5th UK Cereal Genetics & Genomics Workshop

Rothamsted Research, Harpenden, 16th-18th April 2008

Programme and Presentations:

Wednesday 16th April

Session 1: Genomics

Chair: Kim Hammond Kosack (RRes) / Simon Griffiths (JIC)

  • Mike Bevan (JIC) - Progress in Brachypodium distachyon genomics Presentation - Abstract
  • Etienne Paux (INRA) - Exploiting the first integrative map of a hexaploid wheat chromosome - Abstract
  • Graham Moore (JIC) - A story of the application of "ics", "ologies" and "omics" to wheat - Presentation - Abstract
  • Luke Ramsay (SCRI) - Barley genomics: development and application of SNP genotyping - Presentation - Abstract
  • Chris Rawlings (RRes) - Bioinformatics and small grain cereals research - Presentation - Abstract
  • Keith Edwards (University of Bristol) - Bioinformatic and Biological Resources Initiative: a community resource for wheat functional genomics - Abstract
  • Tina Barsby (Monogram) - The future of the Small Grain Cereals Network - Presentation

Session 2: Generation and exploitation of novel variation

Chair: Andy Phillips (RRes) / Tina Barsby (Monogram)

  • Christophe Lacomme (University of Edinburgh) - Virus induced gene silencing-mediated functional characterization of genes associated to pathogen resistance and susceptibility -Abstract
  • Julie King (IGER) - The establishment and application of a forward genetic resource for the development of efficient breeding strategies in grass and the cereals - Presentation - Abstract
  • Eric Huttner (Diversity Arrays) - Whole genome profiling of small grain cereals using Diversity Arrays technology - Presentation - Abstract
  • Arnis Druka (SCRI) - Genomic dissection of barley morphology and development: the ERA-PG BARCODE project - Presentation - Abstract
  • Simon Griffiths (JIC) - Waking dormant germplasm at the John Innes Centre - - Presentation Abstract
  • Neil Hall (University of Liverpool) - Genomes for all: the promise of next generation sequencing - Abstract
  • John Bingham - Special lecture: Plant Breeding Institute, Cambridge, 1948-87 Wheat breeding legacy, a genetic pool or puddle? - Presentation - Abstract

Session 3: Resource use: Nitrogen and Water

Chair: Martin Parry (JIC) / John Foulkes (University of Nottingham)

  • William J. Davies (University of Lancaster) - Impacts of abiotic stress on growth and functioning of cereals: a whole plant perspective - Presentation - Abstract
  • Phillip White (SCRI) - Resource use efficiency in barley - Presentation - Abstract
  • Jonathan Howarth (RRes) - Dissecting processes involved in NUE using integrated 'omics approaches - Presentation - Abstract
  • John Foulkes (University of Nottingham) - The N economy of wheat grown under field conditions - Presentation - Abstract
  • Dimah Habash (RRes) - Establishing durum wheat adaptations to drought using multidisciplinary genetic and physiological approaches - Abstract

Friday 18th April

Session 4: Composition for food, feed and raw material

Chair: Peter Shewry (RRes)

  • Gilles Charmet (INRA) - Improvement of dietary fibre composition in wheat - Presentation - Abstract
  • Iain Donnison (IGER) - Forage and bioenergy quality traits in grasses - Presentation - Abstract
  • Sam Millar (CCFRA) - The genetic control of key quality traits in wheat-based bakery products - Abstract
  • Kay Denyer (JIC) - Development of barley cultivars with altered starch properties - Abstract
  • Steve McGrath (RRes) - Changes in the mineral composition of wheat grain - Abstract
  • Peter Shewry (RRes) - Improving wheat for human nutrition: the EU HEALTHGRAIN programme - Presentation - Abstract



Progress in Brachypodium distachyon genomics

Michael Bevan

John Innes Centre, Colney Lane, Norwich NR4 7UJ, UK

(T) +44 1603 450520, (F) +44 1603 450025, (E) michael.bevan@bbsrc.ac.uk

The small annual grass Brachypodium distachyon is a close relative of wheat and other members of the Pooideae subfamily. It's ~300 Mb genome is very small and contains genes that are highly similar to wheat genes and occur in a closely similar chromosomal order. It has a rapid generation time, small stature and undemanding growth requirements that enables 500 plant/m2 to be grown in simple conditions. It is self-fertile, sets abundant seeds and exhibits natural variation in many important features such as flowering time, vernalisation responses, polyploidy and seed size. These features have led to major interest in developing genomics and functional genomes resources in Brachypodium to support research in cereal and grass crops for food and fuel production. The DOE Joint Genome Laboratory is conducting whole genome shotgun sequencing and transcriptome sequencing projects that will be completed by June 2008. A check point assembly of the 4x sequence has already been distributed to users through dedicated databases (www.brachypodium.org and www.modelcrop.org). Two physical maps of BACs support the sequence assemblies, and genetic maps are currently being produced. By the end of 2008 a thoroughly annotated and well- assembled genome sequence will be available.

