Tree Genetics and Molecular Breeding 2024, Vol.14, No.5, 239-246 http://genbreedpublisher.com/index.php/tgmb 240 2 Genomic Resources for Pitaya 2.1 Genome sequencing projects Recent advancements in genome sequencing have significantly contributed to the understanding of pitaya (Hylocereus spp.) genetics. A notable project involved the assembly of a chromosome-level genome for Hylocereus undatus using various sequencing technologies, including PacBio-SMRT and Illumina HiSeq, which provided a comprehensive genomic resource for studying genome evolution and betalain biosynthesis (Chen et al., 2021). This genome assembly revealed a whole-genome triplication and a recent whole-genome duplication, offering insights into the evolutionary history of pitaya (Chen et al., 2021). Additionally, a high-density genetic map was constructed using whole genome resequencing, which aids in quantitative trait mapping and marker-assisted selection (Wu et al., 2021). 2.2 Transcriptomics and gene expression studies Transcriptomic analyses have been pivotal in understanding gene expression during pitaya fruit development and stress responses. For instance, RNA sequencing has been employed to identify differentially expressed genes during the ripening of red pitaya (Hylocereus polyrhizus), providing a basis for selecting reference genes for qRT-PCR studies (Zheng et al., 2020). Moreover, transcriptomic data have facilitated the construction of gene regulatory networks involved in betalain biosynthesis, enhancing our understanding of the molecular mechanisms underlying this process (Chen et al., 2021; Zhao et al., 2023). 2.3 Functional genomics approaches Functional genomics approaches have been utilized to explore gene functions in pitaya, particularly in stress tolerance. The HuERF1 gene, an ethylene response factor fromHylocereus undatus, was identified and shown to enhance salt tolerance when overexpressed in Arabidopsis, indicating its role in abiotic stress regulation (Qu et al., 2020). Additionally, the development of SSR markers has enabled the assessment of genetic diversity and identification of pitaya accessions, which is crucial for breeding programs (Nashima et al., 2021). These functional genomics tools are essential for advancing molecular breeding and improving pitaya cultivars. 3 Marker-Assisted Breeding in Pitaya 3.1 Development of molecular markers The development of molecular markers is a crucial step in marker-assisted breeding, providing the tools necessary for genetic analysis and selection. In pitaya (Hylocereus spp.), various types of molecular markers have been developed to assess genetic diversity and assist in breeding programs. For instance, Random Amplified Polymorphic DNA (RAPD) markers have been used to study genetic variability among pitaya accessions, revealing significant genetic diversity even within the same species (Junqueira et al., 2010). Additionally, simple sequence repeat (SSR) markers have been developed using next-generation sequencing technologies, which have proven effective in distinguishing genetic differences among pitaya accessions and assessing genetic diversity parameters such as heterozygosity and polymorphic information content (Nashima et al., 2021). These markers are essential for identifying and selecting desirable traits in breeding programs. 3.2 QTL mapping for key traits Quantitative Trait Loci (QTL) mapping is a powerful tool for identifying the genetic basis of important traits in plants. In pitaya, the construction of a high-density genetic map using whole genome resequencing has facilitated QTL mapping for key traits. This map, which includes 6 434 single nucleotide polymorphism (SNP) markers, provides a comprehensive framework for locating QTLs associated with economically important traits in pitaya (Wu et al., 2021). The availability of such detailed genetic maps allows for the precise identification of QTLs, which can be targeted in breeding programs to improve traits such as fruit quality, yield, and stress tolerance. 3.3 Application in breeding programs The application of marker-assisted selection (MAS) in pitaya breeding programs has significantly enhanced the efficiency and accuracy of developing new varieties. By utilizing molecular markers linked to desirable traits, breeders can select plants with the best genetic potential early in the breeding process, thus reducing the time and resources required for traditional breeding methods (Thomson et al., 2009; Hasan et al., 2021). For example, the
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