Understanding the rules of genetic recombination in controlled pollination directly related to the selection of parental genotypes and the utilization of heterosis, and genotype identification is a primary study of the genetic rules. The aims of this study were to investigate the ability of near infrared (NIR) spectroscopy to accurately and efficiently discriminate pure species and hybrids within the genus of Eucalyptus, to evaluate the transmission of genetic pedigree in control pollination, and reveal the genetic variation within the genotypes studied. NIR spectra were collected both from fresh leaves and dried, milled leaves of seedlings from pure species E. urophylla and E. grandis, and their F1 hybrids. Principal component analysis (PCA) scores plots of NIR spectra from fresh leaves and dry, milled powder from pure species showed clear segregation, although the species clusters were scattered, suggesting different base genetics and high genetic variation within families of the two pure species. Classification using soft independent modelling of class analogy of the NIR spectra of dried leaves was significantly better than using spectra acquired on fresh leaves, meaning the water content had an effect on the analysis. The projections and orthogonal distance between hybrids and parents, as calculated using PCA models, demonstrated the visualized spectral distance between each hybrid and the parents was very different. Clouds of individuals within a hybrid clusters varied from tightly packed to scattered, which reflected the genetic additive effects inherited from female and male parents were different, and their genetic variation was also different after genetic recombination. The varying response values for partial least squares discriminant analysis prediction verified the conclusions shown by projections and orthogonal distance. The results of this study demonstrate the potential of using NIR spectroscopy to rapidly discriminate taxon. The application of NIR spectroscopy to non-destructively confirm taxonomic identity will greatly facilitate the evaluation of the genetic basis and genetic variation available within breeding populations and for accessing the levels of contamination by non-target pollen in control pollination.
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