Tree Genetics and Molecular Breeding 2025, Vol.15, No.2, 80-88 http://genbreedpublisher.com/index.php/tgmb 82 intergene interactions. Zhao and Su (2019) detected 33 QTLs related to the seven yield traits of corn and found several stable QTLs on chromosomes 2, 5, 7 and 9. Mekonnen et al. (2021) used three different populations and discovered 105 QTLs related to agronomic traits and yield of sorghum, which were integrated into 25 meta QTLs. 3.3 Applications in breeding programs Researchers can introduce some good traits into newly cultivated varieties through MAS. Kulkarni et al. (2020) found that some of the main QTLs identified in rice are beneficial for breeding excellent hybrid rice varieties. Guo et al. (2020) focused on stable QTL related to protein and starch content in wheat to conduct more detailed localization and identify candidate genes, thereby improving the quality of terminal products such as flour. Zhao and Su (2019) analyzed the differences in gene expression within the QTL region, predicted the candidate genes affecting the size and weight of corn kernels, and provided a clear direction for future molecular breeding. 4 Genomic Studies and Sequencing 4.1 Genome sequencing projects Singh et al. (2021) conducted a comprehensive chloroplast genome analysis of 16 Punica granatum genotypes. Through large-scale sequencing and assembly, they discovered differences in the size and structure of chloroplast genomes among these genotypes. Usha et al. (2022) conducted high-quality genomic assembly of the important diploid Punica granatum variety “Bhagwa” in India, providing detailed information on the genomic characteristics of Punica granatum and identifying 30 803 protein-coding genes, demonstrating its potential in gene function research and breeding. In 2019, Yan et al. analyzed the complete chloroplast genomes of three Punica granatum varieties and found that the genetic content and structure of these varieties changed little in the Lythaceae family. 4.2 Identification of key genes Chen et al. (2023) utilized the data from whole-genome sequencing to identify the U-box gene families that play a key role in the ubiquitination process of plants, discovered 56 U-box genes, determined their positions on chromosomes, analyzed their evolutionary relationships, and studied their expression under abiotic stress conditions. Patil et al. (2020) conducted computational analysis using the draft genome of the Punica granatum variety “Dabenzi”, developed a large number of SSR markers, and discovered 173 633 SSR markers that are very useful in genetic research and breeding. Chang et al. (2019) identified a region-specific 4-O-glycosyltransferase related to gallic acid metabolism using CRISPR/Cas9 technology, indicating that genome editing holds great potential in the study of Punica granatum functional genes. 4.3 Comparative genomics Yan et al. (2019) compared the chloroplast genomes of Punica granatum and other plants in the Lythaceae family and found that their genetic contents and structures were very similar, and the sequence differences among different Punica granatum varieties were not significant. Lu et al. (2023) compared the mitochondrial genomes of Punica granatum and their closely related plants, identified homologous fragments between them, and through phylogenetic analysis, found that the genetic relationship between Punica granatum and Lagerstroemia indica was very close. Chen et al. (2022) analyzed the complete chloroplast genome of wild Punica granatum in Tibet, providing useful information for Punica granatum breeding research and the classification of Lythylaceae plants. 5 Functional Genomics and Gene Expression 5.1 Transcriptome analysis Fu et al. (2021) conducted a combined analysis of the metabolome and transcriptome of Punica granatum seeds throughout the entire process from pre-germination to post-germination, and found that the expression of 6 984 genes changed significantly. Through weighted gene co-expression network analysis (WGCNA), the gene modules related to different germination stages were identified. At the beginning of seed soaking, some key genes involved in RNA transmission and glycolysis were discovered. At the stage when germination truly began, more genes related to metabolic processes were found. Chang et al. (2019) discovered 11 increased expression UDP-dependent glycosyltransferases (UGTs) genes in Punica granatum plants edited with CRISPR/Cas9
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