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Zhuang J, Wang Q. Hyperspectral Indices Developed from Fractional-Order Derivative Spectra Improved Estimation of Leaf Chlorophyll Fluorescence Parameters. PLANTS (BASEL, SWITZERLAND) 2024; 13:1923. [PMID: 39065450 PMCID: PMC11281006 DOI: 10.3390/plants13141923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
Abstract
Chlorophyll fluorescence (ChlF) parameters offer valuable insights into quantifying energy transfer and allocation at the photosystem level. However, tracking their variation based on reflectance spectral information remains challenging for large-scale remote sensing applications and ecological modeling. Spectral preprocessing methods, such as fractional-order derivatives (FODs), have been demonstrated to have advantages in highlighting spectral features. In this study, we developed and assessed the ability of novel spectral indices derived from FOD spectra and other spectral transformations to retrieve the ChlF parameters of various species and leaf groups. The results obtained showed that the empirical spectral indices were of low reliability in estimating the ChlF parameters. In contrast, the indices developed from low-order FOD spectra demonstrated a significant improvement in estimation. Furthermore, the incorporation of species specificity enhanced the tracking of the non-photochemical quenching (NPQ) of sunlit leaves (R2 = 0.61, r = 0.79, RMSE = 0.15, MAE = 0.13), the fraction of PSII open centers (qL) of shaded leaves (R2 = 0.50, r = 0.71, RMSE = 0.09, MAE = 0.08), and the fluorescence quantum yield (ΦF) of shaded leaves (R2 = 0.71, r = 0.85, RMSE = 0.002, MAE = 0.001). Our study demonstrates the potential of FOD spectra in capturing variations in ChlF parameters. Nevertheless, given the complexity and sensitivity of ChlF parameters, it is prudent to exercise caution when utilizing spectral indices for tracking them.
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Affiliation(s)
- Jie Zhuang
- Graduate School of Science and Technology, Shizuoka University, Shizuoka 422-8529, Japan;
| | - Quan Wang
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
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Zhuang J, Wang Q. Integrating leaf spectral and water status information to effectively track chlorophyll a fluorescence parameters during dehydration. PHYSIOLOGIA PLANTARUM 2024; 176:e14391. [PMID: 38894595 DOI: 10.1111/ppl.14391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/14/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Monitoring changes in chlorophyll a (ChlFa) fluorescence during dehydration can provide insights into plant photosynthetic responses to climate change challenges, which are predicted to increase drought frequency. However, the limited knowledge of how ChlFa parameters respond to water deficit hinders the exploration of the photochemical mechanism of the photosynthetic process and the simulation of photosynthetic fluorescence models. Furthermore, how to track such responses of ChlFa parameters, especially at large scales, remains a challenge. In this study, we attempted to use spectral information reflected from leaves to follow the dynamic response patterns of ChlFa parameters of seven species under prolonged dehydration. The results showed that the investigated ChlFa parameters exhibited significant changes as dehydration progressed, with considerable variability among the different species as well as under different water conditions. This study also demonstrated that the integration of both spectral and water content information can provide an effective method for tracking ChlFa parameters during dehydration, explaining over 90% of the total variance in the measured ChlFa parameters. Collectively, these results should serve as a valuable reference for predicting the response of ChlFa parameters to dehydration and offer a potential method for estimating ChlFa parameters under drought conditions.
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Affiliation(s)
- Jie Zhuang
- Graduate School of Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Quan Wang
- Faculty of Agriculture, Shizuoka University, Suruga-ku, Shizuoka, Japan
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Jamil HMA, Gatasheh MK, Ahmad R, Ibrahim KE, Khan SA, Irshad U, Shahzad M, Abbasi AM. Ectomycorrhiza and ethylenediurea reduced the impact of high nitrogen and ozone stresses and increased the growth of Cedrus deodara. Heliyon 2024; 10:e28635. [PMID: 38586366 PMCID: PMC10998246 DOI: 10.1016/j.heliyon.2024.e28635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
Cedrus deodara is the central conifer plant affected by ozone and nitrogen pollutants among forest species worldwide. The growth of C. deodara depends upon the ectomycorrhizal (ECM) association, which is usually disturbed by these factors. This study aims to understand how these factors affect plants at physiological and biochemical levels. Three fungal strain consortiums were inoculated with two-year-old C. deodara seedlings. The stresses of 100 kg N h-1and 100 ppb O3 were applied for six months to study their impact on chlorophyll and antioxidant enzymes (SOD, CAT, and APX). The results showed that C2 (Consortium of Cedrus deodara) positively impacted the growth of selected plant species. The high photosynthesis rate was determined by enhanced chlorophyll content, and C2-treated plants showed high chlorophyll content. Relatively, chlorophyll a and b contents increased significantly in the seedlings treated with Ethylenediurea (EDU) alone and with ozone stress. In addition, a significant difference was observed between EDU and O3-treated plants (14% EDU400-O3 and 23% EDU600-O3) and the control. Overall, antioxidant activities were higher in the treated samples than in the control. The order of SOD activity was C2 (448 U/gFW) and lowest (354.7 U/gFW) in control. APX also showed higher activity in treated plants in C1 ≥ C2 ≥ C3+O3, whereas CAT activity was the highest in C2 treatments. Ozone and nitrogen-stressed plants showed higher activities than EDU-treated plants compared to non-treated ones. Our findings highlight the importance of understanding the signaling effects of numerous precursors. Moreover, an extended investigation of seedlings developing into trees must be conducted to verify the potential of ectomycorrhizal strains associated with C. deodara and comprehend EDU's role as a direct molecular scavenger of reactive toxicants.
