Tree Genetics and Molecular Breeding 2025, Vol.15, No.5, 176-184 http://genbreedpublisher.com/index.php/tgmb 181 6.3 Outcomes: improved cultivars and implications for viticulture and winemaking Through these methods, many high-quality new varieties have been cultivated and applied to production. For example, varieties such as ‘Ecolly’ have both high quality and strong stress resistance through compound selection and multi-gene accumulation, and have good adaptability, promoting the sustainable development of the industry (Wang et al., 2021; Wang et al., 2022b; Wang et al., 2024). ‘Shine Muscat’ is obtained through multi-generation hybridization and molecular-assisted selection. It has the characteristics of large grains, seedless, crisp flesh and excellent aroma, and has strong market competitiveness (Yamada and Sato, 2016). Molecular breeding has also promoted the precise improvement of complex traits such as anthocyanin content and sugar-acid ratio, helping to address climate change and meet the diverse market demands. Improved varieties not only enhance the flavor of fruits and wines, but also strengthen disease resistance and stress resistance, reduce production costs, and promote the high-quality development of viticulture and winemaking (Bigard et al., 2018; Tello et al., 2019; Bigard et al., 2020; García-Abadillo et al., 2024; Gómez et al., 2024). 7 Challenges and Limitations 7.1 Long generation cycles and heterozygosity in grape breeding Grapes are perennial fruit trees with a long generation cycle and a high degree of heterozygosity. This makes the breeding speed of new varieties very slow. Due to the long juvenile period, each round of hybridization and trait screening takes several years, significantly reducing the breeding efficiency. High heterozygosity also makes the stable inheritance of superior traits complex. Many target traits are controlled by multiple genes, and there are complex interactions among genes, which makes directed improvement more difficult (Butiuc-Keul and Coste, 2023; Kumar et al., 2023; Wang et al., 2024). These factors together lead to a long cycle and slow progress in the improvement of grape quality. 7.2 Trade-offs between yield, quality, and stress tolerance In grape breeding, there is often a trade-off between yield, quality (such as flavor and nutrition) and stress resistance (such as disease resistance, cold resistance and salt-alkali resistance). For instance, when introducing disease-resistant or cold-resistant genes, it often brings about some undesirable fruit traits of wild species or American species, making it difficult for hybrid offspring to simultaneously achieve high quality and high resistance (Yamada and Sato, 2016; Wang et al., 2021; Wang et al., 2024). In addition, there is a negative correlation between some quality traits (such as sugar-acid ratio and fruit size) and stress resistance, which makes simultaneous improvement of multiple traits more difficult (Gascuel et al., 2017; Bigard et al., 2018; Bigard et al., 2020). Therefore, how to strike a balance among high yield, high quality and high stress resistance is the core challenge in current grape breeding. 7.3 Limited adoption of molecular tools in traditional breeding programs Although molecular breeding techniques such as molecular marker-assisted selection and genome editing have made progress both theoretically and experimentally, they are still not widely applied in traditional breeding projects. There are several main reasons: First, the genetic background of grapes is complex, with many traits regulated by multiple genes, making the development and application of molecular markers difficult. Second, some molecular tools have not yet achieved high throughput and low cost, making them difficult to commercialize. Thirdly, some breeders have a low acceptance of new technologies and limited operational capabilities (Gascuel et al., 2017; Zhang et al., 2021; Butiuc-Keul and Coste, 2023; Kumar et al., 2023). Furthermore, the application of molecular breeding in complex traits such as fruit flavor and nutrition is still in the exploratory stage, and a complete technical system has not yet been formed (García-Abadillo et al., 2024). 8 Future Perspectives 8.1 Application of multi-omics and systems biology for trait dissection Multi-omics techniques (such as genomics, transcriptomics, metabolomics, etc.) combined with systems biology are becoming important tools for studying the complex quality traits of grape fruits. By integrating transcriptome and metabolome data, the gene-metabolite networks that affect flavor, nutrition and stress resistance can be revealed. These achievements provide theoretical support for the development of molecular markers and precision
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