Xero-Branching: discovering how plant roots adapt to reduced water availability

Project Information

Xerobranching

Grant agreement ID: 891262

DOI

10.3030/891262

Project closed

EC signature date 18 March 2020

Start date 1 March 2022

End date 29 February 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 212 933,76

EU contribution

€ 212 933,76

Coordinated by

THE UNIVERSITY OF NOTTINGHAM
United Kingdom

Periodic Reporting for period 1 - Xerobranching (Xero-Branching: discovering how plant roots adapt to reduced water availability)

Reporting period: 2022-03-01 to 2024-02-29

Summary of the context and overall objectives of the project

Background:
Root branching is a major root trait that determine resource foraging capacity. Recently, the host laboratory discovered that root branching is regulated by heterogenous distribution of soil moisture at finer spatial scales. Using X-ray Computed Tomography (CT), it was demonstrated that root branching is completely suppressed in zones of low water availability in soil (e.g. air-filled gap). This root adaptive response termed as ‘Xerobranching’ (XB) was found conserved across many crop species. Initial studies suggested that Xerobranching was dependent on ABA and auxin responses. However, how these hormone pathways regulate Xerobranching was unclear. Given the agronomic importance of water stress and root branching on crop performance, the project aimed to uncover the molecular mechanism(s) underpinning the Xerobranching response.
Proposed objectives:
1. Do roots exhibit Xerobranching in response to ABA-dependent changes in SUMOylation?
2. Does ABA trigger SUMOylation of auxin response factors during Xerobranching?
3. Does Xerobranching response impacts crop performance?

Conclusion of the action:
The research work provided multiple genetic evidence supporting a role for ABA during Xerobranching. Moreover, a novel method of studying transient stress response was developed which helped to elucidate the molecular basis of Xerobranching. The research revealed how dynamic hormone fluxes enable roots to adapt to heterogeneous soil conditions (Mehra et al., 2022 Science). The study elegantly showed that the Xerobranching response is distinct from auxin-regulated lateral root hydropatterning (Mehra et al., 2023 Curr. Op. Pl. Biol.). The research revealed that Xerobranching is independent of SUMOylation/DeSUMOylation processes of the Auxin Response factors. The study also showed that Xerobranching response and mechanism is conserved across crop species including millets (such as Setaria). Thus, Xerobranching represents an adaptive root response to optimize resource foraging in heterogenous soil environments. Overall, the study has effectively achieved the goals outlined in the proposed objectives and uncovered a universal blueprint for water stress sensing in plant roots, offering invaluable insights into how plants adapt to water scarcity.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Most of the preliminary studies on Xerobranching were performed in crop plants using low-throughput soil assays and X-ray CT imaging. Therefore, I first designed ‘Agar-Based Air-gap Assay’ (AAA) to study XB responses in model plant, Arabidopsis. This allowed me to take best advantage of the wealth of genetic resources available in Arabidopsis and proved instrumental in dissecting the molecular mechanisms underlying XB. With the help of the agar-based bioassay, I endeavoured to address the proposed key questions:

1. Do roots exhibit Xerobranching in response to ABA-dependent changes in SUMOylation?
To determine whether Xerobranching is dependent on ABA, I first examined the XB responses of ABA biosynthetic/signalling mutants. Strikingly, unlike wild-type (WT) the Arabidopsis ABA biosynthetic mutant, aba2-1 produced lateral roots in air-gaps. The mutant phenotype was rescued by expressing the wildtype ABA2 gene using the phloem-expressed SUC2 promoter. This result revealed the importance of ABA originating from the phloem, which is also the source of water a root needs to maintain growth in drying soil (Mehra et al., 2022 Science). I further established that that ABA-dependent XB response pathway acts independently of SUMOylation-dependent ABA response pathway.

2. Does ABA trigger SUMOylation of auxin response factors during Xerobranching?
The hormone auxin regulates transcription of many auxin-responsive genes dependent on ‘Aux/IAA-ARF’ signalling modules. The host laboratory discovered another water-related root adaptive trait termed ‘hydropatterning’ which favours lateral root positioning towards moist agar/soil patches. This phenomenon is regulated by differential SUMOylation of ARF7 on dry vs moist sides of a root. SUMOylation blocks ARF7 activity on the dry side of a root, thereby suppressing expression of its downstream target (e.g. LBD16), resulting in no LR formation. To validate the functional importance of SUMOylation during Xerobranching, I examined XB response of Arabidopsis mutants of several SUMO/DeSUMOylation components, some of which also display hydropatterning defects. However, like WT none of these mutants formed lateral roots in air gap suggesting XB response is independent of SUMO/DeSUMOylation processes.

3. Uncovering Xerobranching’s impact on soil exploration
The Xerobranching response ensures roots only branch when in contact with moist soil. I found that besides monocot cereal crops, the response is also conserved in millets such as Setaria and dicot species such as tomato. Using X-ray CT, I observed that tomato mutants impaired in ABA biosynthesis continue to branch in air gaps in soil. This confirmed the role of ABA in regulating XB in crop plants as well. To discover phenotypic variation in this adaptive trait, a diversity population of >300 Setaria accessions was screened for their branching response. The generated phenotypic datasets will be next utilized to perform GWAS analysis to discover the underlying candidate genes/alleles involved in regulation of Xerobranching as well as other root traits in Setaria.

The project outcomes were disseminated through conferences, press releases and via media platforms:
2023 Concurrent session talk at IPGSA, South Korea
2022 Plenary session talk at ICAR, Belfast

Press release: https://www.nottingham.ac.uk/news/research-reveals-plant-roots-change-shape-and-branch-out-for-water#
Media highlights: The amazing system plants use to shape their roots and why it could help protect crops from climate change. The Conversation

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The research work carried out during this fellowship tenure successfully proved ABA as a repressive signal for root branching during Xerobranching response (Mehra et al., 2022, Science). In this groundbreaking research, I reported how a Xerobranching stimulus triggers the transient release of abscisic acid (ABA) from phloem companion cells. I also discovered that during xerobranching conditions, roots rely on an internal water (phloem-derived) source to sustain growth. The hormone ABA is co-mobilised with phloem-derived water towards outer root tissues, where it triggers closure of inter-cellular pores, termed ‘plasmodesmata’. This disrupts inward movement of the hormone auxin towards vasculature, which inhibits root branching (Fig. 1). Strikingly, once root tips regain contact with moisture, ABA response rapidly attenuates. Xerobranching reveals how dynamic hormone responses enable roots to adapt to heterogeneous soil conditions. In summary, the MSCA fellowship project has made several seminal discoveries which impact the field’s understanding about root-water interactions. Additionally, the project outputs have provided the basis for several follow-up experiments that will ultimately help re-engineer root systems to improve foraging and resource use efficiency in crops particularly during water stress conditions.

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