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Forming a second line of plant defense — capturing disease-resistant DNA

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Credit: Earlham Institute

RenSeq (1) is the method to sequence Resistance (R) genes that confer disease resistance in plants.

Each plant typically carries hundreds of potential R gene sequences, encoding NB-LRR proteins, identified by the presence of specific sequence motifs. R genes are often part of families of closely related sequences.

While shared sequences make it possible to capture the R-genes, it also makes it hard to tell them apart and find the exact gene that enables plants to survive attack. Longer molecules and sequences of DNA allow easier and more accurate genetic analysis to identify variation.

The NB-LRR gene family enables plants to withstand infection from a suite of diseases and form a second line of defence. After a pathogen has managed to invade a plant, it uses 'effector' molecules to weaken a plant's defences – the R gene proteins recognise these 'effector' molecules and signal to the plant to activate defence responses – killing cells around the site of infection in an attempt to stop it spreading.

This constant evolutionary arms race between plants and pathogens, whereby the organisms causing disease in plants are mutating to avoid plant defences, causes the plants to evolve through changes in their own genetic makeup. This is where a huge variety of R genes come into play that are highly similar in structure and DNA sequence.

Researchers at the Earlham Institute (EI), The Sainsbury Laboratory (TSL) and the James Hutton Institute, have found a new way to decipher these large stretches of DNA to discover and annotate pathogen resistance in plants.

Using the PacBio, which can read longer stretches of DNA in their entirety, along with the developed NB-LRR gene workflow 'RenSeq' (Resistance gene enrichment sequencing), the data not only targets R genes, but also the important regulatory regions of DNA – promoters and terminators that signal when to start making a protein and when to stop.

Dr Matt Clark, Head of Technology Development at EI and lead author of the study, said: "Wild relatives of crops contain a huge repertoire of novel genes that could be used to breed more resistant varieties that need less pesticide treatments. When it comes to identifying key genes it can be very difficult for researchers to find the exact resistance gene due to the sheer similarity of their DNA sequences.

"Typical sequencing methods use short reads eg from the Illumina HiSeq, but these are often too short to prise similar genes apart.

"RenSeq diverges from normal DNA sequencing on the PacBio by focussing the sequencing effort on a specific gene family i.e. R-genes. In this study, by optimising multiple steps in the library construction, we can identify the protein-coding sequences and the neighbouring regulatory regions; indeed in many cases we can reconstruct the entire DNA region even if it contains many similar genes which normally are too hard to tell apart. This means we can identify the exact gene that confers resistance to a certain infection, and used in breeding programmes."

Professor Jonathan Jones, Senior Scientist at TSL and co-author, said: "This improvement to the RenSeq method will greatly facilitate building reliable inventories of R genes in multiple plant species, helping us clone additional genes that could protect our crops."

Dr Ingo Hein, Principal Investigator at the James Hutton Institute and co-author, added: "R genes can control diverse plant diseases including major threats to global crop production. The ability to capture and sequence long genomic DNA fragments that contain full-length R genes enables the rapid identification of novel, functional resistance genes from wild species. These genes, if introgressed into new cultivars via breeding or alternative routes, could significantly reduce the dependency on pesticides for crop production."

The paper, "Targeted capture and sequencing of gene sized DNA molecules" is published in BioTechniques.

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Working with the researchers, EI's Platform and Pipelines Group migrated the technology for the new genome analysis technique and is available as a service from the EI's National Capability in Genomics, please contact [email protected] more details.

References

(1) Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing – Nature Biotechnology, DOI: 10.1038/nbt.3540

Notes to Editors

1) Lead researcher Dr Matt Clark is available for interview. For press queries, please contact:
Hayley London
Marcomms Officer, Earlham Institute (EI)
+44 (0)1603 450107
[email protected]

2) Accompanying images can be accessed, here: https://www.dropbox.com/sh/cffmxzj8hca1k1h/AAApIlEdvYnfK3mwBibf8C0aa?dl=0. Images show lead author of study Dr Matt Clark (left) and Michael Giolai, post-graduate student in the Clark Group, by the PacBio Sequel (next-generation sequencing platform used for study) at EI.

3) About EI

The Earlham Institute (EI) is a world-leading research institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) – £6.45M in 2015/2016 – as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities. http://www.earlham.ac.uk / @EarlhamInst

4) About TSL

The Sainsbury Laboratory (TSL) is a world-leading research centre focusing on making fundamental discoveries about plants and how they interact with microbes. TSL not only provides fundamental biological insights into plant-pathogen interactions, but is also delivering novel, genomics-based, solutions which will significantly reduce losses from major diseases of food crops, especially in developing countries. TSL is an independent charitable company and receives strategic funding from the Gatsby Charitable Foundation with the balance coming from competitive grants and contracts from a range of public and private bodies, including the European Union (EU), Biotechnology and Biological Sciences Research Council (BBSRC) and commercial and charitable organisations http://www.tsl.ac.uk.

5) About James Hutton Institute

The James Hutton Institute is a world-leading, multi-site scientific organisation encompassing a distinctive range of integrated strengths in land, crop, waters, environmental and socio-economic science. From its sites in Scotland, it undertakes research for the Scottish and UK governments, the EU and other organisations worldwide. The Institute has a staff of nearly 550 and 125 PhD students, and takes its name from the 18th-century Scottish Enlightenment scientist, James Hutton, widely regarded as the founder of geology and agronomist. http://www.hutton.ac.uk

Media Contact

Hayley London
[email protected]
01-603-450-107

http://www.earlham.ac.uk/

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