Tree Genetics and Molecular Breeding 2024, Vol.14, No.5, 239-246 http://genbreedpublisher.com/index.php/tgmb 243 5.2 Prediction models and accuracy Prediction models in genomic selection are crucial for determining the accuracy and effectiveness of the selection process. Common models include Best Linear Unbiased Prediction (BLUP) and Bayesian approaches, which are used to estimate the effects of markers across the genome (Chen et al., 2021; Wu et al., 2021). The accuracy of these models depends on several factors, including the size of the training population, the heritability of the trait, and the density of the markers used. In pitaya, the construction of high-density genetic maps using whole genome resequencing has enhanced the precision of these models, allowing for more accurate predictions of traits such as fruit quality and yield (Figure 3) (Zheng et al., 2020; Wu et al., 2021). 5.3 Implementation in pitaya breeding The implementation of genomic selection in pitaya breeding programs is facilitated by recent advancements in genomic resources, such as the development of a chromosome-scale genome sequence and high-density genetic maps (Chen et al., 2021; Wu et al., 2021). These resources provide a comprehensive framework for identifying and utilizing genetic markers associated with desirable traits. The integration of genomic selection into pitaya breeding can accelerate the development of new cultivars with improved traits, such as disease resistance and enhanced nutritional content, by enabling breeders to make more informed decisions based on genetic predictions rather than solely on phenotypic observations (Chen et al., 2021; Wu et al., 2021; Tel-Zur, 2022). 6 Epigenomics and Stress Tolerance 6.1 Role of epigenetics in pitaya development Epigenetics plays a crucial role in the development and growth of pitaya (Hylocereus spp.), influencing various physiological and morphological traits. The application of molecular tools, such as DNA isolation and flow cytometry, has facilitated the understanding of genetic relationships and dominant/recessive traits in pitaya, which are essential for breeding programs (Zerpa-Catanho et al., 2019; Tel-Zur, 2022). These tools help in identifying epigenetic modifications that can affect gene expression without altering the DNA sequence, thereby contributing to the plant’s adaptability and development. 6.2 Epigenomics of abiotic stress The study of epigenomics in pitaya has provided insights into how this plant responds to abiotic stresses, such as cold temperatures. The identification of NAC transcription factors, particularly HuNAC20 and HuNAC25, has shown that these genes are highly induced under cold stress conditions. These transcription factors play a significant role in enhancing cold tolerance by regulating stress-responsive genes, thereby reducing ion leakage and oxidative damage (Hu et al., 2022). This epigenomic regulation is crucial for pitaya's survival and productivity in varying environmental conditions. 6.3 Applications in breeding programs The integration of epigenomic insights into breeding programs can significantly enhance the development of pitaya cultivars with improved stress tolerance and desirable traits. The availability of a chromosome-scale genome sequence of pitaya provides a valuable resource for molecular breeding, allowing for the identification and manipulation of genes involved in stress responses and other important traits (Chen et al., 2021). By leveraging epigenetic modifications, breeders can develop new pitaya varieties that are better equipped to withstand environmental stresses, thereby improving yield and quality. Additionally, the use of biotechnological tools such as somatic embryogenesis and molecular marker technology further supports the enhancement of pitaya germplasm (Shah et al., 2023; Khokhar et al., 2024). 7 Case Study Sharing 7.1 Molecular breeding for disease resistance Molecular breeding techniques have been pivotal in enhancing disease resistance in pitaya (Hylocereus spp.). The development of a high-density genetic map using whole genome resequencing has facilitated the identification of single nucleotide polymorphisms (SNPs) that are crucial for marker-assisted selection, which can be used to breed disease-resistant varieties (Wu et al., 2021). Additionally, the use of RAPD markers has revealed significant genetic variability among pitaya accessions, which is essential for selecting disease-resistant traits (Junqueira et al.,
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