Cereals research at the John Innes Centre: From new science to new varieties
James Brown
As a major centre for research in plant science, the JIC is keen to ensure that its work is relevant to
improving food production in the UK, Europe and elsewhere. Much of JIC’s research on crop plants
is strategic in nature, with the aim of providing knowledge and resources to help the farming
industry solve current or foreseeable problems. Furthermore, an important part of our research in
fundamental science is to generate ideas for crop improvement in the longer term. In this meeting,
we have invited UK and European cereal breeders to learn about our current work on cereals and to
discuss with us how JIC’s research can be applied to improving arable farming.
In research on Current Priorities, relevant to arable farming at present, JIC is working closely with
plant breeding companies to improve the yield, grain quality and resistance to currently important
diseases of wheat varieties. We have close links with all the UK’s wheat breeding companies and
aim to strengthen our developing links with those in continental Europe.
The wide range of genetic resources and expertise at JIC will help it to address Emerging Traits,
placing the plant breeding industry in a good position to combat changes in market demands,
environmental stresses and the profile of diseases.
Fundamental research at JIC will enable crop production to underpin Future Advances in crop
production. Here, we are taking a long term view of science and technology to make further
improvements in traits which are always likely to be important or to address traits which have so far
proved intractable.
Contact:
Professor James Brown
Department of Disease and Stress Biology, John Innes Centre, Norwich, NR47UH, England
Email
Phone: 01603-450615
Gene x environmental effects on wheat yields
John Snape
Genomic tools, particularly molecular markers, are letting us dissect the genetic control of complex
traits in terms of the locations of quantitative trait loci (QTL). For the last five years or so, we have
had a programme of large scale QTL analysis of yield and yield components using recombinant
doubled haploid populations to understand the variation still segregating. Our research has focussed
predominately on the UK winter wheat gene pool. This is being combined with physiological
analysis to understand the underlying mechanisms of yield development through collaboration with
ADAS and the University of Nottingham.
A picture of the ‘yield dynamics’ of UK winter wheats is emerging, which is giving us pointers to
what allelic variation is available for further yield improvements and which traits should be focused
on for future selection.
Contact:
Professor John Snape
Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, England
Email
Phone: 01603-450608
Stem-base and ear diseases
Paul Nicholson
Eyespot is caused by two fungi (Oculimacula yallundae and Oculimacula acuformis). Two seedling
resistances are exploited in wheat. Pch1 is a potent resistance (chromosome 7D), derived from
Aegilops ventricosa and Pch2 (7A), from Cappelle-Desprez is of moderate effect. In addition, adult
plant resistance has been identified on 5A of Cappelle Desprez. We are fine-mapping both Pch1 and
Pch2 and undertaking studies to determine the genetic basis and location of the 5A resistance.
While Pch1 and Pch2 appear equally effective against both Oculimacula species, this is not true for
all resistances. We have determined that resistance in T. monococcum accessions may function
differentially against the two species.
Fusarium head (ear) blight (FHB) is caused predominantly by Fusarium graminearum. Resistance
to FHB is quantitative and generally categorised into two types: resistance to initial infection (type
1) and resistance to spread in the head (type 2). Type 2 resistance is relatively easy to detect and
potent type 2 resistance has been well characterised from sources such as Sumai 3. Type 1
resistance is potentially of greater importance but is much more difficult to assess. We have
developed approaches to specifically identify type 1 resistance and have identified a potent type 1
resistance on 4A of Triticum macha. In addition, we are using novel bioassays to identify candidate
pathways and genes involved in resistance and are testing these in crop systems.
The research on both eyespot and FHB is being done in collaboration with wheat breeding
companies, with the aim of developing germplasm and genetic markers for use in improving the
resistance of varieties to these two diseases in the UK and elsewhere in Europe.
Contact:
Dr Paul Nicholson
Department of Disease & Stress Biology, John Innes Centre, Norwich, NR4 7UH, England
Email
Phone: 01603-450616
Septoria tritici blotch
Lia Arraiano
In Europe, the need to understand and use host plant resistance to septoria tritici blotch (STB) has
assumed new urgency with the widespread development of fungicide resistance by the pathogen.
We have investigated factors that contribute to reducing STB levels among wheat cultivars in field
conditions, including resistance genes and disease escape. This has allowed the identification of
cultivars which are useful sources of isolate-non-specific resistance to STB in wheat breeding.
In an association genetic analysis of wheat cultivars and breeding lines, two known resistance genes
were associated with reduction of STB. One of these was the most important predictor of resistance
other than plant height and heading date. Other regions of the genome that may contain hitherto
unknown resistance genes were identified by association with microsatellite markers. We have also
detected cultivars which are likely to be new sources of resistance for wheat breeding programmes
in the UK and elsewhere, because their resistance to STB in the field is not explained by known
genes or escape traits.
