Structural Equation Modeling (SEM) Analysis of Sequence Variation and Green Plant Regeneration via Anther Culture in Barley
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Characterization of Input Data
3.1.1. Model Specification and Estimation
3.1.2. Model Description
3.1.3. Model Matching
3.1.4. Estimation of Model Parameters
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
AGFI | Adjusted Goodness-of-Fit Index |
AMPK | AMP-Activated Protein Kinase |
ATP | Adenosine Triphosphate |
ATR-FTIR | Attenuated Total Reflection Fourier Transform Infrared spectroscopy |
CFI | Comparative Fit Index |
DArTseqMet | Diversity Arrays Technology Sequencing Methylation Analysis |
DM | Demethylation |
DNM | De Novo methylation |
ET | Endogenous ethylene |
ETR1 | Ethylene receptor1 |
GFI | Goodness-of-Fit Index |
GP | Green Plant |
IFI | Incremental Fit Index |
metAFLP | Methylation-Sensitive Amplified Fragment Length Polymorphism |
ML | Maximum Likelihood |
MSAP | Methylation Sensitive Amplification Polymorphism |
NFI | Normed Fit Index |
NNFI | Non-Normed Fit Index |
PCFI | Parsimonious Comparative Fit Index |
PNFI | Parsimonious Normed Fit Index |
RFI | Relative Fit Index |
RMR | Root Mean Squares Residuals |
RMSEA | Root Mean Square Error of Approximation |
ROS | Reactive Oxygen Species |
SAM | S-Adenosyl-L-Methionine |
SEM | Structure Equatation Modeling |
SRMR | Standardized Root Mean Squares Residuals |
SV | Sequence Variation |
TCA | Tricarboxylic Acid Cycle |
TCIV | Tissue Culture-Induced Variation |
References
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Variable | Descriptive Statistics | |||
---|---|---|---|---|
Mean | Variance | Skewness | Kurtosis | |
[F1010.940] 1 | 0.035 | 0.000 | 0.531 | −0.689 |
[Cu2+] | 4.751 | 17.205 | 0.123 | −1.573 |
[Ag+] | 20.286 | 667.546 | 0.900 | −1.129 |
[DNM-DM] | 0.794 | 6.089 | −0.804 | −0.048 |
[CG_DMV] | 0.391 | 0.056 | 0.170 | 0.219 |
[CHG_DMV] | 0.940 | 0.098 | −2.393 | 5.433 |
[SV] | 3.952 | 9.585 | 2.849 | 7.049 |
[GP] | 1.123 | 0.715 | 0.835 | −0.424 |
[Time] | 27.800 | 35.988 | 0.057 | −1.657 |
Variable | [F1010.940] 1 | [Cu2+] | [Ag+] | [DNM_DM] | [CG_DMV] | [CHG_DMV] | [SV] | [GP] | [T] |
---|---|---|---|---|---|---|---|---|---|
[F1010.940] | 1.000 | ||||||||
[Cu2+] | 0.338 a * | 1.000 | |||||||
[Ag+] | −0.017 | −0.107 | 1.000 | ||||||
[DNM_DM] | −0.128 | 0.476 ** | 0.166 | 1.000 | |||||
[CG_DMV] | −0.157 | −0.055 | −0.208 | −0.023 | 1.000 | ||||
[CHG_DMV] | −0.405 * | −0.438** | −0.508 ** | −0.231 | 0.590 ** | 1.000 | |||
[SV] | 0.472 ** | 0.418 * | 0.478 ** | 0.080 | −0.391 * | −0.887 ** | 1.000 | ||
[GP] | 0.050 | 0.347 * | 0.157 | 0.210 | −0.315 | −0.251 | 0.240 | 1.000 | |
