Tree Genetics and Molecular Breeding 2024, Vol.14, No.3, 106-118 http://genbreedpublisher.com/index.php/tgmb 112 Figure 3 Population structure, PCA, and LD decay in Eucalyptus grandis × E. urophylla hybrid breeding populations (Adapted from Müller et al., 2018) Image caption: (a) Bar plots showing the population structure of four unrelated Eucalyptus grandis × E. urophylla hybrid breeding populations with the number of clusters (K) ranging from 2 to 4. (b) Principal Component Analysis (PCA) displaying the first two principal components (PC 1 and PC 2) for the combined dataset. (c) Genome-wide linkage disequilibrium (LD) decay, represented by the correlation coefficient (r²), plotted against pairwise single nucleotide polymorphism (SNP) distances up to 1 Mbp. The dashed line at r² = 0.2 marks the threshold commonly used to determine usable LD in genomic studies (Adapted from Müller et al., 2018) Müller et al. (2018) investigates the genetic diversity and population structure of Eucalyptus grandis × E. urophylla hybrids using SNP genotyping. With over 46 000 SNPs retained after filtering, the research identifies distinct subpopulations within the hybrids, varying from K = 2 to K = 5 depending on the population. The analysis emphasizes the importance of accounting for population stratification in genomic studies, as it affects the accuracy of GWAS and heritability estimates. Linkage disequilibrium (LD) patterns reveal that more advanced breeding populations, like Pop4-CNB, exhibit slower LD decay, reflecting the impact of selective breeding. The study underscores the necessity of integrating genetic structure understanding into breeding programs to optimize selection and improve genetic gains. 6.2 Experimental approaches for functional validation in controlled and natural environments Functional validation of identified genes is crucial for understanding their roles in tree biology and adaptation. Various experimental approaches have been employed to achieve this. For example, the use of quantitative trait loci (QTL) mapping in Scots pine has enabled the identification of QTL linked to complex traits, with validation conducted across multiple environments to account for genotype-by-environment interactions (Calleja-Rodriguez et al., 2019). Additionally, the application of genomic selection (GS) in tree breeding has shown promise in accelerating breeding cycles and improving the accuracy of breeding values by integrating genomic and multi-environment data (Grattapaglia et al., 2018). These approaches highlight the importance of combining controlled experiments with natural environment studies to validate gene functions comprehensively. 6.3 Applications of gene discovery in tree breeding and conservation efforts The discovery of novel genes and their functional validation have significant implications for tree breeding and conservation. For instance, maximizing genetic diversity through strategic breeding programs, as demonstrated in the Norway spruce case study, can enhance ecosystem resilience and stability (Kelblerová et al., 2022). Moreover, predictive genomic approaches, such as those discussed in the context of forest tree adaptation to climate change,
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