This research is providing breeders participating in our Defra-LINK projects with knowledge about
the potential value of genes for resistance to STB and about previously unidentified sources of
resistance within the pool of wheat germplasm adapted to UK conditions. This is expected to lead to
improved selection of wheat varieties with resistance to STB and in due course, to a sustained
improvement in the resistance of European wheat varieties to STB and eventually to a reduced need
for fungicides to control this disease.
Contact:
Dr Lia Arraiano and Professor James Brown
Department of Disease & Stress Biology, John Innes Centre, Norwich, NR4 7UH, England
Email LA, Email JB
Phone: 01603-450185 (LA) and 01603-450615 (JB)
Quality traits
John Flintham
Grain quality is a major focus for JIC expertise in the production and trialling of special genetic
stocks, molecular mapping, and biometrical analyses. Most of this effort is aimed at breadmaking
quality, a complex of characters for which many genetic determinants have yet to be resolved.
Milling characteristics, predictive tests, actual performance in a range of bakery products, and
factors controlling Hagberg falling number are being investigated.
Projects will be presented as examples of multidisciplinary, collaborative strategies for combining
expertise and resources across public- and private-sector research partnerships to target specific
end-user requirements. Dissection of grain quality into component traits, genomic mapping of trait
determinants, co-location of candidate genes and transcripts, are being combined to furnish breeders
with information and materials for directed improvement of elite germplasm.
Contact:
Dr John Flintham
Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, England
Email
Phone: 01603-450505
Ramularia leaf spot
Joanne Makepeace
Until recently Ramularia collo-cygni, which causes the disease Ramularia leaf spot (RLS), was not
considered a major pathogen of barley in the UK. In 1998, however, it was reported in Scotland and
has since become a major concern to barley growers. Today this pathogen is present in many
European countries, causing yield losses of up to 35%. JIC is making use of its facilities for
research on Septoria tritici blotch of wheat, caused by a closely related fungus, to investigate this
disease.
A hypothesis to explain why this fungus has become so important was that, as with some other
hemibiotrophic pathogens, the mlo mildew resistance gene increases the susceptibility of barley
plants to RLS. However, in field trials using near-isogenic lines of spring barley, lines with mlo
lines were more resistant to RLS than those with the Mlo mildew-susceptibility gene. Hence, the
widespread use of mlo in spring barley does not in itself account for the proliferation of RLS in the
past decade.
To facilitate research on RLS, a method of inoculating seedlings in laboratory conditions was
developed. This produced typical RLS symptoms, from which the fungus could be isolated. If
plants were exposed to high light intensities before being inoculated with R. collo-cygni, disease
levels were considerably greater. The development of a seedling inoculation technique provides a
basis for research on RLS in controlled conditions. It should be useful for screening fungicides for
efficacy against R. collo-cygni. It should also be possible to use it to test barley varieties for
resistance but current data show no correlation between the severity of RLS on seedlings in
laboratory tests and on adult plants in the field. This indicates that further development of the
method is required to assess adult-plant resistance to RLS.
Contact
Professor James Brown and Mrs Joanne Makepeace
Department of Disease & Stress Biology, John Innes Centre, Norwich, NR4 7UH, England
Email JB, Email JM
Phone: 01603-450615 (JB) and 01603-450185 (JM)
WGIN populations
Simon Orford
The Defra Wheat Genetic Improvement Network (WGIN) has been formed to enable a close
working relationship between researchers, breeders and the end users of the UK wheat industry.
Since 2003, its aim has been to ensure the sustainable development of the UK wheat industry, and it
has ensured that UK wheat researchers have shared objectives in the promotion of the genetic
improvement of UK wheat.
The overall goal of the project has been to generate pre-breeding material, carrying novel traits, to
the breeders of UK grown wheat. The project also provides access to advanced breeding
technologies which will ultimately allow the targeting of improvements for new varieties.
At the JIC, populations have been developed for the wheat community’s use. The provision and
focus on the 200 line mapping population of Avalon x Cadenza has allowed an important common
reference point for the UK wheat industry.
Around 6500 EMS mutant Paragon lines have been developed to the M6 generation. DNA and seed
are available along with detailed records and photographs of interesting mutations such as height
(25 lines shorter than 50% Paragon control height and 548 lines at least 10% shorter, with 133 lines
higher than average and 5 lines higher than the tallest Paragon control), flowering variants (four
days earlier and up to 25 days later than Paragon control), ear structure (club type, laxness, tapered
spelt type and awn suppressor knockout,) seed shape, (sphaerococcum type), temperature sensitivity
(zebra leaf effect), high and low tiller number, disease responses and senescence variants. Of equal
interest, a population of gamma irradiated seed has also been developed to M3. All populations are
free of intellectual property rights and so are freely available (DNA and seed) for exploitation by all
(contact information below).
