̽��ֱ�� of Cambridge - plant genetics

Planting ideas: Botanic Garden opens access with living collections portal

ta385 — Fri, 02 Oct 2020 07:30:00 +0000

A new web portal to Cambridge ̽��ֱ�� Botanic Garden's entire living collection, 14,000 plants, aims to open access and fast-track urgent global research.

Ancient defence strategy continues to protect plants from pathogens

ta385 — Fri, 12 Jul 2019 07:30:00 +0000

Researchers from the Sainsbury Laboratory at the ̽��ֱ�� of Cambridge compared how two distantly related plants – a common liverwort (Marchantia polymorpha) and a flowering plant, wild tobacco (Nicotiana benthamiana) – defend themselves against an aggressive pathogen (Phytophthora palmivora).

This is the first time such a comparison has been undertaken. By studying how these distantly related plants – which split from their common ancestor roughly 400 million years ago – respond to pathogen infections, the research team discovered a suite of microbe-responsive gene families that date back to early land plant evolution.

Our current understanding of how plants successfully defend against disease-causing pathogens mainly originates from studying economically important crop plants and a small number of closely-related flowering plant model systems. Very distantly-related plants, such as non-flowering liverworts that are believed to resemble some of the first land plants, are often overlooked. As a result, not much was known about how these plants defend themselves from pathogens or how plant defence strategies have evolved.

Published in Current Biology, the study's identification of these evolutionarily conserved genes is shedding new light on the strategies that were likely critical for the expansion of plants onto land.

“We have shown that molecular responses to pathogen infection typical of modern flowering plants are common to very distantly-related land plants and may therefore be more ancient than we previously thought,” said Dr Sebastian Schornack, who led the research team that undertook the study. “Despite fluctuating environmental pressures over a broad evolutionary timescale, these conserved genes have retained their capacity to confer pathogen protection in plants, including in important agricultural crops.”

Bioinformatics expert, Dr Anna Gogleva, identified a subset of one-to-one corresponding genes (single-copy orthologs) in the liverwort and wild tobacco and analysed their level of activity during the infection. A number of different genes were activated in both plants, but a set of metabolic genes involved in phenylpropanoid (flavonoid) biosynthesis were highly activated in response to infection.

These gene families are often associated with the stress-response in flowering plants, providing increased protection against biotic or abiotic stresses caused by chewing insects, pathogens and nutrient or light stress. However, this was the first time that these genes had been functionally linked to pathogen defence strategies in liverworts.

“Pathogen zoospores germinate on the surface of liverworts and eventually colonise the liverwort tissues, but in some areas we saw an accumulation of a purple/red pigment in the liverwort tissues where the pathogen was rarely detected,” said Dr Philip Carella, lead author of the study.

“We produced liverwort plants with mosaic pigment patterns – resembling military camouflage fatigues – that allowed us to compare pathogen resistance in pigmented and non-pigmented areas of the same plant and found the pigment provided some resistance to pathogen infection.”

̽��ֱ��enormous diversity of traits and species that we see in modern plants today speaks to the millions of years of evolution that enabled plants to survive in dynamic and contrasting environments across the globe.

“ ̽��ֱ��conflict between organisms can be a very powerful selective pressure that guides their evolutionary trajectory,” said Dr Schornack. “Genes involved in fighting specific pathogens can evolve rapidly – both in plants and animals. But we have also now found these broadly-conserved genes responding to pathogen infection in very distantly-related plants, which suggests that land plants have retained a likely ancient pathogen deterrence strategy that is much too useful to lose.

“Fossil evidence shows that plants have engaged in close-interactions with microbial life forms throughout their evolutionary history. Our research has uncovered a common set of pathogen-responsive genes shared in early-divergent land plants and more evolutionarily young flowering plants, which are all likely to have been critical for the expansion of plants onto land. Further comparative studies focusing on other distantly related land plants and their aquatic algal predecessors should reveal even more information about the evolution and role of these vital gene families.”

