Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients

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 netw..., , , # Unveiling the Genetic Networks: Exploring the Dynamic Interaction of Photosynthetic Phenotypes in Woody Plants across Varied Light Gradients

## 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

Con...