[Time] | −0.079 | −0.002 | 0.160 | 0.114 | 0.593 ** | 0.306 | −0.252 | −0.138 | 1.000 |
Parameter | Postulated Model |
---|---|
Degrees of freedom (df) | 19 |
Chi-square | 21.125 |
p-value | 0.330 |
Root Mean Squares Residuals (RMR) | 2.836 |
Standardized Root Mean Squares Residuals (SRMR) | 0.134 |
Goodness-of-Fit Index (GFI) | 0.862 |
Adjusted Goodness-of-Fit Index (AGFI) | 0.673 |
Normed Fit Index (NFI) | 0.647 |
Relative Fit Index (RFI) | 0.331 |
Incremental Fit Index (IFI) | 0.948 |
Non-Normed Fit Index (NNFI) | 0.831 |
Comparative Fit Index (CFI) | 0.911 |
Parsimonious Normed Fit Index (PNFI) | 0.341 |
Parsimonious Comparative Fit Index (PCFI) | 0.481 |
Root Mean Square Error of Approximation (RMSEA) | 0.057 |
Parameter | Effect | Estimate (b) | Standard Error | Test Statistic | Standardized Estimate (β) | ||
---|---|---|---|---|---|---|---|
Path coefficients | |||||||
λ1 | [Time] | → | [CHG_DMV] | 0.014 | 0.005 | 2.641 ** | 0.284 |
λ2 | [F1010.940] | → | [CHG_DMV] | −6.230 | 5.127 | −1.215 | −0.139 |
λ3 | [Ag+] | → | [CHG_DMV] | −0.007 | 0.001 | −6.508 ** | −0.695 |
λ4 | [Cu2+] | → | [CHG_DMV] | −0.037 | 0.009 | −4.180 ** | −0.481 |
λ5 | [Time] | → | [Ag+] | 0.800 | 0.834 | 0.959 | 0.173 |
λ6 | [Time] | → | [Cu2+] | −0.023 | 0.127 | −0.179 | −0.036 |
λ7 | [Time] | → | [CG_DMV] | 0.018 | 0.005 | 3.555 ** | 0.592 |
λ8 | [Ag+] | → | [CG_DMV] | −0.003 | 0.001 | −2.404 * | −0.402 |
λ9 | [Cu2+] | → | [CG_DMV] | −0.009 | 0.009 | −1.011 | −0.179 |
λ10 | [CHG_DMV] | → | [GP] | 0.055 | 0.676 | 0.082 | 0.019 |
λ11 | [CG_DMV] | → | [GP] | −2.596 | 0.953 | −2.723 ** | −0.563 |
λ12 | [DNM_DM] | → | [GP] | 0.046 | 0.068 | 0.684 | 0.141 |
λ13 | [Ag+] | → | [DNM-DM] | 0.021 | 0.013 | 1.586 | 0.220 |
λ14 | [Cu2+] | → | [DNM-DM] | 0.454 | 0.109 | 4.161 ** | 0.646 |
λ15 | [CHG_DMV] | → | [SV] | −9.803 | 1.047 | −9.366 ** | −0.985 |
λ16 | [DNM_DM] | → | [SV] | −0.200 | 0.106 | −1.880 | 0.141 |
Covariances | |||||||
φ1 | [F1010.940] | ↔ | [Time] | 0.002 | 0.007 | 0.347 | 0.074 |
Variances | |||||||
δ1 | 0.018 | 0.005 | 3.346 ** | ||||
δ2 | 616.775 | 151.285 | 4.077 ** | ||||
δ3 | 11.636 | 3.407 | 3.415 ** | ||||
δ4 | 0.015 | 0.005 | 3.018 ** | ||||
δ5 | 0.396 | 0.124 | 3.199 ** | ||||
δ6 | 3.083 | 0.930 | 3.313 ** | ||||
δ7 | 1.120 | 0.328 | 3.418 ** | ||||
[Time] | 29.723 | 7.845 | 3.789 ** | ||||
[F1010.940] | 0.000 | 0.000 | 3.015 ** |
Effect | Estimates (b) | Standardized Estimates (β) | ||||||
---|---|---|---|---|---|---|---|---|
Direct Effect | Indirect Effects | Total Effects | Direct Effect | Indirect Effects | Total Effects | |||
[CHG_DMV] | ||||||||
[Time] | → | [CHG_DMV] | 0.014 | −0.005 | 0.009 | 0.284 | −0.103 | 0.181 |
[F1010.940] | → | [CHG_DMV] | −6.230 | — | −6.230 | −0.139 | — | −0.139 |
