Molecular Plant Breeding 2025, Vol.16, No.3, 202-210 http://genbreedpublisher.com/index.php/mpb 202 Research Insight Open Access Improving the Fruit Flavor of Golden Pitaya through Gene Editing: Applications of CRISPR/Cas9 in Metabolic Pathways Zhen Li, Zhonggang Li Tropical Specialty Crops Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: zhonggang.li@hitar.org Molecular Plant Breeding, 2025, Vol.16, No.3 doi: 10.5376/mpb.2025.16.0020 Received: 20 May, 2025 Accepted: 22 Jun., 2025 Published: 30 Jun., 2025 Copyright © 2025 Li and Li, 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: Li Z., and Li Z.G., 2025, Improving the fruit flavor of golden pitaya through gene editing: applications of CRISPR/Cas9 in metabolic pathways, Molecular Plant Breeding, 16(3): 202-210 (doi: 10.5376/mpb.2025.16.0020) Abstract This study analyzed the current status and application prospects of gene editing technology in improving the flavor of tropical fruit bird's nest fruit (golden pitaya, Selenicereus megalanthus). This study analyzed the flavor composition and metabolic pathways of bird's nest fruit, including the accumulation mechanism of key substances such as sugars, organic acids and aromatic volatiles, and discussed the key gene selection strategies that affect flavor, such as enzymes and inhibitors that regulate sugar accumulation, genes that control organic acid synthesis and transportation, and pathway enzymes involved in the biosynthesis of aromatic substances. The application strategies of CRISPR/Cas9 technology in flavor improvement are mainly introduced, including targeted gene knockout to increase sugar content and reduce acidity, metabolic pathway reprogramming to increase the content of aromatic substances, and multi-gene editing to achieve comprehensive improvement of flavor. At the same time, the latest progress in fruit flavor improvement at home and abroad is outlined, such as the simultaneous editing of multiple genes in tomatoes to significantly increase the soluble sugar content, the identification and functional verification of aroma regulatory genes in fruits such as strawberries, etc., and based on this, the feasibility and potential effect of flavor improvement of bird's nest fruit through gene editing are prospected. The targeted flavor improvement of bird’s nest fruit provides new ideas and new ways for tropical fruit breeding and industrial upgrading. Keywords Golden pitaya; Fruit flavor; Metabolic pathway; Gene editing; CRISPR/Cas9 1 Introduction Flavor is one of the key factors in judging the quality and market value of fruits. The sweetness and sourness of fruits are mainly determined by the content of soluble sugars and organic acids, while the aroma depends on the complex composition of volatile organic compounds (Miao et al., 2024). As a tropical specialty fruit, bird’s nest fruit (commonly known as golden pitaya, Selenicereus megalanthus) is favored by consumers for its unique sweet and sour flavor and aroma. Golden pitaya is native to the Andes Mountains in Central America and is currently cultivated in South America and Southeast Asia. It is a fruit crop with important economic value in the Cactaceae family (Chen et al., 2021). Compared with red or white pitaya (Hylocereus undatus, etc.), golden pitaya has golden flesh, smaller seeds, sweet taste and not watery and astringent taste, and has unique competitiveness in the international market (Valero et al., 2025). Recent studies have sequenced and annotated the genome of golden pitaya and assembled a high-quality reference genome (Chen et al., 2021). The acquisition of genomic information lays the foundation for analyzing the flavor formation mechanism of golden pitaya and exploring flavor-related genes. Traditional breeding has been effective in improving fruit yield and disease resistance, but quality traits such as flavor are often neglected due to complex genetic mechanisms and breeding trade-offs, resulting in the phenomenon of “high yield but not delicious” (Kaur et al., 2023). For emerging fruits such as golden pitaya, how to balance yield and flavor in breeding and achieve targeted improvement of flavor is the key to improving their market competitiveness. The gene editing technology that has emerged in recent years, especially the genome fixed-point editing tools represented by CRISPR/Cas9, has provided a new way to accurately improve fruit flavor (Ma et al., 2023; Tiwari et al., 2023).
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