Reference

Philip Carella, Anna Gogleva, David John Hoey, Anthony John Bridgen, Sara Christina Stolze, Hirofumi Nakagami, and Sebastian Schornack. Conserved Biochemical Defenses Underpin Host Responses to Oomycete Infection in an Early-Divergent Land Plant Lineage. Current Biology (11 July 2019); DOI: 10.1016/j.cub.2019.05.078

Scientists at the ̽��ֱ�� of Cambridge have uncovered striking similarities in how two distantly related plants defend themselves against pathogens despite splitting from their common ancestor more than 400 million years ago.

Land plants have retained a likely ancient pathogen deterrence strategy that is much too useful to lose

Sebastian Schornack

̽��ֱ��Sainsbury Laboratory, ̽��ֱ�� of Cambridge

Sebastian Schornack and Philip Carella of the Sainsbury Laboratory, ̽��ֱ�� of Cambridge

Funding

This work was funded by the Gatsby Charitable Foundation, the Royal Society, the BBSRC OpenPlant initiative, the Natural Environment Research Council (NERC; NE/N00941X/1), and a Natural Sciences and Engineering Research Council of Canada (NSERC) postdoctoral fellowship to Philip Carella. Proteomic work performed in the Nakagami lab was supported by the Max-Planck-Gesellschaft.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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Enemy at the gates: the battle to save our crops

ta385 — Wed, 22 May 2019 07:00:00 +0000

A gene newly-linked to plant self-defence may hold the key to saving important crops from a deadly disease, scientists at Cambridge's Sainsbury Laboratory now hope.

Opinion: GM crops already feed much of the world today – why not tomorrow’s generations too?

Anonymous — Tue, 24 May 2016 13:19:58 +0000

My parents researched malnutrition and under-nutrition in India, especially among children, and found that many diets recommended by Western nutritionists were in fact completely inapplicable to the poor. So they formulated cheap, healthy diets based on indigenous food with which people were familiar. Yet despite their many other efforts, a quarter of people in Indian and nearly one in nine people around the world do not have enough food to live a healthy active life.

̽��ֱ��World Bank estimates that we will need to produce about 50% more food by 2050 to feed a population of nine billion people. And the past 50 years have seen agricultural productivity soar – corn yields in the US have doubled, for example. But this has come with sharp increases in the use of fertilisers, pesticides and water which has brought its own problems. There is also no guarantee that this rate of increase in yields can be maintained.

Just as new agricultural techniques and equipment spurred on food production in the Middle Ages, and scientific crop breeding, fertilisers and pesticides did so for the Green Revolution of the 20th century, so we must rely on the latest technology to boost food production further. Genetic modification, or GM, used appropriately with proper regulation, may be part of the solution. Yet GM remains a highly contentious topic of debate where, unfortunately, the underlying facts are often obscured.

Views on GM differ across the world. Almost half of all crops grown in the US are GM, whereas widespread opposition in Europe means virtually no GM crops are grown there. In Canada, regulation is focused on the characteristics of the crop produced, while in the EU the focus is on how it has been modified. GM crops do not damage the environment by nature of their modification; GM is merely a technology, and it is the resulting product that we should be concerned about and regulate, just as we would any new product.

There are outstanding plant scientists who work on GM in the UK, but the Scottish, Welsh and Northern Irish governments have declared their opposition to GM plants. Why is there such strong opposition in a country with great trust in scientists?

About 15 years ago when GM was just emerging, its main proponents and many of the initial products were from large multinational corporations – even though it was publicly funded scientists who produced much of the initial research. Understandably, many felt GM was a means for these corporations to impose a monopoly on crops and maximise their profits. This perception was not helped by some of the practices of these big companies, such as introducing herbicide resistant crops that led to the heavy use of herbicides – often made by the same companies.

̽��ֱ��debate became polarised, and any sense that the evidence could be rationally assessed evaporated. There have been claims made about the negative health effects and economic costs of GM crops – claims later shown to be unsubstantiated. Today, half of those in the UK do not feel well informed about GM crops.

Everyday genetic modification

GM involves the introduction of very specific genes into plants. In many ways this is much more controlled than the random mutations that are selected for in traditional plant breeding. Most of the commonly grown crops that we consider natural actually bear little resemblance to their wild ancestors, having been selectively modified through cross-breeding over the thousands of years that humans have been farming crops – in a sense, this is a form of genetic modification itself.

