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Dissecting the genomes of crop plants to improve breeding potential

Visit The Genome Analysis Centre website Visit John Innes Centre website

1 August 2011

BBSRC-funded scientists on the Norwich Research Park, working with colleagues in China, have developed new techniques that will aid the application of genomics to breeding the improved varieties of crop needed to ensure food security in the future. By dissecting the complicated genome of oilseed rape they have been able to produce maps of the genome that are needed for predictive breeding.

Traditional breeding involves crossing two varieties and selecting the best performing among the progeny. Predictive breeding is a more advanced technique where specific parts of the genome most likely to contain beneficial genes are identified.

Genomic sequencing and the availability of genetic linkage maps can play a major part in predictive breeding efforts by linking beneficial traits to specific parts of the genome. Researchers and breeders use genetic markers to construct linkage maps, which help to identify useful genes. They are also vital to marker-assisted crop breeding, where the maps and markers can greatly accelerate the breeding in of new improved traits.

However, for key crops such as bread wheat and oilseed rape, the use of this kind of genomics-based predictive crop breeding is severely hampered due to the complicated genomes that these species possess. Many important crop plants are polyploid, possessing several sets of chromosomes. Bread wheat, for example, contains three pairs of chromosomes derived from multiple hybridisation events that occurred between two other wheat species relatively recently in its ancestry. To try to overcome this problem, a team from the John Innes Centre and The Genome Analysis Centre (TGAC), which are strategically supported by the BBSRC, combined sequence data from different sources to construct genetic linkage maps.

The team led by Professor Ian Bancroft worked on oilseed rape, which as well as being an important oil crop also plays a key role in crop rotation strategies. Its oil has industrial applications and its straw can be used for biofuel production. Like bread wheat, oilseed rape (Brassica napus) has a complicated genome, having recently been formed from related species Brassica rapa and Brassica oleracea.

The strategy adopted by the group involves integrating the available sequence data for oilseed rape with that of its ancestral progenitors, and also that of a more distantly-related species for which high-quality genome sequence data is available, in this case the model plant Arabidopsis thaliana.

Instead of trying to sequence the DNA, the team focussed on the RNA transcribed from the DNA when the genetic code is expressed. The complete set of all of this transcribed RNA is known as the transcriptome.

TGAC used the Illumina GAII platform for the study, producing a series of consistently high quality sequence datasets from expressed genes.

The team analysed the transcriptome in juvenile leaves, which gives an overview of all of the genes that are expressed in that tissue. Using the sequence variation the researchers were able to construct genetic linkage maps in oilseed rape, eventually identifying over 23,000 markers. This allowed them to align the oilseed rape genome with that of Arabidopsis thaliana and also to sequence data from oilseed rape's two progenitor species.

This method of dissecting the genome of polyploid crops is likely to be equally applicable to other important crops. Bread wheat is a prime candidate for this, using the model grass Brachypodium distachyon in the place of Arabidopsis.

"Dissecting the genome of oilseed rape like this opens up the possibility of using predictive breeding techniques that will really help with the production of improved varieties" said Prof. Bancroft.

This study was published in Nature Biotechnology and funded by the BBSRC, the Department for Environment, Food and Rural Affairs and the China National Basic Research and Development Program.

Reference: "Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing" will be published online by Nature Biotechnology at 18:00 London time/13:00 US Eastern time on 31 July. doi: 10.1038/nbt.1926.

ENDS

About the John Innes Centre

The John Innes Centre, www.jic.ac.uk, is a world-leading research centre strategically funded by the BBSRC based on Norwich Research Park www.nrp.org.uk. Its mission is to generate knowledge of plants and microbes through innovative research, to train scientists for the future, and to apply its knowledge to benefit agriculture, human health and well-being, and the environment. JIC delivers world class bioscience outcomes leading to wealth and job creation, and generating high returns for the UK economy.

About TGAC

TGAC is a centre for the application of genomics and bioinformatics to key strategic areas of biological science and a specialist in next generation sequencing. It is located on the Norwich Research Park. It was established by the Biotechnology and Biological Sciences Research Council in partnership with the East of England Development Agency, Norfolk County Council, South Norfolk Council, Norwich City Council and the Greater Norwich Development Partnership. For more information on TGAC visit www.tgac.ac.uk.

About BBSRC

BBSRC is the UK funding agency for research in the life sciences and the largest single public funder of agriculture and food-related research.

