DOI: 10.5061/dryad.2fqz612wf
title: Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients

description: 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.
description: # 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 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.