Integrative Modelling of Gene Expression and Digital Phenotypes to Describe Senescence in Wheat

Abstract

Senescence is the final stage of leaf development and is critical for plants’ fitness as nutrient relocation from leaves to reproductive organs takes place. Although senescence is key in nutrient relocation and yield determination in cereal grain production, there is limited understanding of the genetic and molecular mechanisms that control it in major staple crops such as wheat. Senescence is a highly orchestrated continuum of interacting pathways throughout the lifecycle of a plant. Levels of gene expression, morphogenesis, and phenotypic development all play key roles. Yet, most studies focus on a short window immediately after anthesis. This approach clearly leaves out key components controlling the activation, development, and modulation of the senescence pathway before anthesis, as well as during the later developmental stages, during which grain development continues. Here, a computational multiscale modelling approach integrates multi-omics developmental data to attempt to simulate senescence at the molecular and plant level. To recreate the senescence process in wheat, core principles were borrowed from Arabidopsis Thaliana, a more widely researched plant model. The resulted model describes temporal gene regulatory networks and their effect on plant morphology leading to senescence. Digital phenotypes generated from images using a phenomics platform were used to capture the dynamics of plant development. This work provides the basis for the application of computational modelling to advance understanding of the complex biological trait senescence. This supports the development of a predictive framework enabling its prediction in changing or extreme environmental conditions, with a view to targeted selection for optimal lifecycle duration for improving resilience to climate change.

Rapid Investigation of Functional Roles of Genes in Regulation of Leaf Senescence Using Arabidopsis Protoplasts

“…Plants evolve sophisticated genetic programs for determining the appropriate senescence onset and coordinating senescence progression. The onset of senescence is triggered by various endogenous and environmental signals through the coordinated actions of multiple senescence induction pathways ( Woo et al, 2019 ; Camargo Rodriguez, 2021 ). A well-studied genetic pathway for senescence onset in Arabidopsis is the trifurcate death circuit consisting of ORE1, EIN2 as an ORE1 activator, and miRNA164 as an ORE1 repressor.…”

Transcriptome Analysis of Early Senescence in the Post-Anthesis Flag Leaf of Wheat (Triticum aestivum L.)

“…Many identified NAC and WRKY TFs have been associated with leaf senescence in Arabidopsis, barley, and wheat [ 15 , 21 , 61 , 62 ]. Over half the NAC genes identified in this study showed a correlation with senescence based on their expression patterns, including NAC21/22 , NAC29 , NAC8 , NAC7 , and three other characterized NAM genes.…”

“…Although various factors are interrelated and influence each other, the internal factors play a leading role. Different techniques have been used to identify many senescence-associated genes (SAGs), which are mainly involved in degradation, biosynthetic and regulatory processes, stress responses, and transport [ 13 , 14 , 15 , 16 ]. In SAGs, NAC (no apical meristem (NAM), ATAF1/2, and cup-shaped cotyledon (CUC)) and WRKY transcription factors (TFs) play important roles in regulating gene expression changes during leaf senescence.…”