A multi-tissue genome-scale model of Populus trichocarpa elucidates overexpression targets for improving drought tolerance

Abstract

Populus trichocarpa (poplar) is a fast-growing model tree whose lignocellulosic biomass is a promising biofuel feedstock. Enhancing its viability and yield in non-arable drought-prone lands can reduce biomass costs and accelerate adoption as a biofuel crop. Data from extensive -omics and phenotypic studies were leveraged herein to reconstruct a multi-tissue (root, stem and leaf) genome-scale model (GSM) of poplar, iPotri3463, encompassing 14 360 reactions, 12 402 metabolites and 3463 genes. Two condition-specific GSMs were extracted from iPotri3463: iPotri3016C (control) and iPotri2999D (drought), supported by condition-specific transcript levels and reaction essentiality for growth. Physiological constraints consistent with experimental measurements of drought-stressed plants were imposed on growth, photorespiration and carbon assimilation rates. Calculated increased flux capacity through the violaxanthin cycle and GABA biosynthetic pathways agree with established key strategies for improving drought tolerance. Differential gene expression analysis was performed on existing transcriptomes of poplar under different watering regimes. Computational flux knockdown was applied to reactions with increased flux capacity under drought that were associated with at least one downregulated gene. Several such reactions were essential for maintaining observed biomass yield and their associated genes are candidates for overexpression to improve drought tolerance. Glutamine synthetase is one whose overexpression in poplar confirms in silico predictions. However, the two most promising candidates are genes encoding ferulate-5-hydroxylase, Potri.007G016400 and Potri.005G117500, as their overexpression in other plant species led to demonstrably improved drought tolerance while previous overexpression in poplar reduced biomass recalcitrance. iPotri3463 is the first poplar-specific whole-plant GSM and the second one available for a woody plant.