Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and<i>Brassica rapa</i>cultivars

Calderwood, Alexander; Hepworth, Jo; Woodhouse, Shannon; Bilham, Lorelei; Jones, D. Marc; Tudor, Eleri; Ali, ME; Dean, Caroline; Wells, Rachel; Irwin, Judith A.; Morris, Richard J.

doi:10.1017/qpb.2021.6

Cited by 6 publications

(9 citation statements)

References 66 publications

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“…Dynamic genes require dynamic methods: many of the critical nodes change quantitatively over time, so time-course analyses are essential ( Shindo et al 2006 ; Duncan et al 2015 ; Nagano et al 2019 ; Schiessl et al 2019 ; Calderwood et al 2021a ), and tools are becoming available for easier comparison of transcriptomics ( Calderwood et al 2021b ).…”

Section: Analyzing Flowering In a New Speciesmentioning

confidence: 99%

Flowering time: From physiology, through genetics to mechanism

Maple,

Zhu,

Hepworth

et al. 2024

Plant Physiology

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Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signalling input pathways converge to regulate a common set of ‘floral pathway integrators’. Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.

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Section: Analyzing Flowering In a New Speciesmentioning

confidence: 99%

Flowering time: From physiology, through genetics to mechanism

Maple,

Zhu,

Hepworth

et al. 2024

Plant Physiology

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“…Brassica rapa , a close relative of A. thaliana , is a globally relevant crop that is considered a model dicotyledon for genetic studies because of its small genome size among the Brassica genus, morphological diversity and fast life cycle of some genotypes (Itabashi et al, 2018; X. Wang et al, 2011). The main A. thaliana flowering time regulatory genes are conserved in B. rapa although they usually appear in several copies (Akter et al, 2021; Calderwood et al, 2021; Schiessl et al, 2017; X. Wang et al, 2011). There are two B. rapa FT homologs that have been shown relevant for flowering time regulation by quantitative trait loci analysis (Lou et al, 2007; Zhang et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Most of what we know about the regulation of flowering time in Brassica crops is inferred from previous A. thaliana studies (Schiessl et al, 2017). To fix this problem, we recently started characterizing the flowering time response in B. rapa R‐o‐18, a rapid‐cycling variety that is becoming a model Brassica oilseed crop due to its genetic resources (Calderwood et al, 2021; del Olmo et al, 2019; Stephenson et al, 2010). In this study, we study the two related H3K27me3 demethylases BraA.REF6 and BraA.ELF6 and characterize novel B. rapa mutant lines.…”

Section: Introductionmentioning

confidence: 99%

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Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa

Poza-Viejo

Payá‐Milans

Martín-Úriz

et al. 2022

Plant Cell & Environment

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Epigenetic regulation is necessary for optimal organism development and preservation of gene expression profiles in the cell. In plants, the trimethylation of histone H3 lysine 27 (H3K27me3) is a silencing epigenetic mark relevant for developmental transitions like flowering. The floral transition is a key agronomic trait; however, the epigenetic mechanisms of flowering time regulation in crops remain poorly understood. Here we study the Jumonji H3K27me3 demethylases BraA.REF6 and BraA.ELF6 in Brassica rapa. Phenotypic characterization of novel mutant lines and genome-wide H3K27me3 chromatin immunoprecipitation and transcriptomic analyses indicated that BraA.REF6 plays a greater role than BraA.ELF6 in fine-tuning H3K27me3 levels. In addition, we found that braA.elf6 mutants were early flowering due to high H3K27me3 levels at B. rapa homologs of the floral repressor FLC. Unlike mutations in Arabidopsis thaliana, braA.ref6 mutants were late flowering without altering the expression of B. rapa FLC genes. Remarkably, we found that BraA.REF6 regulated a number of gibberellic acid (GA) biosynthetic genes, including a homolog of GA1, and that GA-treatment complemented the late flowering mutant phenotype. This study increases our understanding of the epigenetic regulation of flowering time in B. rapa, highlighting conserved and distinct regulatory mechanisms between model and crop species.

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“…This is a total revolution in plant science as the focus will shift away from yield increase and optimisation (only relevant to a stable, controlled, environment), to the mechanisms supporting robustness and adaptability (relevant to a fluctuating environment). For instance, this involves analysing how time can tune regulatory networks (Calderwood et al, 2021 ), how incoherence generates stability (Creff et al, 2023 ; Joanito et al, 2018 ), how local variability generates global reproducibility (Roeder, 2021 ) or how delays support adaptability (Vidal et al, 2010 ).…”

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confidence: 99%

The 1972 Meadows report: A wake-up call for plant science

Hamant

2023

Quant Plant Bio.

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The 1972 Meadows report, ‘the limits to growth’, predicted a global socio-economic tipping point during the twenty-first century. Now supported by 50 years of empirical evidence, this work is a tribute to systems thinking and an invitation to take the current environmental crisis for what it is: neither a transition nor a bifurcation, but an inversion. For instance, we used matter (e.g., fossil fuel) to save time; we will use time to preserve matter (e.g., bioeconomy). We were exploiting ecosystems to fuel production; production will feed ecosystems. We centralised to optimise; we will decentralise to support resilience. In plant science, this new context calls for new research on plant complexity (e.g., multiscale robustness and benefits of variability), also extending to new scientific approaches (e.g., participatory research, art and science). Taking this turn reverses many paradigms and becomes a new responsibility for plant scientists as the world becomes increasingly turbulent.

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Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis andBrassica rapacultivars

Cited by 6 publications

References 66 publications

Flowering time: From physiology, through genetics to mechanism

Flowering time: From physiology, through genetics to mechanism

Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa

The 1972 Meadows report: A wake-up call for plant science

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