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

Meacham-Hensold, Katherine; Montes, Christopher M.; Wu, Jin; Guan, Kaiyu; Fu, Peng; Ainsworth, Elizabeth A.; Pederson, Taylor; Moore, Caitlin E.; Brown, Kenny Lee; Raines, Christine; Bernacchi, Carl J.

doi:10.1016/j.rse.2019.04.029

Title: 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 (Vc,max), maximum electron transport rate (Jmax) 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 Vc,max, Jmax and [N] for all plantsmore »« less

Authors:

; Montes, Christopher M.; Wu, Jin; Guan, Kaiyu;

; Ainsworth, Elizabeth A.; Pederson, Taylor; Moore, Caitlin E.; Brown, Kenny Lee; Raines, Christine;

Publication Date:: Sun Sep 01 00:00:00 EDT 2019

Research Org.:: Univ. of Illinois at Urbana-Champaign, IL (United States); Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Org.:: USDOE Advanced Research Projects Agency - Energy (ARPA-E)

OSTI Identifier:: 1545645

Alternate Identifier(s):: OSTI ID: 1613661

Grant/Contract Number:: AR0000598; SC0012704

Resource Type:: Published Article

Journal Name:: Remote Sensing of Environment

Additional Journal Information:: Journal Name: Remote Sensing of Environment Journal Volume: 231 Journal Issue: C; Journal ID: ISSN 0034-4257

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Subject:: 54 ENVIRONMENTAL SCIENCES; 47 OTHER INSTRUMENTATION; Environmental Sciences & Ecology; Remote Sensing; Imaging Science & Photographic Technology; Hyperspectral reflectance; Partial least squares regression (PLSR); Photosynthesis; Leaf nitrogen; Food security; Gas exchange; Spectroscopy

Citation Formats


                    Meacham-Hensold, Katherine, Montes, Christopher M., Wu, Jin, Guan, Kaiyu, Fu, Peng, Ainsworth, Elizabeth A., Pederson, Taylor, Moore, Caitlin E., Brown, Kenny Lee, Raines, Christine, and Bernacchi, Carl J. High-throughput field phenotyping using hyperspectral reflectance and partial least squares regression (PLSR) reveals genetic modifications to photosynthetic capacity.  United States: N. p., 2019. 
Web.  doi:10.1016/j.rse.2019.04.029.

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                    Meacham-Hensold, Katherine, Montes, Christopher M., Wu, Jin, Guan, Kaiyu, Fu, Peng, Ainsworth, Elizabeth A., Pederson, Taylor, Moore, Caitlin E., Brown, Kenny Lee, Raines, Christine, & Bernacchi, Carl J. High-throughput field phenotyping using hyperspectral reflectance and partial least squares regression (PLSR) reveals genetic modifications to photosynthetic capacity.  United States.  https://doi.org/10.1016/j.rse.2019.04.029

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                    Meacham-Hensold, Katherine, Montes, Christopher M., Wu, Jin, Guan, Kaiyu, Fu, Peng, Ainsworth, Elizabeth A., Pederson, Taylor, Moore, Caitlin E., Brown, Kenny Lee, Raines, Christine, and Bernacchi, Carl J. Sun .  
"High-throughput field phenotyping using hyperspectral reflectance and partial least squares regression (PLSR) reveals genetic modifications to photosynthetic capacity".  United States.  https://doi.org/10.1016/j.rse.2019.04.029.

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@article{osti_1545645,

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

  author       = {Meacham-Hensold, Katherine and Montes, Christopher M. and Wu, Jin and Guan, Kaiyu and Fu, Peng and Ainsworth, Elizabeth A. and Pederson, Taylor and Moore, Caitlin E. and Brown, Kenny Lee and Raines, Christine and Bernacchi, Carl J.},

  abstractNote = {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 (Vc,max), maximum electron transport rate (Jmax) 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 Vc,max, Jmax 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 Vc,max, but not for Jmax, and not for genotypes unique to 2017. Building a new model including data collected in 2017 resulted in more robust predictions, with R2 increases of 17% for Vc,max. and 13% Jmax. Plants generally have a positive correlation between leaf nitrogen and photosynthesis, however, tobacco with reduced Rubisco (SSuD) had significantly higher [N] despite much lower Vc,max. The PLSR model was able to accurately predict both lower Vc,max and higher leaf [N] for this genotype suggesting that the spectral based estimates of Vc,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.},

  doi          = {10.1016/j.rse.2019.04.029},

  journal      = {Remote Sensing of Environment},

  number       = C,

  volume       = 231,

  place        = {United States},

  year         = {Sun Sep 01 00:00:00 EDT 2019},

  month        = {Sun Sep 01 00:00:00 EDT 2019}

}

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Works referencing / citing this record:

Natural genetic variation in photosynthesis: an untapped resource to increase crop yield potential?
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Hyperspectral Leaf Reflectance as Proxy for Photosynthetic Capacities: An Ensemble Approach Based on Multiple Machine Learning Algorithms
journal, June 2019

Fu, Peng; Meacham-Hensold, Katherine; Guan, Kaiyu
Frontiers in Plant Science, Vol. 10
DOI: 10.3389/fpls.2019.00730

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

Abstract

Citation Formats

Natural genetic variation in photosynthesis: an untapped resource to increase crop yield potential? journal, November 2019

Assessing durum wheat ear and leaf metabolomes in the field through hyperspectral data journal, January 2020

Hyperspectral Leaf Reflectance as Proxy for Photosynthetic Capacities: An Ensemble Approach Based on Multiple Machine Learning Algorithms journal, June 2019

Natural genetic variation in photosynthesis: an untapped resource to increase crop yield potential?
journal, November 2019

Assessing durum wheat ear and leaf metabolomes in the field through hyperspectral data
journal, January 2020

Hyperspectral Leaf Reflectance as Proxy for Photosynthetic Capacities: An Ensemble Approach Based on Multiple Machine Learning Algorithms
journal, June 2019