SEGN: Inferring real-time gene networks mediating phenotypic plasticity

Characterization, costs, cues and future perspectives of phenotypic plasticity

BACKGROUND

Plastic responses of plants to the environment are ubiquitous. Phenotypic plasticity occurs in many forms and at many biological scales, and its adaptive value depends on the specific environment and interactions with other plant traits and organisms. Even though plasticity is the norm rather than the exception, its complex nature has been a challenge in characterizing the expression of plasticity, its adaptive value for fitness and the environmental cues that regulate its expression.

SCOPE

This review discusses the characterization and costs of plasticity and approaches, considerations, and promising research directions in studying plasticity. Phenotypic plasticity is genetically controlled and heritable; however, little is known about how organisms perceive, interpret and respond to environmental cues, and the genes and pathways associated with plasticity. Not every genotype is plastic for every trait, and plasticity is not infinite, suggesting trade-offs, costs and limits to expression of plasticity. The timing, specificity and duration of plasticity are critical to their adaptive value for plant fitness.

CONCLUSIONS

There are many research opportunities to advance our understanding of plant phenotypic plasticity. New methodology and technological breakthroughs enable the study of phenotypic responses across biological scales and in multiple environments. Understanding the mechanisms of plasticity and how the expression of specific phenotypes influences fitness in many environmental ranges would benefit many areas of plant science ranging from basic research to applied breeding for crop improvement.

An eco-evo-devo genetic network model of stress response

The capacity of plants to resist abiotic stresses is of great importance to agricultural, ecological and environmental sustainability, but little is known about its genetic underpinnings. Existing genetic tools can identify individual genetic variants mediating biochemical, physiological, and cellular defenses, but fail to chart an overall genetic atlas behind stress resistance. We view stress response as an eco-evo-devo process by which plants adaptively respond to stress through complex interactions of developmental canalization, phenotypic plasticity, and phenotypic integration. As such, we define and quantify stress response as the developmental change of adaptive traits from stress-free to stress-exposed environments. We integrate composite functional mapping and evolutionary game theory to reconstruct omnigenic, information-flow interaction networks for stress response. Using desert-adapted Euphrates poplar as an example, we infer salt resistance-related genome-wide interactome networks and trace the roadmap of how each SNP acts and interacts with any other possible SNPs to mediate salt resistance. We characterize the previously unknown regulatory mechanisms driving trait variation; i.e. the significance of a SNP may be due to the promotion of positive regulators, whereas the insignificance of a SNP may result from the inhibition of negative regulators. The regulator-regulatee interactions detected are not only experimentally validated by two complementary experiments, but also biologically interpreted by their encoded protein-protein interactions. Our eco-evo-devo model of genetic interactome networks provides an approach to interrogate the genetic architecture of stress response and informs precise gene editing for improving plants' capacity to live in stress environments.

Modeling genome-wide by environment interactions through omnigenic interactome networks

How genes interact with the environment to shape phenotypic variation and evolution is a fundamental question intriguing to biologists from various fields. Existing linear models built on single genes are inadequate to reveal the complexity of genotype-environment (G-E) interactions. Here, we develop a conceptual model for mechanistically dissecting G-E interplay by integrating previously disconnected theories and methods. Under this integration, evolutionary game theory, developmental modularity theory, and a variable selection method allow us to reconstruct environment-induced, maximally informative, sparse, and casual multilayer genetic networks. We design and conduct two mapping experiments by using a desert-adapted tree species to validate the biological application of the model proposed. The model identifies previously uncharacterized molecular mechanisms that mediate trees' response to saline stress. Our model provides a tool to comprehend the genetic architecture of trait variation and evolution and trace the information flow of each gene toward phenotypes within omnigenic networks.

Heterophylly Quantitative Trait Loci Respond to Salt Stress in the Desert Tree Populus euphratica

Heterophylly, or leaf morphological changes along plant shoot axes, is an important indicator of plant eco-adaptation to heterogeneous microenvironments. Despite extensive studies on the genetic control of leaf shape, the genetic architecture of heterophylly remains elusive. To identify genes related to heterophylly and their associations with plant saline tolerance, we conducted a leaf shape mapping experiment using leaves from a natural population of Populus euphratica. We included 106 genotypes grown under salt stress and salt-free (control) conditions using clonal seedling replicates. We developed a shape tracking method to monitor and analyze the leaf shape using principal component (PC) analysis. PC1 explained 42.18% of the shape variation, indicating that shape variation is mainly determined by the leaf length. Using leaf length along shoot axes as a dynamic trait, we implemented a functional mapping-assisted genome-wide association study (GWAS) for heterophylly. We identified 171 and 134 significant quantitative trait loci (QTLs) in control and stressed plants, respectively, which were annotated as candidate genes for stress resistance, auxin, shape, and disease resistance. Functions of the stress resistance genes ABSCISIC ACIS-INSENSITIVE 5-like (ABI5), WRKY72, and MAPK3 were found to be related to many tolerance responses. The detection of AUXIN RESPONSE FACTOR17-LIKE (ARF17) suggests a balance between auxin-regulated leaf growth and stress resistance within the genome, which led to the development of heterophylly via evolution. Differentially expressed genes between control and stressed plants included several factors with similar functions affecting stress-mediated heterophylly, such as the stress-related genes ABC transporter C family member 2 (ABCC2) and ABC transporter F family member (ABCF), and the stomata-regulating and reactive oxygen species (ROS) signaling gene RESPIRATORY BURST OXIDASE HOMOLOG (RBOH). A comparison of the genetic architecture of control and salt-stressed plants revealed a potential link between heterophylly and saline tolerance in P. euphratica, which will provide new avenues for research on saline resistance-related genetic mechanisms.