Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients
Data files
Nov 28, 2023 version files 3.77 MB
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examplegen.Rdata
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examplegeninfo.Rdata
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expheno.Rdata
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README.md
Abstract
Background:
Understanding the mechanisms by which genes control and regulate complex quantitative traits during periods of fluctuating resources remains a challenging and uncertain task in photosynthesis studies. Most studies have focused on the structure of photosynthesis, the photosynthetic response under stress, or the genetic mechanisms involved in photosynthetic effects and neglected the interactive genetic mechanism that governs various traits through significant quantitative trait loci (QTLs). Results In this study, we have developed a differential dynamic system that enables the identification of QTLs based on the photosynthetic phenotypic and genotypic data under varying levels of light intensity gradients. The framework not only allows for the assessment of the direct effects of QTLs on phenotypes but also captures how they influence interactions among phenotypes as light intensities change. We have analyzed the genetic effects and genetic variance, visualized the genetic network associated with photosynthesis interactions, and validated the effectiveness and stability of the DDS framework. Pivotal QTLs were identified individually to uncover the process and pattern of interaction. Through functional annotation, we made an intriguing discovery that seemingly unimportant QTLs can still have significant genetic effects on phenotypic changes through their regulation with other QTLs. Conclusions This finding emphasizes the significance of considering the interactive genetic architecture when seeking to understand the genetic interaction mechanism of photosynthesis in natural populations of woody plants. Moreover, our research provides a novel framework that can be extended to explore the interactive genetic architecture among organisms, contributing to a deeper understanding of stress resistance mechanisms in woody plants.
README: Unveiling the Genetic Networks: Exploring the Dynamic Interaction of Photosynthetic Phenotypes in Woody Plants across Varied Light Gradients
https://doi.org/10.5061/dryad.2fqz612wf
Datasets included:
- expheno.Rdata
Phenotypes data of the chlorophyll fluorescence under 11 segments of excitation light irradiation from 102 samples (including maximal Fluorescence (Fm), Electron Transfer Rate (ETR), Quantum Photochemical Yield (Yield), Photochemical Quenching Coefficient (qP), and Non-Photochemical Quenching coefficient (qN))
- examplegen.Rdata
Genotypes of 100000 SNPs in 012 format
- examplegeninfo.Rdata
SNP informations of 100000 SNPs
Sharing/Access information
Links to other publicly accessible locations of the data:
Code/Software
- main.R
The total running commands. When running these commands, all functions in the following R files will be called as required. Please make sure that these files are in your working directory.
- Net Function.R
Network construction
- lvcovar.R
Construct covariance matrix using the first-order forward dependent SAD model
- lvcurve.R
Solve the likelihood function value and parameter set of the original hypothesis
- lvoptim.R
Solve the likelihood function value and parameter set of the alternative hypothesis
- renewode.R
Differential Dynamic System (DDS) model
All of the files runs in R.