Norwich gene hunters tackle crop diseases
9th December 2010
Norwich scientists are on the trail of some of the most economically damaging organisms that infect crops worldwide. Their latest targets are two types of mildew and the water mold that causes late blight in potatoes and tomatoes.
John Innes Centre scientists contributed to a project, led by Imperial College London, that sequenced the genome of Blumeria, the fungus that causes the economically important disease powdery mildew in barley.
Publishing in the journal Science, the researchers show that the Blumeria genome contains an unexpectedly large number of elements within its genome known as transposons. They believe that these transposons allow Blumeria to rapidly adapt its genome to help it avoid detection by plant defences, which has made developing resistant crop varieties difficult. The genome information and the new understanding of how Blumeria overcomes resistance will help in the development of new more durable resistant crops.
“A major focus of our research is sustainable agriculture,” said John Innes Centre Director Professor Dale Sanders.
“We need to help breeders and farmers generate good quality food and other agricultural products in an environmentally sustainable way. One way of doing so will be to develop crops that are resistant to pathogens and pests. Such crops will reduce the need to spray pesticides and fungicides and they will give better yields, as less will be lost to disease.”
Also published in the same edition of the journal Science are two studies of other plant pathogen genomes involving other researchers from the Norwich Research Park. One of these studies was led by Professor Sophien Kamoun, head of The Sainsbury Laboratory, which has examined how the genome of the pathogen that causes potato late blight evolves as it jumps from one host plant to another.
“New strains of the late blight pathogen cause regular new epidemics, as with the tomato strain that emerged in the US last year and is still spreading,” said Professor Kamoun.
“It is important to understand how the pathogen adapts to its plant hosts. In this latest study we have learnt more about how the pathogen evolves to attack new hosts.”
The scientists compared the genome of the late blight pathogen, Phytophthora infestans, with the genomes of sister species from Mexico, where the pathogen originated. Each pathogenic species infects different plant families. Some sections of the pathogens’ genomes have tightly packed genes, are slow to evolve and are passed through generations. Other sections are dynamic and gene-sparse. Most genes involved in infection are in the rapidly evolving, gene-sparse regions. This genome architecture appears to enable the pathogen to adapt to its new plant species after it jumps host.
Developing resistance by targeting genes from the slowly-evolving, gene-rich regions will help scientists to create more durable resistance.
“Such in-depth knowledge of the genetics of the pathogen will help us and other scientists worldwide find new ways to manage it,” said Professor Kamoun.
“We can now suggest that the most evolutionarily stable genes are better targets for genetic resistance.”
The scientists think they may have also stumbled on new findings that seem to confirm our emerging understanding of evolution. The basal genetic information carried by every cell is the sequence of genes, a protein assembly manual written in a four-letter code. On top of this, genes can carry chemical highlights, known as epigenetic marks. These marks are imprinted in response to changes in the environment. They affect the way genes are expressed and maintained in the genome. Epigenetic marks may therefore have an impact on how the genome evolves.
The scientists were surprised to find, in the dynamic region of the genome of the blight pathogen, a concentration of genes known to modulate the epigenetic imprinting pattern. These genes may play a role in promoting the rapid evolution of restricted areas of the genome and may have contributed to the pathogen genome adaptation to their host plants.
“The discovery of rapidly-evolving epigenetic genes in particular regions of the genome will enable us to hypothesise on how genome evolution is regulated,” said co-lead author Dr Sylvain Raffaele from The Sainsbury Laboratory.
“It will be exciting to build on our discovery to explore the role of epigenetics in the evolution of pathogens.”
Published in the same edition of the journal Science are two studies focusing on the parasite that causes downy mildew, which, like the potato late blight pathogen, is a kind of water mold or oomycete. The oomycetes are fungal-like organisms that have evolved from marine algae. Downy mildew causes yellow patches and fuzzy white mould on the leaves of many crops including crucifers, maize, grapes and lettuce. Powdery mildew is a fungal disease of barley that is most damaging in cool, wet climates.
The genomes of the parasites have been sequenced in separate research collaborations, one involving John Innes Centre scientists and the other The Sainsbury Laboratory. The genomes were compared with those of closely related species.
Analysis revealed that the parasites have discarded many genes. They have become specialised to live solely on their plant host and have dispensed with the genes that would be needed to survive elsewhere. Instead they have focussed on genes that help them stealthily take control of host cells. The genome sequences reveal large numbers of effector proteins, the molecules that invade plant cells to suppress plant immunity.
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Contacts:
JIC/TSL Press Office
Zoe Dunford, Tel: 01603 255111, email: zoe.dunford@jic.ac.uk
Andrew Chapple, Tel: 01603 251490, email: andrew.chapple@jic.ac.uk
Notes to Editors
Paper references:
Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage, Raffaele et al., published in Science on 10th December 2010 doi: 10.1126/science.1193070 [This project was funded by the Gatsby Charitable Foundation, a Marie Curie Intra-European Fellowship, the U.S. Department of Agriculture, a National Science Foundation grant, and the research funding programme LOEWE of the Ministry of Research, Science and the Arts of Hesse (Germany).]
Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora Arabidopsidis Genome, published in Science on 10th December 2010 doi: 10.1126/science.1195203 This project was supported by the U.S. NSF and the U.S.Department of Agriculture National Institute of Food and Agriculture, the BBSRC, the EPSRC, and The Gatsby Charitable Foundation
Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Functional Tradeoffs in Parasitism, Spanu et al., published in Science on 10th December 2010 doi: 10.1126/science.1194573 [This project was supported by the BBSRC, INRA, the BioExploit European Union Framework 6 project, Deutsche Forschungsgemeinschaft, the Leverhulme Trust, and the Max Planck Society.]
About the Sainsbury Laboratory
The Sainsbury Laboratory (TSL) is based on Norwich Research Park and is a world-leading research centre focusing on making fundamental discoveries about plants and how they interact with microbes. TSL is evolving its scientific mission so that it not only provides fundamental biological insights into plant-pathogen interactions, but also delivers novel, genomics-based, solutions which will significantly reduce losses from major diseases of food crops, especially in developing countries. www.tsl.ac.uk
About the John Innes Centre
The John Innes Centre, www.jic.ac.uk is an institute of the BBSRC and is a world-leading research centre in plant and microbial sciences. JIC is based on Norwich Research Park and carries out high quality fundamental, strategic and applied research to understand how plants and microbes work at the molecular, cellular and genetic levels. The JIC also trains scientists and students, collaborates with many other research laboratories and communicates its science to end-users and the general public.
The institutes deliver innovative, world class bioscience research and training, leading to wealth and job creation, generating high returns for the UK economy. They have strong links with business, industry and the wider community, and support policy development.
The institutes' research underpins key sectors of the UK economy such as agriculture, bioenergy, biotechnology, food and drink and pharmaceuticals. In addition, the institutes maintain unique research facilities of national importance.
Research at the John Innes Centre and the Sainsbury Laboratory is supported by the Biotechnology and Biological Sciences Research Council (BBSRC)