In any case, we accept genetic modification in many other contexts: insulin used to treat diabetes is now made by GM microbes and has almost completely replaced animal insulin, for example. Many of the top selling drugs are proteins such as antibodies made entirely by GM, and now account for a third of all new medicines (and over half of the biggest selling ones). These are used to treat a host of diseases, from breast cancer to arthritis and leukaemia.

Millions of acres growing GM crops worldwide. Fafner/ISSSA, CC BY-SA

GM has been used to create insect-resistance in plants that greatly reduces or even eliminates the need for chemical insecticides, reducing the cost to the farmer and the environment. It also has the potential to make crops more nutritious, for example by adding healthier fats or more nutritious proteins. It’s been used to introduce nutrients such as beta carotene from which the body can make vitamin A – the so-called golden rice – which prevents night blindness in children. And GM can potentially create crops that are drought resistant – something that as water becomes scarce will become increasingly important.

More than 10% of the world’s arable land is now used to grow GM plants. An extensive study conducted by the US National Academies of Sciences recently reported that there has been no evidence of ill effects linked to the consumption of any approved GM crop since the widespread commercialisation of GM products 18 years ago. It also reported that there was no conclusive evidence of environmental problems resulting from GM crops.

GM is a tool, and how we use it is up to us. It certainly does not have to be the monopoly of a few multinational corporations. We can and should have adequate regulations to ensure the safety of any new crop strain (GM or otherwise) to both ourselves and the environment, and it is up to us to decide what traits in any new plant are acceptable. People may be opposed to GM crops for a variety of reasons and ultimately consumers will decide what they want to eat. But the one in nine people in poor countries facing malnutrition or starvation do not enjoy that choice. ̽��ֱ��availability of cheap, healthy and nutritious food for them is a matter of life and death.

Alongside other improvements in farming practices, genetic modification is an important part of a sustainable solution to global food shortages. However, the motto of the Royal Society is nullius in verba; roughly, “take nobody’s word for it”. We need a well-informed debate based on an assessment of the evidence. ̽��ֱ��Royal Society has published GM Plants: questions and answers which can play its part in this. People should look at the evidence – not just loudly voiced opinions – for themselves and make up their own minds.

Venki Ramakrishnan, Professor and Deputy Director, MRC Laboratory of Molecular Biology, ̽��ֱ�� of Cambridge

This article was originally published on ̽��ֱ��Conversation. Read the original article.

̽��ֱ��opinions expressed in this article are those of the individual author(s) and do not represent the views of the ̽��ֱ�� of Cambridge.

Professor Sir Venki Ramakrishnan (MRC Laboratory of Molecular Biology) discusses how genetically modified crops could help solve the problem of food security.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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‘Smoke detector’ enables fungal partnership that allowed plants to first survive on land

fpjl2 — Fri, 18 Dec 2015 10:56:53 +0000

New research has revealed that a plant protein known to detect growth-promoting compounds in smoke from burning vegetation has a much older and broader role: recognising initial signals sent from the beneficial soil fungi that deliver nutrients directly into plant cells.

By identifying the molecular signals emitted through the soil by friendly fungi, the protein enables a plant to “roll out the red carpet” for cell colonisation by the fungi, and all the survival advantages this mutually-beneficial relationship brings – the fungi feeds minerals such as phosphate into plant cells in return for sugar extraction.

This “symbiosis” between plants and certain microbial fungi is prevalent across the plant kingdom, and thought to date back to the earliest transitions of plant life from water to land some 450 million years ago, as plants had to develop ways of surviving on land by acquiring nutrients from soil many millennia before they evolved roots.

Scientists believe this ancient relationship with fungi was likely critical to the early terrestrial survival of plants, and consequently the evolution of “all higher life on earth”.

While previous research had shown that plants can clearly tell the difference between beneficial fungi and those that offer nothing or cause disease, how they make the distinction had proved mysterious. Now, latest research has unravelled the genetic code of the plant protein that enables the “cross-kingdom dialogue” between plants and fungi – allowing plants to let the right fungi in.

