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
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.