The availability of high quality annotated genome sequence has raised considerable interest in Brachypodium both as a comparative genomics resource for "bridging" into the largest more complex genomes of closely related wheat, barley and forage grasses, but also as an experimental system for exploring the biology of environmental adaptation, growth control and disease resistance in temperate grasses. Biological studies in Brachypodium can also form a useful "bridge" between the extensive biological research conducted in Arabidopsis and strategic research goals in wheat, barley, forage and bioenergy grass crops, especially projects focussed on grass-specific traits. Consequently there has been an increased demand from the research community for resources to conduct biological research in Brachypodium.

In my lecture I will describe recent progress in the Brachypodium genome project and illustrate how comparative genomics can aid genomics research in wheat and barley.


Exploiting the first integrative map of a hexaploid wheat chromosome

Etienne Paux

Genetics, Diversity & Ecophysiology of Cereals, INRA, 63100 Clermont-Ferrand, France

(T) +33 473 62 43 86, (F) +33 473 62 44 53, (E) etienne.paux@clermont.inra.fr

In the framework of the International Wheat Genome Sequencing Consortium that aims at constructing an integrative map of the hexaploid wheat genome, we are establishing a physical map of chromosome 3B, the largest wheat chromosome (1 Gb) following a chromosome-specific approach. Using flow cytometry, chromosome 3B of cv. Chinese Spring was isolated and used for the construction of the first chromosome-specific wheat BAC library. High Information Content Fingerprints were generated from the 67 968 BAC clones of the 3B BAC library by SNaPshot fingerprinting procedure and were assembled into contigs using FPC software. About 1000 contigs ranging from 300kb to 4 Mb and covering roughly 82% of the chromosome were obtained during the first phase. Approximately 1400 SSR, EST and ISBP markers were used to anchor these contigs to genetic maps by (i) PCR screening of plate pools of the whole library and analysis of screening results with elephant, a new software combining screening results with FPC data and (ii) PCR screening of 3D pools of the minimal tiling path (MTP) of the physical map. This MTP of 7440 clones has also been used to accelerate map-based cloning of genes located on 3B, sequence megabase-sized contigs representing different chromosomal regions, study the recombination distribution and evolution along the chromosome and identify the expressed part of the chromosome. An update of the status and exploitation of this first integrative map of a hexaploid wheat chromosome will be presented.


A story of the application of "ics", "ologies" and "omics" to wheat

Graham Moore

John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

(T) +44 1603 450000, (F) +44 1603 450045, (E) graham.moore@bbsr.ac.uk


Despite possessing multiple sets of chromosomes, hexaploid wheat and tetraploid wheat behave as diploids at meiosis. Correct pairing of homologous chromosomes is controlled by the Ph1 locus which stabilises this polyploid genome. By exploiting comparative genomics, bioinformatics, deletion and genetic mapping we have defined the Ph1 locus to a cluster of Cdk-like (CDKL2) genes containing a segment of heterochromatin. This dominant 5B locus arose by gene amplification and insertion during wheat's polyploidisation. The 5B locus suppresses the expression of the corresponding loci on the homoeologous chromosomes, 5A and 5D. The Cdk-like genes show homology to Cdk2 in mammals. Cdk2 affects chromatin remodelling for replication and the recombinational machinery. Its disruption causes non-homologous synapsis at meiosis. Cell biology of Ph1 shows that it affects replication, controls the remodelling of heterochromatin and the recombinational machinery Our working hypothesis is that CDKL2 is functional similar to Cdk2 and this explains the Ph1 phenotypes observed., all important controls for stabilising the genome. With Peter Shaw group, we have now developed cutting edge proteomic approaches for wheat so that we can assess whether the biochemical activity and interacting factors of CDK2L are similar to Cdk2 in mammals.


Barley genomics: development and application of SNP genotyping

Luke Ramsay, Jordi Comadran, William T.B. Thomas, David F. Marshall, Arnis Druka, Katrin Mackenzie*, Prasanna Bhat**, Timothy J. Close** and Robbie Waugh

SCRI, Invergowrie, Dundee, DD2 5DA, Scotland, UK

(T) +44 1382 562731, (F) +44 1382 568587, (E) Luke.Ramsay@scri.ac.uk

* Biomathematics and Statistics Scotland, SCRI, Invergowrie, Dundee, DD2 5DA, Scotland, UK

** Dept of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

The genomic resources available in barley, in particular the substantial numbers of EST sequences derived from multiple cultivars, has enabled the development of high through-put SNP genotyping capa used on a much larger scale. The generation of large data sets has necessitated the parallel development of inforbility in this crop. The SNPs used in pilot assays for mapping in bi-parental crosses and germplasm surveys have enabled the development of a robust subset of <3000 SNP markers, 1500 of which have been matics resources that can act as a conduit between the raw data and the utilisation of the information generated through graphical interpretation and efficient databasing. These technologies underpin a project entitled eAssociation Genetics of UK Elite Barley's (http://www.agoueb.org/) funded by BBSRC and RERAD under the Defra Sustainable Arable LINK scheme that includes UK barley breeders and representatives from end-user industries including growers, maltsters, brewers and distillers. This project aims to relate the variation shown by the molecular genotyping of UK adapted cultivars with their phenotypic variation. Information on the latter comes from a combination of existing data from official trials and additional phenotypic data generated de novo within the project. The SNP genotyping capability and associations found offer the breeding industry a means of deploying genome-wide marker-aided selection to accelerate breeding progress.