Sponsored by Government, BBSRC’s budget for 2011-12 is around £445M which it is investing in a wide range of research that makes a significant contribution to the quality of life in the UK and beyond and supports a number of important industrial stakeholders, including the agriculture, food, chemical, healthcare and pharmaceutical sectors.

BBSRC provides institute strategic research grants to the following:

  • The Babraham Institute
  • Institute for Animal Health
  • Institute of Biological, Environmental and Rural Sciences (Aberystwyth University)
  • Institute of Food Research
  • John Innes Centre
  • The Genome Analysis Centre
  • The Roslin Institute (University of Edinburgh)
  • Rothamsted Research

The Institutes conduct long-term, mission-oriented research using specialist facilities. They have strong interactions with industry, Government departments and other end-users of their research.

External contact

11 October 2005

The following stories appear in the October 2005 edition of Business, the quarterly magazine of research highlights from the Biotechnology and Biological Sciences Research Council (BBSRC).


Controlling 'superpests'
Scientists have developed a new technique that helps make pesticides more effective by removing insects’ ability to exhibit resistance. Their research will extend the effective life of current pesticides, reduce the amount that needs to be sprayed and remove the need for farmers to move to stronger and more harmful chemicals. The new technique relies on applying a chemical to block the insect’s processes that can degrade a pesticide. With the pests newly rendered helpless farmers can apply pesticide to kill them.
(Page 13)

Contact:
Dr Graham Moores, Rothamsted Research, Tel: 01582 763133 ext 2483, e-mail:graham.moores@rothamsted.ac.uk


Fruit fly studies open new avenue in cancer research
Researchers have discovered a family of amino acid transporters that are powerful growth promoters in fruit flies. When the transporters were overexpressed in a fly, its cells became hypersensitive to insulin-like molecules in the body that have a long-term role in promoting cell growth in development and cancer, and the cells grew excessively. If the equivalent genes in humans have the same effect then this discovery could lead to new drugs or even dietary advice that could block their activity and slow down the growth of tumours.
(Page 20)

Contact:
Dr Deborah Goberdhan, University of Oxford, Tel: 01865 282662, e-mail: deborah.goberdhan@anat.ox.ac.uk


Gene delivery vehicle for skeletal regeneration
UK scientists are working on new methods to regenerate cartilage and bone by delivering genes to stem cells within the body to instruct them to turn into bone cells. The new research will use tiny nanoscopic systems that cross the surface of a stem cell and then deliver the genes into that prompt the cell to turn into a bone cell. This method of gene delivery could provide significant healthcare benefits as trauma, degenerative disease and bone loss with old age all lead to patients needing orthopaedic procedures that require new bone.
(Page 26)

Contact:
Professor Richard Oreffo, University of Southampton, Tel: 023 8079 8502, e-mail: roco@soton.ac.uk


'Ending up' with antibody production
Scientists are pioneering a new technique to produce large numbers of antibodies quickly and reliably and this is being used to help the study of dangerous bacteria. The new technique harnesses the unique properties of the C-terminus of a protein to produce a large number of antibodies that will only bind to a specific protein. The antibodies can then be used to identify, count and track the proteins. Proteins are central to many areas of bioscience research as they are often the targets for vaccines, the raw materials for bioprocessing or are employed as environmental biomarkers. Production of panels of antibodies that previously took years may now be possible in just weeks.
(Page 14)

Contact:
Dr Rob Edwards, Imperial College Hammersmith Hospital, Tel: 020 8383 2055, e-mail:r.edwards@imperial.ac.uk


Building proteins on demand
A multidisciplinary team of researchers is developing new tools to direct the evolution of proteins, a move that will help the search for new anti-HIV drugs. The scientists have developed an efficient methodology for generating every possible mutation of a single protein and then assembling this into a library to identify which variations are resistant to drugs and which are not. This information can then be used to develop and validate new drugs.
(Page 9)

Contact:
Dr Cameron Neylon, University of Southampton, e-mail: d.c.neylon@soton.ac.uk


Bringing physical forces to bear
World-leading laser facilities at the Rutherford Appleton Laboratory in Oxfordshire will be harnessed for biological studies thanks to joint funding from two Research Councils. A new laser system will study the bonds between atoms by looking at the unique frequency of their vibration. The new system will be able to take measurements of these ‘vibrational fingerprints’ at a scale so small that they will by able to study how cells repair damaged DNA, how proteins fold and develop new ways of detecting cancerous and pre-cancerous cells.
(Page 6)

