Genomics and Applied Biology 2024, Vol.15, No.6, 320-332 http://bioscipublisher.com/index.php/gab 325 (QTLs) with higher precision, accelerating the breeding process. These high-density genetic maps facilitate marker-assisted selection (MAS) in Cactaceae breeding, improving efficiency and accuracy (Chen et al., 2021). 5.2 Genetic diversity analysis and hybrid breeding using molecular markers Molecular marker technologies, especially inter-simple sequence repeat (ISSR) markers, play a critical role in analyzing the genetic diversity of Cactaceae plants. Studies have shown that out of 16 ISSR primers screened, 14 primers produced 178 reproducible amplification bands with polymorphism percentages ranging from 20% to 92.8%, and the polymorphic information content (PIC) values reached as high as 0.91 (Abirami et al., 2021; Nashima et al., 2021). These markers effectively distinguish the three major cultivars of dragon fruit, clustering them into different genetic groups based on flesh color and geographic origin. For instance, DGF1 and DGF3 showed 52% genetic similarity, while DGF2 and DGF4 exhibited a higher genetic similarity of 76%. These findings elucidate genetic relationships among cultivars, providing scientific insights for the classification, identification, and breeding of dragon fruit germplasm resources. Moreover, combining morphological and molecular marker analyses enhances the reliability of germplasm studies. ISSR marker analysis has revealed significant differences among dragon fruit cultivars in traits such as fruit morphology, peel, and flesh color, which are highly consistent with molecular data (Abirami et al., 2021). This integrative approach effectively supports the development and utilization of germplasm resources, offering valuable references for the conservation and genetic improvement of Cactaceae plants such as dragon fruit. 5.3 Trait improvement through gene regulation and functional genomics Functional genomics, which deciphers transcriptome data and gene regulatory networks, provides essential support for trait improvement in Cactaceae plants. In the study of pitaya (Selenicereus spp.), the transcription factor HmoWRKY40 was identified as a key regulator of betacyanin synthesis, activating the biosynthesis of secondary metabolites by binding to the W-box region of the CYP76AD1 gene promoter (Zhang et al., 2021). Silencing of HmoWRKY40 resulted in a significant reduction in betacyanin content, further demonstrating the importance of this transcription factor in betalain biosynthesis (Figure 2). Additionally, multi-omics analyses have shown that genes related to stress resistance, such as those encoding antioxidant enzymes (POD and APX), and signal transduction genes are significantly upregulated under stress conditions. These genes, along with transcription factors such as WRKY and MYB, participate in stress responses and metabolic regulation. Through functional enrichment analyses and weighted gene co-expression network analysis (WGCNA), researchers have identified key gene modules involved in antioxidant defense, signal transduction, and metabolic regulation. Functional genomic studies have positioned transcription factor networks as a significant research direction for dragon fruit breeding. For example, the silencing of HmoWRKY40 using virus-induced gene silencing (VIGS) confirmed its role in enhancing fruit coloration and betacyanin content, demonstrating that its overexpression significantly improves these traits (Khokhar et al., 2024). In the future, combining functional genomics with molecular breeding technologies will further enhance the quality and stress resistance of dragon fruit while providing potential applications for the genetic improvement of other crops. 6 Case Studies 6.1 Study on root structure and genetic mechanism of Pachycereus pringlei Cactaceae species often thrive in arid or semi-arid environments, and their root structure and growth patterns are crucial for adapting to extreme conditions (Martino et al., 2018). Pachycereus pringlei, as a representative species, exhibits determinate growth of its primary root due to the exhaustion of root apical meristem (RAM). Rodriguez-Alonso et al. (2018) constructed the transcriptome of P. pringlei root apex at three developmental stages through RNA sequencing, revealing specific gene expression patterns and their relationship to RAM maintenance. The results indicated that the RAM of P. pringlei's primary root becomes exhausted at specific developmental stages, leading to determinate growth (Figure 3). This growth pattern is possibly an adaptive strategy to extreme arid environments, enhancing water absorption efficiency and promoting lateral root development.
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