Incorporating chemical traits in breeding requires the estimation of quantitative genetic parameters, especially the levels of additive genetic variation. This requires large numbers of samples from pedigreed populations. Conventional wet chemistry procedures for chemotyping are slow, expensive and not a practical option. This study focuses on the chemical variation in Pinus radiata, where the near infrared (NIR) spectral properties of the needles, bark and roots before and after exposure to methyl jasmonate (MJ) and artificial bark stripping (strip) treatments were investigated as an alternative approach. The aim was to test the capability of NIR spectroscopy to (i) discriminate samples exposed to MJ and strip assessed 7, 14, 21 and 28 days after treatment from untreated samples, and (ii) quantitatively predict individual chemical compounds in the three plant parts. Using principal components analysis (PCA) on the spectral data, we differentiated between treated and untreated samples for the individual plant parts. Based on partial least squares–discriminant analysis (PLS-DA) models, the best discrimination of treated from non-treated samples with the smallest root mean square error cross-validation (RMSECV) and highest coefficient of determination (r2) was achieved in the fresh needles (r2 = 0.81, RMSECV= 0.24) and fresh inner bark (r2 = 0.79, RMSECV = 0.25) for MJ-treated samples 14 days and 21 days after treatment, respectively. Using partial least squares regression, models for individual compounds gave high (r2), residual predictive deviation (RPD), lab to NIR error (PRL) or range error ratio (RER) for fructose (r2 = 0.84, RPD = 1.5, PRL = 0.71, RER = 7.25) and glucose (r2 = 0.83, RPD = 1.9, PRL = 1.14, RER = 8.50) and several diterpenoids. This provides an optimistic outlook for the use of NIR spectroscopy-based models for the larger-scale prediction of the P. radiata chemistry needed for quantitative genetic studies.
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