Chapter 03, Near-Infrared, Mid-Infrared, and Raman Spectroscopy

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  1. Peter R. Griffiths' Chapters
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Using FT-IR spectroscopy combined with chemometrics e. Finally, they used chemical fingerprints from healthy xylem tissue to separate resistant U. More recently, Hardoim et al. They found that control seedlings from an unfavorable maternal environment, which were previously found to be less tolerant to F.

The authors concluded that variation in the intensity of the MIR spectrum may be associated with seedling carbohydrate content, and changes in carbohydrate content of seedlings following infection may impact their tolerance to F. In our own work, we used a combined FT-IR spectroscopy and chemometric approach to distinguish between resistant and susceptible Q. In addition, PLSR was used to estimate the concentration of specific phenolic compounds previously associated with Q. Even though NIR reflectance spectroscopy has been used widely, the technique has not been used extensively to screen trees for disease resistance.

The ability to detect chemical differences between groups is important, because plant-derived chemicals are often associated with tree defense responses. For example Moore et al. FPCs are known deterrents of koala feeding Moore et al. These authors were able to estimate the total concentration of FPC in Eucalyptus foliage using calibration models that were created using NIR spectra and concentrations of FPC in Eucalyptus foliage quantitated by high performance liquid chromatography.

Estimates were then combined with spatial tree distribution data to produce palatability maps based on koala feeding preferences of Eucalyptus foliage. A similar approach could be used to map the distribution of disease resistant trees on a landscape scale. Most recently, O'Reilly-Wapstra et al. While the authors did not use this method to screen trees for disease resistance, they clearly showed that the technique can be used to discriminate between groups based on genetic differences in chemistry. Since tree disease resistance is genetically based and often an inherited trait, it is plausible that NIR spectroscopy and chemometrics could also be used to distinguish between genetic-based differences in resistance that manifest as differences in chemical composition.

Further applications and examples of NIR spectroscopy for analyzing the chemical composition, anatomical features, mechanical properties, and other attributes of trees can be found in a recent review by Tsuchikawa and Kobori We were unable to find any papers where Raman spectroscopy and chemometrics were used to distinguish between trees that varied in disease susceptibility.

Peter R. Griffiths' Chapters

However, it has been used to measure and estimate various chemical constituents of trees. For example, FT-Raman spectroscopy was used to study chemical changes in waterlogged Pinus spp. The authors assessed the depletion of cellulose, hemicellulose, and lignin in ancient wood samples from these tree species. Finally, a portable Raman spectrometer equipped with a laser diode and optical fiber was used to assess the quality of fruit from olive trees and could differentiate between sound i. Raman spectroscopy is clearly capable of detecting chemical differences between sample groups.

Since plant-derived chemicals e. In the preceding sections, we described methods for chemically fingerprinting trees using IR and Raman spectroscopy. Chemical fingerprinting, when combined with chemometrics, is a powerful tool that can be used to distinguish between groups of trees that vary in disease susceptibility.

Alternatively, these methods could be used to estimate quantitative traits of interest, like the concentration of plant-derived chemicals, which may be associated with resistant tree responses. Many of the studies referenced above utilized benchtop spectrometers for chemical fingerprinting of samples; however, there are many portable and handheld devices available that could be used directly in the forest to screen larger numbers of trees for disease resistance, once protocols to deal with fresh tissues have been optimized see reviews by Sorak et al. Handheld devices have not yet been used for this purpose, though on-site screening methods using NIR spectroscopy have been developed to predict sugarcane smut resistance for plant breeding Purcell et al.

Although Meder et al. Handheld or automated laboratory devices will need to be utilized if chemical fingerprinting by IR and Raman spectroscopy is to be implemented on more high-throughput scales to efficiently screen trees for disease resistance. Instruments for these types of analyses are commercially available and chemometric pipelines for analyzing large data sets are well established. The next steps will be to scale-up existing experiments using handheld and portable devices, increase sample diversity within training and testing data sets, and validate predictive models for in-forest assessment of tree resistance.

Once these steps have been completed, chemical fingerprinting and chemometrics should be viewed as a reliable method for screening individuals in tree breeding programs and for managing forest diseases by identifying and utilizing naturally resistant trees. AC and PB discussed content and structure of review prior to writing review. AC reviewed relevant literature and compiled initial draft of review. PB reviewed first and subsequent drafts and contributed content.