Contact:
Professor Tony Parker, CCLRC Rutherford Appleton Laboratory, Tel: 01235 445109, e-mail: a.w.parker@cclrc.ac.uk


‘Model gut’ moves to commercialisation
Researchers at the Institute of Food Research in Norwich are moving closer to turning ten years of research on the workings of the human gut into a computer controlled model that will enable scientists to predict the digestive processes of human gut using real food and medicines. The result will be a revolutionary research tool that will enable researchers to examine the physical, chemical and biochemical functions of the gut as a whole.
(Page 3)

Contact:
Zoe Dunford, Institute of Food Research, Tel: 01603 255111, e-mail: zoe.dunford@nbi.ac.uk

ENDS

About BBSRC

The Biotechnology and Biological Sciences Research Council (BBSRC) is the UK funding agency for research in the life sciences. Sponsored by Government, BBSRC annually invests around £380 million in a wide range of research that makes a significant contribution to the quality of life for UK citizens and supports a number of important industrial stakeholders including the agriculture, food, chemical, healthcare and pharmaceutical sectors. http://www.bbsrc.ac.uk

5 November 2009

Scientists from the John Innes Centre in Norwich, UK and the University of Freiburg in Germany have uncovered a gene in plants that is responsible for controlling the size of seeds, which could lead to ways of improving crops to help ensure food security in the future.

Increasing seed or grain size has been key in the domestication of the crops used in modern agriculture, and with a growing world population, further increasing the yield of crops is one goal of agricultural research. Michael Lenhard, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), has identified a gene in the model plant Arabidopsis that determines overall seed size, and is now investigating how this could be used to for the improvement of crops.

Publishing in the Proceedings of the National Academy of Sciences, the team from the John Innes Centre, an institute of the BBSRC, demonstrated that the gene acts locally at the base of the growing seed. It produces an as yet unidentified mobile growth signal that determines final seed size. If the gene is turned off, smaller seeds are produced, but crucially if the gene is turned on at a higher level than normal, seeds a third larger in size and weight are produced. This is the first time such a reciprocal effect on seed size has been observed, and points to the fundamental importance of this gene in plant development.

More work is now needed before this research can be applied to crop plants. One effect of increasing the seed size in the experimental plants was to decrease the total number of seeds produced, so there was no overall increase in yield. The scientists did notice an increase in the relative oil content of the larger seeds, so the effects of altering this gene in oil seed rape is currently being investigated.

Unravelling this gene’s role in determining the final seed size will also be important for other strategies for increasing yield, an example of how fundamental plant science can inform and drive efforts to ensure food security

Professor Mike Bevan, Acting Director of the John Innes Centre, said “This work shows how JIC's focus on understanding the mechanisms controlling plant growth can have immediate useful application for crop improvement.”

ENDS

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Nikolai Adamski and Michael Lenhard examining Arabidopsis (323KB)


 

Notes to editors

Reference: Local maternal control of seed size by KLUH/CYP78A5-dependent growth
Signalling, PNAS.

Funding: BBSRC David Phillips Fellowship.

About the John Innes Centre

The John Innes Centre, www.jic.ac.uk, is an independent, world-leading research centre in plant and microbial sciences with over 800 staff. 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 JIC is grant-aided by the Biotechnology and Biological Sciences Research Council.

About BBSRC

The Biotechnology and Biological Sciences Research Council (BBSRC) is the UK funding agency for research in the life sciences. Sponsored by Government, BBSRC annually invests around £450M in a wide range of research that makes a significant contribution to the quality of life for UK citizens and supports a number of important industrial stakeholders including the agriculture, food, chemical, healthcare and pharmaceutical sectors. BBSRC carries out its mission by funding internationally competitive research, providing training in the biosciences, fostering opportunities for knowledge transfer and innovation and promoting interaction with the public and other stakeholders on issues of scientific interest in universities, centres and institutes.

The Babraham Institute, Institute for Animal Health, Institute of Food Research, John Innes Centre and Rothamsted Research are Institutes of BBSRC. The Institutes conduct long-term, mission-oriented research using specialist facilities. They have strong interactions with industry, Government departments and other end-users of their research.

External contact

Andrew Chapple, John Innes Centre

tel: 01603 251490

Zoe Dunford, John Innes Centre

tel: 01603 255111