New MutChromSeq technique makes valuable genes easier to find

Identifying the gene for an interesting trait that might help you breed better crops isn't always easy - especially if you're working with wheat or barley. But scientists at the John Innes Centre in Norwich have applied an innovative technique to the wheat and barley genomes that makes it easier to pinpoint specific genes that might be used in crop improvement programmes.

Plant breeders are on a mission to develop new and improved crop varieties that can better cope with the effects of climate change, new pests and diseases, and which can produce higher yields to feed a growing human population. To do this, it is useful to know exactly where to find the genes that are responsible for advantageous traits: disease resistance genes, for example, or genes that help plants to withstand drought.

But locating the gene for a particular plant trait can be like trying to find a needle in a haystack - it's a small, specific sequence of DNA mixed up in a jumble of other genes, regulatory sequences and non-coding DNA. For some plants, like the model plant Arabidopsis, or rice, the genomes are like small 'haybales', so the gene 'needles' are somewhat easier to find - but for wheat and barley, two of the most important cereal crops across the globe, the genomes are so large it's like searching a whole barn full of haystacks.

Working with colleagues in Switzerland and the Czech Republic, Dr Brande Wulff and his team from the John Innes Centre have succeeded in applying an innovative technique - MutChromSeq - to the wheat and barley genomes, which reduces the complexity of the search for a gene. It works by eliminating parts of the genome where we know the gene will definitely not be found.

So how does MutChromSeq work?

"It is based on a known technique called chromosome flow sorting, in which we can separate chromosomes one from the other by tagging them with fluorescent markers," explained Dr Wulff. "Take the bread wheat genome, for example: this has 21 chromosomes, so with flow sorting, we can separate Chromosome 1 from Chromosome 2, and from Chromosome 3, and so on. If we know that a particular gene is located on, say, Chromosome 21, but we don't know precisely where, then we can filter out Chromosomes 1-20 to narrow down the search. It's much quicker, easier and cheaper to sequence just one chromosome than all 21!"

In MutChromSeq, chromosome flow sorting is combined with classical mutagenesis. Seeds from a plant with the interesting trait are subjected to a chemical that disrupts their DNA, and mutants that have lost the trait are identified by screening. Then, by running MutChromSeq analysis on these mutant plants, the sequence of the mutated chromosomes can be compared with that of the unmutated chromosome.

Dr Wulff said: "By looking for the differences in sequence between the mutated and wild-type chromosomes, we can identify genes without knowing anything about their structure beforehand. So long as we already know which chromosome a particular gene is on, this technique is going to make it much easier to clone any wheat or barley gene of interest, which is great news for researchers!"

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This research was funded by the JIC Innovation Fund, the Biotechnology and Biological Sciences Research Council, Swiss National Science Foundation grants, the Czech Science Foundation, the Czech Republic National Program of Sustainability and the Plant Fellows Programme.

Notes to editors

1. The paper "Rapid gene isolation in barley and wheat by mutant chromosome sequencing" will be published in Genome Biology on Monday 31 October. Advance copies can be accessed here: http://bit.ly/2efmsRF

2. Images to accompany this press release can be downloaded from: http://bit.ly/2eflW6k

3. If you have any questions or would like to interview Dr Wulff, please contact:
Geraldine Platten
Head of External Relations, The John Innes Centre
E: Geraldine.platten@jic.ac.uk

4. About the 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 £30.1 million from the BBSRC.

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

5. About the BBSRC

The Biotechnology and Biological Sciences Research Council (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 over £473M in world-class bioscience 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.

For more information about BBSRC, our science and our impact see: http://www.bbsrc.ac.uk

For more information about BBSRC strategically funded institutes see: http://www.bbsrc.ac.uk/institutes

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