Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System

Aaron J Ogden,Yuliya Farris,Gabriel L Myers,Tanya Winkler,Thomas W Wietsma,Amir H Ahkami

doi:10.1038/s41598-020-63224-z

Abstract

Root systems are dynamic and adaptable organs that play critical roles in plant development. However, how roots grow and accumulate biomass during plant life cycle and in relation to shoot growth phenology remains understudied. A comprehensive time-dependent root morphological analysis integrated with molecular signatures is then required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root morphology, biomass production, and C/N ratios during developmental stages. To provide insight into gene regulation that accompanies root growth, we generated comprehensive transcript profiles of Brachypodium whole-root system at four developmental stages. Our data analysis revealed that multiple biological processes including trehalose metabolism and various families of transcription factors (TFs) were differentially expressed in root system during plant development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated as plant entered the booting/heading stage, while ARFs and GRFs were downregulated suggesting these TF families as important factors involved in specific phases of rooting, and possibly in regulation of transition to plant reproductive stages. We identified several Brachypodium candidate root biomass-promoting genes and cis-regulatory elements for further functional validations and root growth improvements in grasses.

Highlights

Roots are the central core of the plant system which play a critical role during plant growth and development
We identified 35 Transcription Factors (TFs) associated with ethylene signaling using partial least squares discriminant analysis (PLS-DA) (PC1 variable of importance in projection (VIP) score >1, supplemental Table S6), 33 of which belonged to the ethylene response factors (ERFs) or ERF-like TF families
Our data showed a significant increase in expression of the trehalose phosphate synthases (TPSs) Bd4g41580 and Bd1g69420 in T4 compared to T1, suggesting altered root trehalose metabolism during Brachypodium developmental stages, possibly as a signaling pathway triggering root growth responses[51]

Summary

Introduction

Roots are the central core of the plant system which play a critical role during plant growth and development. In this context, Brachypodium displays all the characteristics of a monocotyledon root system; its complexity is minimal compared to many other strategic food and bioenergy crops[5]. Though, only one gene has been characterized to date that modulates a relatively subtle shift to root architecture in a monocot, DEEPER ROOTING 1 (DRO1) as a major quantitative trait loci (QTL) for deeper rooting in rice[9] It is well-documented that almost all aspects of plant growth and development (including root formation) are governed in part by Transcription Factors (TFs)[8,10]. Our results provide the most comprehensive dataset of Brachypodium rooting process at the transcript level to date, and the identified putative root growth-promoting genes and regulatory elements in this work are potential targets to generate genetically modified crops for biomass increase in future studies

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