Surprisingly, the protein is an enzyme known to science as the receptor for Karrikin, a plant hormone created when vegetation is burned. Karrikin – from karrik, the Aboriginal word for fire – triggers seed germination in certain species of plant known as “fire-chasers”: plants that are first to sprout once wildfires have devastated their competitors.

While only those few fire-following species such as eucalyptus and some members of the tobacco family use the protein (called D14L) to “tune into smoke signals”, the latest study shows that this same protein is used by the vast majority of plant life on Earth to tune into fungi – perceiving the molecular signals from friendly fungi, and enabling a relationship that helped sustain plant life on land hundreds of millions of years before the evolution of roots and seeds.

“This protein had already been seen to detect smoke hormones in a few fire-chasing plant species, but now we’ve shown it’s the same protein that is central to the everyday interaction of plants with beneficial fungi. This primary, ancestral role of forging a symbiosis with fungi is harnessed by over 80% of all plant species on the planet,” said Dr Uta Paszkowski, from Cambridge ̽��ֱ��’s Department of Plant Science, senior author of the study published today in the journal Science.

“Such fungal symbioses assisted plants to make the transition to land. We are beginning to unlock a process which is taking us back to the first stages of plant life on land some 450 million years ago, one of the key evolutionary steps of life on planet Earth,” she said.

For the new study, scientists found the first “mutant” rice plant that had no susceptibility at all to the friendly fungi. ̽��ֱ��team was able to work out the missing gene, and isolated the D14L protein as the critical element for the detection of these fungi in plants.

“Fungi and plants secrete all sorts of molecules, like a dialogue through the soil, and what we captured is the ‘hearing’ side in plants. Removal of the protein renders the plant insensitive to the fungus – in other words, the plant has become deaf,” said Paszkowski.

When colonising a plant, the beneficial fungus blooms within individual plant cells, growing thin tendrils called hyphae that extend into surrounding soil and pump minerals and nutrients straight into the heart of plant cells. Plants colonised by friendly fungi get between 70 to 100% of their phosphate directly from these hyphae, for example. In return, the fungus gets its sugars from the plant.

Plants monitor their surrounding for the presence of other bacterial or fungal invaders normally using ‘receptor-kinases’. “We and others had assumed the protein mechanism plants use for identifying beneficial fungi would be related to those,” said Paszkowski.

She describes it as a “real surprise” to find the D14L protein, a ‘hydrolase’ protein which functions deep inside the cell, to be necessary for the communication with the friendly fungi.

As the D14L protein is also involved in plants developmental responses to light Paszkowski talks of a “gut feeling” that – with this ancient protein responding to light, atmosphere (through smoke detection) and soil environment (through fungal symbiosis) – it could have been a developmental crossroads vital to plants’ evolutionary leap out of the oceans.

“Light; atmosphere; soil: all aspects crucially different when making that change from water to land, and all adaptations that would be influenced by this one protein. ̽��ֱ��D14L protein may take us back to the earliest days of life on land,” she said.

A protein that detects hormones in smoke has a much wider and more ancient role in the plant kingdom – detecting microscopic soil fungi which colonise plants and feed nutrients to their cells. This ancient symbiosis with soil fungi is thought to be how plants survived on land millions of years before they evolved roots.

Fungi and plants secrete all sorts of molecules, like a dialogue through the soil, and what we captured is the ‘hearing’ side in plants

Uta Paszkowski

Paszkowski lab

This microscopic image shows the spores and hyphae of 'friendly' arbuscular mycorrhizal fungus interacting with a plant root.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

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Fungus enhances crop roots and could be a future 'bio-fertiliser'

fpjl2 — Mon, 04 May 2015 19:02:39 +0000

New research has found that the interaction of roots with a common soil fungus changes the genetic expression of rice crops – triggering additional root growth that enables the plant to absorb more nutrients.

In addition to causing extra root growth, the mycorrhizal fungus also enmeshes itself within crop roots at a cellular level – blooming within individual plant cells. ̽��ֱ��fungus grows thin tendrils called hyphae that extend into surrounding soil and pump nutrients, phosphate in particular, straight into the heart of plant cells.

