High-throughput field phenotyping using hyperspectral reflectance and partial least squares regression (PLSR) reveals genetic modifications to photosynthetic capacity

Abstract

Spectroscopy is becoming an increasingly powerful tool to alleviate the challenges of traditional measurements of key plant traits at the leaf, canopy, and ecosystem scales. Spectroscopic methods often rely on statistical approaches to reduce data redundancy and enhance useful prediction of physiological traits. Given the mechanistic uncertainty of spectroscopic techniques, genetic modification of plant biochemical pathways may affect reflectance spectra causing predictive models to lose power. The objectives of this research were to assess over two separate years, whether a predictive model can represent natural and imposed variation in leaf photosynthetic potential for different crop cultivars and genetically modified plants, to assess the interannual capabilities of a partial least square regression (PLSR) model, and to determine whether leaf N is a dominant driver of photosynthesis in PLSR models. In 2016, a PLSR analysis of reflectance spectra coupled with gas exchange data was used to build predictive models for photosynthetic parameters including maximum carboxylation rate of Rubisco ( V c , max ), maximum electron transport rate ( J max ) and percentage leaf nitrogen ([N]). The model was developed for wild type and genetically modified plants that represent a wide range of photosynthetic capacities. Results show that hyperspectral reflectance accurately predicted V c ,max , J max and [N] for all plants measured in 2016. Applying these PLSR models to plants grown in 2017 resulted in a strong predictive ability relative to gas exchange measurements for V c ,max , but not for J max , and not for genotypes unique to 2017. Building a new model including data collected in 2017 resulted in more robust predictions, with R 2 increases of 17% for V c , max . and 13% J max . Plants generally have a positive correlation between leaf nitrogen and photosynthesis, however, tobacco with reduced Rubisco (SSuD) had significantly higher [N] despite much lower V c ,max . The PLSR model was able to accurately predict both lower V c , max and higher leaf [N] for this genotype suggesting that the spectral based estimates of V c , max and leaf nitrogen [N] are independent. These results suggest that the PLSR model can be applied across years, but only to genotypes used to build the model and that the actual mechanism measured with the PLSR technique is not directly related to leaf [N]. The success of the leaf-scale analysis suggests that similar approaches may be successful at the canopy and ecosystem scales but to use these methods across years and between genotypes at any scale, application of accurately populated physical based models based on radiative transfer principles may be required.

Plant phenotyping relevance

植物の光合成生理形質をハイパースペクトル反射とPLSRで推定する手法を開発・検証し、年次・遺伝子型間の予測性能を評価しているため、フェノタイピング手法が中心です。

Code and data availability

The article describes hyperspectral reflectance and gas-exchange data used to build PLSR models, but no public repository, dataset deposit, or author code URL is mentioned. Supplementary data is only referenced via the article DOI, with no explicit statement of publicly deposited spectra, phenotypes, or scripts.

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