaloids and are the main active components in Theobroma
RkJQdWJsaXNoZXIy MjQ4ODYzNA==