AC revised manuscript based on PB contributions and feedback. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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The authors thank Dr. Caterina Villari and Dr. Luis Rodriguez-Saona for pre-submission reviews, and two reviewers of the first submission for providing constructive feedback that led to significant improvements in the quality of the document. Her research interests are in mechanisms of tree resistance to biotic and abiotic stresses. Metabolomic technologies and their application to the study of plants and plant-host interactions.

Standard normal variate transformation and de-trending of near-infrared diffuse reflectance spectra. The restoration of the American chestnut: Identification of Quercus agrifolia coast live oak resistant to the invasive pathogen Phytophthora ramorum in native stands using Fourier-transform infrared FT-IR spectroscopy.

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Use of infrared spectroscopy for in-field measurement and phenotyping of plant properties: Introduction to Modern Vibrational Spectroscopy. Metabolic fingerprinting in disease diagnosis: Resilience of forests to pathogens: Qualitative and quantitative changes of beech wood degraded by wood-rotting basidiomycetes monitored by Fourier transform infrared spectroscopic methods and multivariate data analysis.

Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Metabolomics — the link between genotypes and phenotypes. Non-destructive prediction of decay resistance of Pinus sylvestris heartwood by near infrared spectroscopy.

Ecological applications of near infrared reflectance spectroscopy - a tool for rapid, cost-effective prediction of the composition of plant and animal tissues and aspects of animal performance. Sudden oak death and Phytophthora ramorum in the USA: Rapid prediction of natural durability of larch heartwood using Fourier transform near-infrared spectroscopy. Infrared spectroscopy in the study of edible oils and fats. A portable Raman sensor for the rapid discrimination of olives according to fruit quality.

Temporal metabolic profiling of the Quercus suber - Phytophthora cinnamomi system by middle-infrared spectroscopy. A review of imaging techniques for plant phenotyping. Seven Ulmus minor clones tolerant to Ophiostoma novo-ulmi registered as forest reproductive material in Spain. Fourier transform-infrared spectroscopy as a new method for evaluating host resistance in the Dutch elm disease complex.

Metabolic distinction of Ulmus minor xylem tissues after inoculation with Ophiostoma novo-ulmi. Metabolic fingerprinting allows discrimination between Ulmus pumila and U.

Focused Review ARTICLE

Detection of differential changes in lignin composition of elm xylem tissues inoculated with Ophiostoma novo-ulmi using Fourier transform-infrared spectroscopy. Towards the in-forest assessment of Kraft pulp yield: Potential for marker-assisted selection for forest tree breeding: Genetic analysis of the near-infrared spectral phenome of a global Eucalyptus species.

Port-Orford-cedar resistant to Phytophthora lateralis. Fourier-transform Raman spectroscopic study of a Neolithic waterlogged wood assemblage.

Learning from history, predicting the future: On-site rapid screening for sugarcane smut resistance using near-infrared NIR spectroscopy. Accuracy of genomic selection methods in a standard data set of loblolly pine Pinus taeda L.

Raman vs infrared spectroscopy

Use of FTIR for rapid authentication and detection of adulteration of food. Changing Climate, Changing forests: A review of advanced techniques for detecting plant diseases. Application of hand-held and portable infrared spectrometers in bovine milk analysis. Department of Agriculture , 65— New developments and applications of handheld Raman, mid-infrared, and near-infrared Spectrometers. Climate change and forest diseases. Can we protect forests by harnessing variation in resistance to pests and pathogens? A review of recent application of near infrared spectroscopy to wood science and technology.

Maternal effects and carbohydrate changes of Pinus pinaster after inoculation with Fusarium circinatum. Handheld near infared spectroscopy for the prediction of leaf physiological status in tree seedlings. Phenolic metabolites in the resistance of northern forest trees to pathogens - past experiences and future prospects. Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst.

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Griffiths in Handbook of Near Infrared Spectroscopy eds. Cziurczak , Academic Press, New York, pp. Jinno , Elsevier Science Publishers, Amsterdam, pp. In Situ Investigation" K.

Scheuing , ACS Symp. Griffiths in Analytical Applications of Spectroscopy eds. Davies , Royal Society of Chemistry, London, pp.

Griffiths in Infrared Microspectroscopy: Theory and Applications ed. Harthcock , Marcel Dekker, New York, pp. Pariente in Instrumentation for the 21st Century ed. Beecher , Martinus Nijhoff Publishers, Boston, pp.