Plants 'colonised' by the fungi get between 70 to 100% of their phosphate directly from these fungus tendrils, an enormous mineral boost which may eventually mitigate the need for farmers to saturate crop fields with phosphate fertiliser to ensure maximum yield.

̽��ֱ��hope is that mycorrhizal fungi could one day act as a 'bio-fertiliser' that ultimately replaces the need to mine phosphate from the ground for industrial fertiliser. Finding a replacement for mined phosphate is a critical issue as not only is the resultant fertiliser a pollutant – causing algal growth which chokes water supplies – but the big phosphate mines are now depleted to the point where they are expected to run out in the next 30 to 50 years. Many experts are predicting a 'phosphate crisis'.

" ̽��ֱ��big question we are trying to answer is whether and how we can make use of the biofertiliser capacity of mycorrhizal symbiosis in modern and more high input agricultural settings, meaning more intensive farming methods. We need alternatives to phosphate fertiliser if we are to feed growing populations," said Dr Uta Paszkowski from the ̽��ֱ�� of Cambridge's Department of Plant Sciences, who co-authored the research published today in the journal PNAS.

"Cereals such as rice, wheat and maize are the most important crops in the world, feeding billions of people every day. Mycorrhizal fungi have a mutualistic relationship with plants, including cereals, going back to the earliest days of plant life on land, before roots were 'invented'. By analysing this ancient and common relationship we are gaining insights that could be used to breed crops with the best possible root architectural and symbiotic properties – towards 'designing crops' with very high food outputs," she said.

̽��ֱ��new research pioneers the examination of the root system building units of adult rice plants at a molecular level, as rice can be used as a model for cereal crops generally. Cereal root 'architecture' involves a few big, thickset roots called crown roots that act as a scaffold from which all the smaller, lateral roots spread out into the different layers of soil, which contain the various nutrients.

Researchers found that plants colonised by mycorrhizal fungi have a different genetic expression which causes the cell walls within crown roots to soften, triggering the growth of many more lateral roots which are able to suck in more nutrients, contributing to a healthier plant with a higher yield. This is in addition to the phosphate provided by the fungal 'hyphae' tendrils, which in effect act as extra roots themselves (in return for which, the fungus gets its carbohydrate from the plant).

"Plant roots that have the capacity to explore the widest soil area absorb the most nutrients as a consequence and so are likely to have a greater crop yield. By finding out which parts of the genome are responsible for the best plant root systems we can start breeding for the best root 'architecture'," said Paszkowski.

"Designer crops with the best possible root systems will mean greater crop yield, which means more people fed."

Rice is best grown in highly irrigated paddy fields, but there are many parts of the world where this isn't an option, and 40% of the world's area for rice crop is grown 'dry'. However, the plant-fungi relationship that creates enhanced crops actually works best in dry environments. Mycorrhizal fungi could be of huge benefit to those who rely on dry rice crops in some of the poorest areas of Asia and sub-Saharan Africa.

̽��ֱ��main hurdle for researchers to overcome is the self-regulation of plants, which means the fungi cannot be tested on an industrial scale alongside traditional fertiliser.

"Plants monitor their own nutritional state. If a plant has enough phosphate it will not allow fungus to enter root – so at the moment it's one or the other. We are working on ways to circumvent this blockage so we can allow symbiosis to contribute in agricultural practices in better developed countries " said Paszkowski.

Mycorrhizal fungi are extremely common in all soils around the world, and are an ingredient in many 'bio' plant foods found in domestic garden centres, but have yet to be used for industrial agriculture.

Inset image: Mycorrhizal fungi blooming within a plant cell

“Ancient relationship” between fungi and plant roots creates genetic expression that leads to more root growth. Common fungus could one day be used as ‘bio-fertiliser’, replacing mined phosphate which is now depleted to the point of impending fertiliser crisis.

By analysing this ancient and common relationship we are gaining insights that could be used to breed crops with the best possible root architectural and symbiotic properties

Uta Paszkowski

Ahmad Nizam Awang

Dry rice field at dusk

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

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