Evaluation of core collections held within the National Wheat Collection at the JIC has shown the
immense diversity of material held in the A.E.Watkins collection. Collated in the 1930s, the 800
lines from 32 countries have been scored for ear emergence (77-120 days), height (50 to 150cm)
and homeogenous nature.
Along with core objectives, the network has enabled the spin-off of satellite projects as a result of
the regular meetings between partners of the project. Updates of current and past activities are
posted to an electronic newsletter which can be subscribed to or viewed at www.wgin.org.uk
Contact and supply of material:
Dr Simon Griffiths and Mr Simon Orford
Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, England
Email SG, Email SO
Phone: 01603-450611 (SG) and 01603-450584 (SO)
Germplasm collections
Mike Ambrose
The John Innes Centre hosts a number of important small grain cereal germplasm collections
focused on wheat, barley and oats. A number of these are in the public domain and act as reference
collections. Material and information from these collections is regularly requested by breeders and
researchers. The reduction in costs and improvements in reproducibility of molecular markers has
seen a steady increase in the screening of these resources for studies of allelic diversity.
This presentation will provide an up overview of these collections, their availability and recent
developments in web searchable databases. I will show a new database application (GERMINATE)
aimed at linking the more traditional data associated with germplasm such as origin and pedigree to
link with phenotypic and marker datasets from a range of studies within the new a single database
system.
Contact:
Mr Mike Ambrose
Genetic Resources Unit, Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH,
England
Email
Phone: 01603-450630
Genetic resources
Simon Griffiths
In collaboration with European wheat breeders and producers, JIC wheat geneticists are defining the
alleles controlling variation in yield and quality traits that are widely exploited in European wheat
breeding programs. With this information we can build predictive models for optimal combinations
of known alleles and conduct searches for novel variation. The backbone of our approach is the
production of segregating populations with associated genetic maps. Genetic effects are identified
as quantiative trait loci (QTL), then the QTLs are backcrossed into uniform genetic backgrounds to
produce near isogenic lines (NILs). Specific examples of this approach will be discussed. NILs are
a key resource, allowing effects to be defined physiologically and genetically so delivering a
biological understanding of how key traits are manifested and exactly where they are so that close
flanking markers can be produced using gene based genetic markers. Ultimately markers based on
the polymorphism which changes function will emerge, as is already the case for the Rht alleles.
Our searches for novel alleles focus on the use of mutagenised populations and non-adapted
germplasm. It is worth noting that all the agronomically important allelic variation that has been
identified to date in wheat, barley, rice, and maize could have been generated in a conventional
mutagenesis program. Opportunities for targetted mutagenesis using our mutant populations of the
UK spring variety Paragon will be discussed as will a range of resources for achieving the goals
outlined above.
Contact:
Dr Simon Griffiths
Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, England
Email
Phone: 01603-450611
Photoperiod sensitivity
David Laurie
To fit crop production to the available growing conditions, farmers and breeders have selected
various flowering time variants during the domestication and development of wheat. Winter/spring
and photoperiod sensitive/insensitive differences are the best known. Several of the genes
underlying these differences have now been isolated, allowing allele specific markers to be
designed.
My work has focused on photoperiod genes, and we can now diagnose alleles on 2A, 2B and 2D.
Further alleles are likely to be identified as germplasm collections are explored. Analysing the
distribution of alleles in wheat varieties will shed light on what is needed for good adaptation to
particular regions. As well as diagnosing photoperiod and vernalization effects, accounting for the
effects of these major genes will help uncover additional more subtle QTLs that provide fine-tuning
for adaptation to specific regions.
In the talk I will outline what we know about the wheat photoperiod genes, how we think
photoperiod insensitivity is conferred, how many alleles we have found and what we can provide in
the way of diagnostic markers.
Contact:
Dr David Laurie
Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, England
Email
Phone: 01603-450610
Cereal transformation
Wendy Harwood
There is an increasing demand for cereal transformation, mainly as a tool to determine gene
function. Wheat and barley have historically been difficult to transform. Initially, the ‘gene gun’
was used to introduce genes to cereal crops but this method has now been largely replaced by
methods using the soil bacterium, Agrobacterium tumefaciens to transfer the genes of interest. This
bacterial method has a number of advantages and recently the Agrobacterium-mediated
transformation method for barley has been significantly improved at JIC so that it is now highly
efficient. This means that we can now easily set up experiments to either over-express or to silence
genes of interest. We also have the opportunity to develop new transformation-based resources that
could be used to speed up the determination of gene function in both wheat and barley. Such
resources would be useful for conventional breeding programmes as well as leading to new
possibilities for genetically modified varieties.
