Regulation of stem initiation and its role in plant architecture

Lead Research Organisation: John Innes Centre
Department Name: Cell and Develop Biology


Development of a vertical shoot axis capable of bearing organs above the ground was one of the key steps in the evolution of land plants. In spite of its ancient and central role in shaping plants, formation of the stem remains one of the least understood processes in plant development. This process also has practical importance: mutations that reduce stem growth have been widely used to improve crop yield but also have undesired side effects on plant growth, for example during seed germination. A better understanding of how genes control stem growth is required to develop more precise genetic tools to increase plant productivity by modifying plant height and shape.

One way to develop new tools to modify plant height is to study how genes modulate stem growth at different stages of the plant's life. This modulation is seen markedly in plants with a rosette habit, such as Arabidopsis, beet, radish, lettuce and cabbage, in which stem elongation is initially inhibited, but later activated during flowering. This transition is triggered by environmental conditions such as day length and temperature, and initiates growth of the stem in a specific region of the shoot apex, called the rib zone (RZ).

Our laboratory has been studying how the RZ functions in the in the reference plant Arabidopsis. We found that a gene called ATH1 has a key role in controlling when the stem is formed: ATH1 is initially active in the RZ to prevent stem growth but is inhibited by flowering signals to initiate the stem. However, it is not known how flowering signals control ATH1 and how ATH1 inhibits stem growth. Our initial results indicate that ATH1 controls stem initiation by acting as a "gatekeeper" for two hormone signals that are known to promote stem growth: gibberellin and brassinosteroid. To test this idea, we propose to follow how ATH1 affects genes involved in signalling by these hormones. In addition, we will test whether these genes mediate the effects of ATH1 on stem growth.

We also aim to understand how flowering signals connect to ATH1 to co-ordinate flower development and stem elongation. We will initially focus on regulatory sequences within the ATH1 gene, which suggest direct links to known regulators of flowering. We will introduce mutations in these sequences and look for plants in which stem growth is uncoupled from flowering. Depending on the regulatory sequences involved, we will then test whether they mediate the input of specific regulatory proteins that regulate the transition to flowering.

Another motivation for studying regulatory sequences in ATH1 is that they may play a role in existing diversity in stem growth in vegetable Brassicas, and could be used to create useful, new variation in plant height and shape. Previous work showed that variation in stem height in Brassica crops is associated with differences in the genomic region containing ATH1, and that crops with a rosette habit (cabbage, kale) have specific differences in ATH1 in comparison to those with elongated stems. To test whether these differences are responsible for variation in stem growth, we will generate plants that carry ATH1 from long-or short-stemmed Brassica, but are otherwise genetically identical. If existing variation in Brassica ATH1 cannot explain differences in stem height, we will use the findings from Arabidopsis to generate novel regulatory mutations to uncouple stem growth from flowering in Brassica.

Overall, this work will reveal the genetic mechanism controlling stem initiation, will shed light on how a variety of plant shapes have been selected during crop breeding, and will produce novel genetic tools to control the height and shape of plants.

Technical Summary

Stem development has a major role on plant architecture and crop value and is initiated in region of the shot apical meristem called the rib zone (RZ). The Bel1-like transcription factor ATH1 is a central regulator of RZ activity and is repressed to activate stem growth during flowering. Here, we aim to understand how ATH1 is regulated and how it controls RZ activity. Based on this knowledge, we will explore regulatory changes in ATH1 as a source of diversity in plant architecture in both Arabidopsis and Brassica.

Our recent results suggest that ATH1 antagonizes RZ activity by inhibiting the function of two hormones with key roles in stem growth: gibberellin (GA) and brassinosteroid (BR). To test this hypothesis, we will monitor expression of GA and BR-related genes in response to ATH1, and test whether localised gain and loss of BR signalling can mimic or bypass ATH1 function in the RZ.

ChIP-seq results and conserved sequences in the ATH1 promoter suggest direct control by flowering regulators (RPL, FD, PIF). To identify regulatory sequences, we will mutagenise the endogenous ATH1 promoter using CRISPR/Cas9, then screen for phenotypes expected for loss of ATH1 expression (elongation of vegetative internodes after GA treatment) and gain of function (short inflorescence stems). Functionally important sequences will be tested for interaction with the relevant flowering regulators.

The results in Arabidopsis will inform the analysis of ATH1 regulation in Brassica. Current data suggest that genetic variation in ATH1 is associated with diversity in shoot architecture in B. oleracea. To verify this, we will compare the function of ATH1 from B. oleraceae lines with a compressed stem (kale) and elongated stem (TO1000) in isogenic backgrounds.

This project will reveal the mechanisms by which RZ activity is controlled, will give insight into the genetic basis for shape variation in Brassica and will explore novel genetic tools to improve crop architecture.

Planned Impact

This project will benefit four main non-academic beneficiaries in the following ways:

1. Plant breeders

Breeders will benefit from novel strategies to increase crop yield by modifying stem architecture, with fewer pleiotropic effects than existing semi-dwarf mutations. The gene network controlling rib meristem activity and stem growth is an attractive target for engineering or selecting regulatory mutations, particularly to obtain dwarfing alleles with disrupted cis-elements that mediate repression rib meristem activity. These dominant regulatory alleles would be especially useful in polyploid species such as Brassica.

The most immediate uses of our results will be genetic tools and markers for translation in Brassica crops. The knowledge and strategy developed in this project also have the potential to be extended more widely to modify crop architecture. The expected time frame for this beneficial impact will be 7-10 years after the start of the project

2. Agricultural businesses

These will benefit from our work indirectly, through future use of the resources and knowledge made available to academic peers and to breeders. The most obvious potential benefits will be in the development of novel strategies to produce semi-dwarf crop varieties with reduced pleiotropy. The channels to these beneficiaries will be breeders, as mentioned above, and licensing of patented knowledge through PBL Technologies. The time frame for this type of impact is expected to be 10-20 years.

3. The general public

The wider public will benefit from interacting with researchers working in areas of public concern, such as food security and genetic modification. The channels for interaction with the public include school activities, press communications and user-friendly web interfaces (3-4 years). In the long term, the public may benefit through a reduction in the volatility of food prices caused by unstable crop yields.


BBSRC will benefit from research relevant to its Strategic Framework for research in agriculture and food security. Specifically, this project is relevant to the Strategic Framework focus on "Accessing under-researched traits for public good", in part by "exploiting the links between target species and model systems"


10 25 50
Description The project started a few months ago, so it is too early to report key findings.
Exploitation Route Too early to report
Sectors Agriculture, Food and Drink