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

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

Research output: Contribution to journalArticle

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 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.

Original languageEnglish (US)
Article number111176
JournalRemote Sensing of Environment
Volume231
DOIs
StatePublished - Sep 15 2019

Fingerprint

genetic engineering
reflectance
least squares
Throughput
phenotype
leaves
Genetically modified plants
genotype
Photosynthesis
ribulose-bisphosphate carboxylase
Nitrogen
gas exchange
Ecosystems
genetic modification
nitrogen
photosynthesis
canopy
Carboxylation
prediction
Tobacco

Keywords

  • Food security
  • Gas exchange
  • Hyperspectral reflectance
  • Leaf nitrogen
  • Partial least squares regression (PLSR)
  • Photosynthesis
  • Spectroscopy

ASJC Scopus subject areas

  • Soil Science
  • Geology
  • Computers in Earth Sciences

Cite this

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; Pederson, Taylor; Moore, Caitlin E.; Brown, Kenny Lee; Raines, Christine; Bernacchi, Carl.

In: Remote Sensing of Environment, Vol. 231, 111176, 15.09.2019.

Research output: Contribution to journalArticle

Meacham-Hensold, Katherine ; Montes, Christopher M. ; Wu, Jin ; Guan, Kaiyu ; Fu, Peng ; Ainsworth, Elizabeth ; Pederson, Taylor ; Moore, Caitlin E. ; Brown, Kenny Lee ; Raines, Christine ; Bernacchi, Carl. / High-throughput field phenotyping using hyperspectral reflectance and partial least squares regression (PLSR) reveals genetic modifications to photosynthetic capacity. In: Remote Sensing of Environment. 2019 ; Vol. 231.
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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 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.",
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AU - Ainsworth, Elizabeth

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