Cereal transformation requires specific expertise, tissue culture facilities and controlled plant
growth facilities. To make cereal transformation widely available, we have set up the BRACT
project (Biotechnology Resources for Arable Crop Transformation). BRACT can offer a
transformation service on a cost recovery basis and can also provide training and a range of other
transformation resources (www.bract.org).
Contact:
Dr Wendy Harwood
Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, England
Email
Phone: 01603-450609
Dwarfing genes
Margaret Boulton
The Rht gibberelic acid (GA) insensitive semi-dwarfing genes are key components of the genotypes
of modern wheat cultivars in the UK and world-wide. They encode mutant forms of DELLA
proteins, which, in Arabidopsis, have been shown to be important elements of the pathways that
regulate plant growth in response to multiple signals from the environment. DELLA proteins inhibit
plant growth, while GA promotes growth by destabilising them and marking them for destruction
by the cell’s protein turnover machinery. Although different Arabidopsis DELLA proteins all
function as GA signalling molecules, they are responsible for different aspects of the plant GAmodulated response to the environment.
The work I will describe is an example of ‘Model-to-Crop’ research, in which the JIC aims to
exploit fundamental discoveries about model plants such as Arabidopsis to generate ideas and
resources for breeding of crop species. We are investigating the way that modulation of the function
of DELLA proteins in cereal plants has variable effects on plant growth – and thus grain yield – in
response to environmental stresses and disease. We have been funded by the BBSRC Crop Science
Initiative to study the roles of allelic variation in Rht genes which are currently used in UK wheat
breeding and also other alleles which are not. The long-term aim is to increase the adaptability of
the UK’s wheat to changing environmental conditions and disease pressures.
Contact:
Dr Margaret Boulton
Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR47UH, England
Email
Phone: 01603-450267
Take-all
Anne Osbourn
Take-all is the most damaging root disease of wheat worldwide and is a major constraint for wheat
production in Europe and in other cereal-growing areas of the world. It represents a substantial
challenge for disease control because of the yield losses that it incurs and the constraints that it imposes
on rotational practices. In the UK, 20-50% of cereal crops are in rotational positions that put them at
risk from take-all. The disease can reduce yields of wheat by up to 4t/ha, with 1-1.5t/ha being common
on second and third wheats. Costs to the UK cereal industry are currently in the region of ~£25-50 m
per annum. Control of take-all has been confounded by lack of economically viable chemical control
agents and lack of genetic resistance and there is an urgent need for simple, economic and sustainable
methods of disease control. The identification and deployment of suitable sources of genetic resistance
would provide the most sustainable means of achieving this goal.
We have shown that preformed antimicrobial compounds (avenacins) produced by oat roots provide
broad-spectrum protection against take-all and other soil-borne diseases. We have identified the genes
for most of the steps in the biosynthetic pathway for these compounds and are now in the process of
transferring these genes, alone and in combination, into wheat to establish which steps are required for
production of defence compounds in this background. The development of wheat lines that synthesise
structural variants (different “flavours”) of antimicrobial compounds is expected to provide durable
resistance against take-all and other root-infecting pathogens.
Contact:
Professor Anne Osbourn
Department of Metabolic Biology, John Innes Centre, Norwich, NR4 7UH, England
Email
Phone: 01603-450407
Use of Ph1 in breeding
Tracie Foote
The Ph1locus is present in the genomes of all hexaploid and tetraploid wheats. Its main function is
to allow homologous chromosomes to pair, while preventing homoeologous chromosomes from
pairing & recombining. This stabilises the genomes and ensures the plant’s fertility. The downside
of Ph1 is that it also prevents wheat chromosomes from pairing with homoeologous chromosomes
of related species and genera, thereby preventing the transfer of useful traits into wheat. If Ph1 is
absent, however, related chromosomes are able to pair and recombine.
In a new project we will determine whether we can use specific drugs, such as okadaic acid, to
reproduce the effect of removing Ph1. We will examine how we can use the drugs to inhibit Ph1
(and thus override the pairing control mechanism) in one generation, with it being switched back on
in the next. This will enable pairing between wheat chromosomes and chromosomes from wild
relatives, and allow the introduction of novel variation into wheat.
Contact:
Professor Graham Moore and Miss Tracie Foote
Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, England
Email GM, Email TF
Phone: 01603-450577 (GM) and 01603-450508 (TF)