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Affiliation(s)
- Hafiz Muhammad Ansab Jamil
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22060, Abbottabad, Pakistan
| | - Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O. Box. 2455, Riyadh, 11451, Saudi Arabia
| | - Rafiq Ahmad
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22060, Abbottabad, Pakistan
| | - Khalid Elfaki Ibrahim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sabaz Ali Khan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22060, Abbottabad, Pakistan
| | - Usman Irshad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, 22060, Abbottabad, Pakistan
| | - Muhammad Shahzad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, 22060, Abbottabad, Pakistan
| | - Arshad Mehmood Abbasi
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, 22060, Abbottabad, Pakistan
- University of Gastronomic Sciences of Pollenzo, Piazza V. Emanuele II, I-12042, Bra/Pollenzo, Italy
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Li Y, Gu M, Liu X, Lin J, Jiang H, Song H, Xiao X, Zhou W. Sequencing and analysis of the complete mitochondrial genomes of Toona sinensis and Toona ciliata reveal evolutionary features of Toona. BMC Genomics 2023; 24:58. [PMID: 36726084 PMCID: PMC9893635 DOI: 10.1186/s12864-023-09150-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives. RESULTS (1) T. sinensis and T.ciliata are both circular structures with lengths of 683482 bp and 68300 bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other. CONCLUSIONS This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.
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Affiliation(s)
- Youli Li
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Min Gu
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Xuanzhe Liu
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Jianna Lin
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Huier Jiang
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Huiyun Song
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Xingcui Xiao
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry Sciences, Chengdu, 61008 Sichuan China
| | - Wei Zhou
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
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Wu H, Song Z, Niu X, Liu J, Jiang J, Li Y. Classification of Toona sinensis Young Leaves Using Machine Learning and UAV-Borne Hyperspectral Imagery. FRONTIERS IN PLANT SCIENCE 2022; 13:940327. [PMID: 35837456 PMCID: PMC9274089 DOI: 10.3389/fpls.2022.940327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Rapid and accurate distinction between young and old leaves of Toona sinensis in the wild is of great significance to the selection of T. sinensis varieties and the evaluation of relative yield. In this study, UAV hyperspectral imaging technology was used to obtain canopy hyperspectral data of biennial seedlings of different varieties of T. sinensis to distinguish young and old leaves. Five classification models were trained, namely Random Forest (RF), Artificial Neural Network (ANN), Decision Tree (DT), Partial Least Squares Discriminant Analysis (PLSDA), and Support Vector Machine (SVM). Raw spectra and six preprocessing methods were used to fit the best classification model. Satisfactory accuracy was obtained from all the five models using the raw spectra. The SVM model showed good performance on raw spectra and all preprocessing methods, and yielded higher accuracy, sensitivity, precision, and specificity than other models. In the end, the SVM model based on the raw spectra produced the most reliable and robust prediction results (99.62% accuracy and 99.23% sensitivity on the validation set only, and 100.00% for the rest). Three important spectral regions of 422.7~503.2, 549.2, and 646.2~687.2 nm were found to be highly correlated with the identification of young leaves of T. sinensis. In this study, a fast and effective method for identifying young leaves of T. sinensis was found, which provided a reference for the rapid identification of young leaves of T. sinensis in the wild.
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Affiliation(s)
- Haoran Wu
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Zhaoying Song
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xiaoyun Niu
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Jun Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Jingmin Jiang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yanjie Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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