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Peeling back the layers: scientists use new techniques to uncover hidden secrets of plant stem development

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News from: The John Innes Centre

Scientists from the John Innes Centre have pioneered innovative new cell imaging techniques to shed light on cells hidden deep inside the meristem. This new development has made it possible to explore further below the outer surface of plants and has uncovered how a key gene controls stem growth.

The limitations of current live-imaging techniques mean typically only easily accessible parts of plants can be accurately visualised. Studies on areas such as leaves and flowers, have therefore often taken centre stage in plant developmental research. The cellular origins of plant stem growth are buried under several layers of other cells, and as a consequence, it has previously been difficult to explore how stem growth is controlled.

To address this oversight, Professor Robert Sablowski and his team from the John Innes Centre developed new cell imaging techniques to allow them to visualise changes in cells below the plant surface. In particular the group focussed on the shoot apical meristem (SAM), a cluster of cells at the shoot tip, which differentiate to form different kinds of plant tissues and determine the size and overall shape of the plant. The research is published in a new paper in the scientific journal Developmental Cell.

Copyright: JIC

Professor Sablowski said: “To understand how genes control plant shape, we need to understand how they affect growth and division of the cells that make up the plant. The cells that go on to form stem tissue are located in a part of the SAM called the ‘rib zone’, which is buried underneath layers of cells all doing other things. The two main methods that scientists usually use to look at cells under a microscope weren’t suitable in this case: live imaging reveals how cells grow and divide over time, but the rib zone is too deep to give clear live images. The other method is to slice through the SAM to see the rib zone cells. However, you can’t do that with living, growing cells, so the resulting data is not in ‘real-time’. To make things worse, the rib zone is not clearly demarcated, so it’s hard to differentiate it from the rest of the SAM.”

To get around these problems, the scientists combined two approaches. First, using normal ‘wild-type’ Arabidopsis thaliana plants, they marked single cells with a bright fluorescent marker and followed the descendants of these cells in the rib meristem. In the second approach, the researchers used information recorded in the cell walls to infer how the rib zone grows: thinner walls produced during recent cell divisions glowed less brightly than older, thicker cell walls, and the orientation of new cell walls in three-dimensional images revealed the directions of cell growth and division.

Next, the researchers repeated this experiment, but used SAM tissues from a mutant Arabidopsis plant lacking a gene called REPLUMLESS, or RPL for short, to see what effect this had on cell growth.

“It was already known that RPL must be involved in stem development, because it is expressed throughout the SAM, including in the rib zone, and mutation of this gene results in short stems – we just didn’t know how, until now,” said Dr Stefano Bencivenga, first author of the paper. “This time, in the images of SAMs from the rpl mutant, we noticed that although the cells grew at the same rate, they were arranged at different angles instead of all neatly facing in the same direction.”

Professor Sablowski said: “This showed us that RPL doesn’t affect the speed or number of cells growing in the rib zone, rather it affects the orientation in which cells divide as they form new plant stem tissue. In other experiments, also described in our paper, we demonstrate that RPL represses other genes involved in creating organ boundaries. This is important because these organ boundary genes are known to reduce growth in the regions that separate the SAM from new organs such as leaves and flowers. As well as being an important advancement in our understanding of stem development, we might be able to use this knowledge to influence plant traits with key practical importance.”

This research was funded by the Biotechnology and Biological Sciences Research Council (BBSRC).


Notes to editors

The a copy of the paper “Control of oriented tissue growth through repression of organ boundary genes promotes stem morphogenesis” and images to accompany this press release can be found at:

If you would like to interview Professor Sablowski or Dr Stefano Bencivenga, please see external contacts below.

About John Innes Centre

The John Innes Centre is an independent, international centre of excellence in plant science and microbiology.

Our mission is to generate knowledge of plants and microbes through innovative research, to train scientists for the future, to apply our knowledge of nature’s diversity to benefit agriculture, the environment, human health and wellbeing, and engage with policy makers and the public.

To achieve these goals we establish pioneering long-term research objectives in plant and microbial science, with a focus on genetics. These objectives include promoting the translation of research through partnerships to develop improved crops and to make new products from microbes and plants for human health and other applications. We also create new approaches, technologies and resources that enable research advances and help industry to make new products. The knowledge, resources and trained researchers we generate help global societies address important challenges including providing sufficient and affordable food, making new products for human health and industrial applications, and developing sustainable bio-based manufacturing.

This provides a fertile environment for training the next generation of plant and microbial scientists, many of whom go on to careers in industry and academia, around the world.

The John Innes Centre is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC). In 2015-2016 the John Innes Centre received a total of £30.1M from BBSRC.

The John Innes Centre is the winner of BBSRC’s 2013 – 2016 Excellence With Impact award.


BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.

Funded by government, BBSRC invested £473 million in world-class bioscience, people and research infrastructure in 2015-16. We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.

More information about BBSRC, our science and our impact.
More information about BBSRC strategically funded institutes.


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