Tree Genetics and Molecular Breeding 2025, Vol.15, No.3, 108-116 http://genbreedpublisher.com/index.php/tgmb 108 Feature Review Open Access Integrated Transcriptome and Metabolome Analysis Reveals the Genetic Regulation of Aroma Biosynthesis in Citrus Xingzhu Feng Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: xingzhu.feng@hibio.org Tree Genetics and Molecular Breeding, 2025, Vol.15, No.3 doi: 10.5376/tgmb.2025.15.0013 Received: 29 Apr., 2025 Accepted: 31 May, 2025 Published: 10 Jun., 2025 Copyright © 2025 Feng., 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., 2025, Integrated transcriptome and metabolome analysis reveals the genetic regulation of aroma biosynthesis in Citrus, Tree Genetics and Molecular Breeding, 15(3): 108-116 (doi: 10.5376/tgmb.2025.15.0013) Abstract This study mainly aims to clarify how the aroma of Citrus is produced. By using a combined analysis method of transcriptomics and metabolomics, it identifies the genes and pathways related to aroma synthesis, sorts out the main volatile components in the aroma of Citrus, and then introduces how these components are synthesized step by step. It was found that the expression changes of key enzyme genes such as TPS, LOX and ADH are related to the accumulation of aroma substances. This study also summarized some important regulatory factors and signaling pathways from different studies, all of which are related to the regulation of aroma synthesis. It emphasized the significance of multi-omics joint analysis, believing that it can help better improve the aroma traits of Citrus and also provide useful theoretical support and methodological ideas for breeding new varieties with better aroma. Keywords Citrus aroma; Transcriptomic analysis; Metabolomics; Aroma biosynthetic pathway; Molecular breeding 1 Introduction Citrus fruits have always been popular among global consumers because of their good aroma and taste (Wang et al., 2024b). These aromas come from some particular compounds, such as volatile terpenoids, aldehydes, alcohols and esters, which determine the flavor and quality of Citrus (Lu et al., 2024). These substances not only affect the taste of fruits when eaten, but also help plants resist pests and diseases and adapt to the environment. Among them, terpene components such as valencene and nootkatone are particularly important. They can make Citrus more fragrant and more likely to be favored by consumers (Sharon-Asa et al., 2003; Alquézar et al., 2017). At present, scientists do not know much about the key enzymes, transcription factors that regulate the synthesis of these aroma substances and the relationships among them (Sharon-Asa et al., 2003; Lu et al., 2024). It is still unclear which genes control the synthesis of aroma, how the expression of these genes is regulated, how the oil glands develop, and what the relationship is between these processes and aroma accumulation (Alquézar et al., 2017; Wang et al., 2024a). The genetic basis for the differences in aroma among various Citrus varieties has not yet been fully understood. This study combined transcriptome and metabolome data to identify several key genes and metabolites related to Citrus aroma. It also analyzed how these genes are regulated, explored how oil glands develop, and investigated the connection between them and aroma accumulation. These results can provide some scientific basis for improving the flavor of Citrus and enhancing the quality of varieties in the future. 2 Citrus Aroma: Composition and Biological Significance 2.1 Major aroma volatiles in Citrus: terpenoids, aldehydes, alcohols, esters The fragrance of Citrus mainly comes from many kinds of volatile organic compounds (VOCs). Among them, the most important ones are terpenoids, aldehydes, alcohols and esters. Terpenoids, such as limonene, β -farnene, β -caryophyllene and β -humulene, are particularly abundant in the essential oils of Citrus peels and leaves. Limonene is particularly abundant, accounting for more than 90% in the essential oil of sweet orange peel, and it is the main component of Citrus fragrance (Baccati et al., 2021; Ferrer et al., 2021; Ferrer et al., 2023). Aldehydes, such as octanal and decal, make fruits smell fresher and more fruity. Alcohols, such as linalool and α -terpineol,
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