Molecular Plant Breeding 2025, Vol.16, No.1, 1-12 http://genbreedpublisher.com/index.php/mpb 10 7.2 Functional validation of QTLs through gene editing technologies (e.g., CRISPR) The functional validation of QTLs is crucial for confirming their roles in trait expression and for potential application in breeding programs. Gene editing technologies, such as CRISPR/Cas9, offer powerful tools for this purpose. By precisely targeting and modifying specific genes within QTL regions, researchers can validate the effects of these genes on phenotypic traits. For example, the identification of candidate genes for fruit shape and size QTLs in cucumber can be followed by CRISPR-mediated knockout or overexpression studies to confirm their functional roles (Gao et al., 2020; Pan et al., 2022). This approach not only validates the QTLs but also provides insights into the underlying molecular mechanisms, paving the way for the development of improved cucumber varieties with desirable traits. 7.3 Integrating QTL data with transcriptomic and proteomic studies for comprehensive trait analysis To achieve a comprehensive understanding of the genetic basis of agronomic traits, it is essential to integrate QTL mapping data with transcriptomic and proteomic analyses. This integrative approach can reveal the regulatory networks and pathways involved in trait expression. For instance, transcriptome profiling of near-isogenic lines (NILs) has been used to identify differentially expressed genes associated with fruit size and shape QTLs in cucumber, highlighting the role of auxin-mediated cell division and expansion (Pan et al., 2022). Similarly, combining QTL mapping with RNA-seq data has led to the identification of key genes and transcription factors involved in fruit length regulation (Xing et al., 2023). By incorporating proteomic data, researchers can further elucidate the protein interactions and modifications that contribute to trait development, providing a holistic view of the genetic and molecular basis of agronomic traits in cucumber. 8 Conclusion The genetic basis of agronomic traits in cucumber has been widely investigated through QTL mapping and genome-wide association studies (GWAS), leading to substantial advancements in identifying and characterizing genes and QTLs linked to key phenotypic traits. A notable review documented 81 simply inherited trait genes or major-effect QTLs that have been cloned or fine-mapped, alongside 322 QTLs for 42 quantitative traits, such as disease resistance to seven pathogens. For parthenocarpy- a critical trait in cucumber production—six loci have been identified via GWAS, showing its polygenic nature. Genetic studies on cucumber populations reveal high heritability for most agronomic traits, underscoring their strong genetic basis. Additionally, research using microsatellite markers and SNPs has provided valuable insights into cucumber germplasm’s genetic diversity and structure, which are essential for effective breeding programs. Key discoveries, such as the NS gene for fruit spine density and the Ef1.1 QTL for early flowering, further underscore the progress in understanding the genetic regulation of important agronomic traits in cucumber. These findings have profound implications for future cucumber breeding and crop enhancement efforts. Identifying specific genes and QTLs offers valuable markers for marker-assisted selection (MAS), allowing breeders to target desirable traits like disease resistance, parthenocarpy, and early flowering more efficiently. High heritability of major traits suggests that genetic improvements through selective breeding could yield substantial gains in crop performance.The genetic diversity found within cucumber germplasm collections provides a rich resource for developing new varieties with improved traits, enhancing both crop resilience and productivity. Furthermore, knowledge of genetic pathways controlling traits like leaf morphology, fruit development, and plant architecture can guide breeding strategies for better crop management. The use of molecular techniques, such as CRISPR/Cas9 for precise gene editing, offers potential for targeted trait modifications, expediting the creation of superior cucumber varieties. These advances in genetic research lay a strong foundation for ongoing improvement in cucumber breeding, equipping agriculture to tackle present and future challenges. Acknowledgments Thanks to the reviewers for providing detailed comments and guidance on the manuscript of this study. The reviewers’ keen insights into the issues and attention to detail have greatly benefited the authors. Funding This research was supported by Zhoushan Municipal Basic Research Foundation of Zhejiang Province under Grant No.2024C31028.
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