Tree Genetics and Molecular Breeding 2024, Vol.14, No.4, 177-184 http://genbreedpublisher.com/index.php/tgmb 182 breeders to introduce desirable traits such as improved yield, enhanced nutritional content, and increased resistance to biotic and abiotic stresses directly into elite cultivars (Zheng et al., 2021; Kostick et al., 2023). This method circumvents the lengthy and resource-intensive processes associated with traditional breeding techniques, such as backcrossing and selection. Moreover, the ability to perform transgene-free genome editing through CRISPR-Cas9 can facilitate public acceptance of genetically modified crops, as it reduces concerns associated with transgenic modifications (Vassilev et al., 2006). The potential to manipulate consumer-friendly traits, such as fruit quality and stress tolerance, further underscores the transformative impact of CRISPR-Cas9 on breeding programs, paving the way for sustainable agricultural practices and improved crop resilience (Kostick et al., 2023). 5 Challenges and Future Directions 5.1 Gaps in genomic resources for dragon fruit Despite the economic importance of dragon fruit, there are significant gaps in its genomic resources. The draft genome of Hylocereus undatus provides a foundational resource, yet it highlights the need for more comprehensive genomic data to fully understand the genetic basis of key traits such as drought resistance and fruit flavor (Zheng et al., 2021). The current genomic resources are limited, and there is a need for more extensive sequencing efforts and the development of high-density genetic maps to facilitate advanced breeding programs. Additionally, the lack of genomic resources in underutilized fruit crops, including dragon fruit, is a barrier to exploiting their full potential in breeding applications (Tchokponhoué et al., 2020). 5.2 Integrating multi-omics approaches for trait analysis Integrating multi-omics approaches, such as genomics, transcriptomics, and metabolomics, can significantly enhance the understanding of complex traits in dragon fruit. The co-localization of betacyanin biosynthetic genes in the dragon fruit genome suggests that multi-omics approaches could elucidate the regulatory networks involved in pigment biosynthesis and other important traits (Zheng et al., 2021). By combining data from different omics layers, researchers can identify key regulatory genes and pathways, leading to more targeted breeding strategies (Salazar et al., 2017). This integration is crucial for dissecting polygenic traits and improving the efficiency of marker-assisted selection in dragon fruit breeding (Salazar et al., 2017). 5.3 Climate-resilient breeding strategies Developing climate-resilient dragon fruit varieties is essential in the face of increasing environmental challenges. The genetic diversity observed in dragon fruit accessions, as revealed by morphological traits and ISSR markers, provides a valuable resource for breeding programs aimed at enhancing drought tolerance and other stress-related traits (Tao et al., 2014). Genomic selection and genome-assisted parental selection are promising strategies to accelerate the breeding of climate-resilient varieties by reducing the generation interval and increasing the accumulation of favorable alleles (Muranty et al., 2015). These strategies can help develop dragon fruit cultivars that are better adapted to changing climatic conditions, ensuring sustainable production and economic viability. 6 Conclusions The study on the functional genomics of key traits in dragon fruit for breeding applications highlights significant advancements in the field of plant genomics and breeding. The integration of functional markers (FMs) and genomic resources has been pivotal in enhancing the precision and efficiency of breeding programs. These tools allow for the direct selection of genes associated with desirable phenotypic traits, thereby increasing the efficiency of developing new cultivars with improved agronomic traits and resistance to biotic and abiotic stresses. Functional genomics offers practical applications in dragon fruit breeding by utilizing high-throughput sequencing and genome editing techniques. These methods facilitate the identification of genes linked to important horticultural traits, enabling breeders to develop cultivars with enhanced fruit quality, yield, and stress resistance. The use of marker-assisted selection (MAS) further supports the breeding process by providing reliable genetic markers that assist in selecting superior parent plants and progeny.
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