[Ag+] | → | [CHG_DMV] | 0.007 | — | 0.007 | −0.695 | — | −0.695 |
[Cu2+] | → | [CHG_DMV] | −0.037 | — | −0.037 | −0.481 | — | −0.481 |
[Ag+] | ||||||||
[Time] | → | [Ag+] | 0.800 | — | 0.800 | 0.173 | — | 0.173 |
[Cu2+] | ||||||||
[Time] | → | [Cu2+] | −0.023 | — | −0.023 | −0.036 | — | −0.036 |
[SV] | ||||||||
[CHG_DMV] | → | [SV] | −9.803 | — | −9.803 | −0.985 | — | −0.985 |
[Time] | → | [SV] | — | −0.088 | −0.088 | — | −0.181 | −0.181 |
[F1010.940] | → | [SV] | — | 61.073 | 61.073 | — | 0.137 | 0.137 |
[Ag+] | → | [SV] | — | 0.067 | 0.067 | — | 0.644 | 0.644 |
[Cu2+] | → | [SV] | — | 0.275 | 0.275 | — | 0.356 | 0.356 |
[DNM_DM] | → | [SV] | −0.200 | — | −0.200 | −0.182 | — | −0.182 |
[GP] | ||||||||
[CHG_DMV] | → | [GP] | 0.055 | — | 0.055 | 0.019 | — | 0.019 |
[Time] | → | [GP] | — | −0.042 | −0.042 | — | −0.292 | −0.292 |
[F1010.940] | → | [GP] | — | −0.344 | −0.344 | — | −0.003 | −0.003 |
[Ag+] | → | [GP] | — | 0.008 | 0.008 | — | 0.245 | 0.245 |
[Cu2+] | → | [GP] | — | 0.042 | 0.042 | — | 0.183 | 0.183 |
[CG_DMV] | → | [GP] | −2.596 | — | −2.596 | −0.563 | — | −0.563 |
[DNM_DM] | → | [GP] | 0.046 | — | 0.046 | 0.141 | — | 0.141 |
[CG_DMV] | ||||||||
[Ag+] | → | [CG_DMV] | −0.003 | — | −0.003 | −0.402 | — | −0.402 |
[Cu2+] | → | [CG_DMV] | −0.009 | — | −0.009 | −0.179 | — | −0.179 |
[Time] | → | [CG_DMV] | 0.017 | — | 0.017 | 0.591 | — | 0.529 |
[DNM_DM] | ||||||||
[Ag+] | → | [DNM_DM] | 0.021 | — | 0.021 | 0.220 | — | 0.220 |
[Cu2+] | → | [DNM_DM] | 0.454 | — | 0.454 | 0.646 | — | 0.646 |
[Time] | → | [DNM_DM] | — | 0.006 | 0.006 | — | 0.015 | 0.015 |
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Bednarek, P.T.; Orłowska, R.; Mańkowski, D.R.; Oleszczuk, S.; Zebrowski, J. Structural Equation Modeling (SEM) Analysis of Sequence Variation and Green Plant Regeneration via Anther Culture in Barley. Cells 2021, 10, 2774. https://doi.org/10.3390/cells10102774
Bednarek PT, Orłowska R, Mańkowski DR, Oleszczuk S, Zebrowski J. Structural Equation Modeling (SEM) Analysis of Sequence Variation and Green Plant Regeneration via Anther Culture in Barley. Cells. 2021; 10(10):2774. https://doi.org/10.3390/cells10102774
Chicago/Turabian StyleBednarek, Piotr Tomasz, Renata Orłowska, Dariusz Rafał Mańkowski, Sylwia Oleszczuk, and Jacek Zebrowski. 2021. "Structural Equation Modeling (SEM) Analysis of Sequence Variation and Green Plant Regeneration via Anther Culture in Barley" Cells 10, no. 10: 2774. https://doi.org/10.3390/cells10102774
APA StyleBednarek, P. T., Orłowska, R., Mańkowski, D. R., Oleszczuk, S., & Zebrowski, J. (2021). Structural Equation Modeling (SEM) Analysis of Sequence Variation and Green Plant Regeneration via Anther Culture in Barley. Cells, 10(10), 2774. https://doi.org/10.3390/cells10102774