Tree Genetics and Molecular Breeding 2024, Vol.14, No.3, 106-118 http://genbreedpublisher.com/index.php/tgmb 109 angustifolia, a subtropical conifer. This SNP array has provided a comprehensive look at the genetic diversity and structure of the species, revealing a major north-south genetic cline and enabling more accurate assessments of regional differentiation (Silva et al., 2020). These case studies highlight the diverse adaptive strategies employed by different tree species to thrive in their respective environments. Figure 1 Genomic structure and hybrid composition in spruce species (Adapted from Gagalova et al., 2022) Image caption: (a) Collinearity between super-scaffolds and the genetic map for spruce species. Mapped cDNAs were aligned to each species’ genome assembly, identifying the best matching scaffolds. These scaffolds were ordered according to the genetic map, forming super-scaffolds representative of each of the 12 chromosomes. The plot shows the alignment of cDNA start positions against their genetic map positions. (b) Shared SNP composition in the hybrid interior spruce genotype PG29. For each PG29 linkage group super-scaffold, the proportion of SNPs unique to interior spruce (gray) and those shared with Sitka (red), Engelmann (blue), and white spruce (green) were plotted. The ideograms depict regions with the highest shared SNP densities. Base genome contributions were estimated to be approximately 68.4% from white spruce, 16.1% from Engelmann spruce, and 12.9% from Sitka spruce, with unassigned portions indicated in light gray (Adapted from Gagalova et al., 2022) 4 Functional Genomics: Decoding Gene Functions in Trees 4.1 Strategies for annotation and characterization of tree genomes Functional annotation of tree genomes is a critical step in understanding the biological roles of genes and their contributions to growth, development, and stress responses. Various strategies have been developed to annotate
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