5th UK Cereal Genetics and Genomics Workshop

The SNP genotyping platform is integrating barley genetics and genomics data from the whole barley research community. It is being adopted by colleagues throughout the world and this will lead to an integrated world-wide survey of the genotypes of a broad range of barley germplasm. The high density gene mapping data, together with data from other sources, are facilitating the development of high density gene maps that are in turn clarifying the relationships between barley, rice and now Brachypodium. Already the data are facilitating both map based cloning projects (see presentation by Arnis Druka) and the development of the barley physical map.


Bioinformatics and small grain cereals research

Chris Rawlings(1), Jo Dicks(2), Helen Ougham(3), David Marshall(4)

1-Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK

(T) +44 1582 763133, (E) chris.rawlings@bbsrc.ac.uk

2-John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

3-IGER, Plas Gogerddan, Aberystwyth SY23 3EG, Wales, UK

4-SCRI, Invergowrie, Dundee DD2 JDA, Scotland, UK

This presentation will be an update from the informatics working group of the MONOGRAM Cross-Institute programme. The topics to be covered will include recent progress in the development of new and existing bioinformatics tools and resources that are available from the MONOGRAM participating institutions and will be relevant to SGCN members. Future plans will be described for extending support and information for SGC bioinformatics users through the MONOGRAM website using documented data analysis workflows.


Bioinformatic and biological resources initiative - A community resource for wheat functional genomics

Gary Barker, Jane Coghill and Keith J. Edwards

School of Biological Sciences, University of Bristol, Woodlands Road, Bristol BS8 1UG, UK

(T) +44 117 331 7079, (F) +44 117 3317985, (E) edwards@bristol.ac.uk

In February of this year the BBSRC's Tools and Resources BBR Committee funded the five year project "A community resource for wheat functional genomics" The stated objectives of this project are to:

1. Engage with the UK wheat community to locate further resources and build tools to search for these via the SGCN web site portal. Actively promote awareness of the SGCN web site and its use as a portal to wheat resources for future projects and new datasets

2. Redevelop the existing SGCN web site to make it fit for purpose as a portal to all the UK's wheat data and resources.

3. Update the analysis tools, currently within cerealsdb, to incorporate all array-based technologies such as Agilent and Affymetrix GeneChip data.

4. Add genotyping data and analysis tools, including those for the padlock probe technology to the portal facilities.

5. Publicise the available knockout mutants.

6. Update the digital differential display tool to incorporate libraries other than those generated by the Bristol IGF program (where external library provenance can be guaranteed) and replace the existing simple statistics with pre-cached randomisation tests.

7. In collaboration with Rothamsted, explore ways of linking wheat to Arabidopsis genomics data where homology exists between the two taxa and develop a wheat ENSEMBL database.

8. Expand the facilities currently within wheatbp.net to include more farmer, breeder and end user relevant data.

9. Provide training (practical and bioinformatics) to academic and industrial personnel in the use of technologies developed by the Bristol group.

Hence the purpose of my talk at this year's SGCN meeting will be to initiate this process and to find out from you the community, what in this initial period, we should focus our efforts on.



Virus induced gene silencing-mediated functional characterization of genes associated to pathogen resistance and susceptibility

Christophe Lacomme

Institute of Molecular Plant Sciences, University of Edinburgh, South Bridge, Edinburgh EH8 9YL, Scotland, UK. (T) +44 131 6513324, (F) +44 131 6507256, (E) c.lacomme@ed.ac.uk

RNA silencing is conserved in a broad range of eukaryotes and is referred to as RNA interference in animals and posttranscriptional gene silencing (PTGS) in plants. In plants, PTGS acts as an antiviral system; a successful virus infection requires suppression or evasion of the induced silencing response. Small interfering RNAs (siRNAs) accumulate in plants infected with positive-strand RNA viruses and provide specificity to this RNA-mediated defence mechanism against virus infection. These properties offer the possibility to use plant viruses as a functional genomic platform to elucidate plant gene function through gene silencing. We developed a Barley stripe mosaic virus (BSMV) viral induced gene silencing (VIGS) vector for the functional characterization of barley genes potentially involved in resistance (Mla-mediated) and susceptibility to the fungal pathogen Blumeria graminis f.sp. hordei (Bgh, barley powdery mildew). Such approach successfully demonstrated that Rar1 (small zinc-binding protein with two highly similar domains CHORD-I and .II), Sgt1 (associates with Skp1-Cullin-Fbox type E3 ubiquitin ligase complexes) and as well cytosolic heat shock protein 90 (HSP90, Takahashi et al., 2003) are required for Mla-mediated mildew resistance in barley. The functional characterisation of genes associated to pathogen resistance and susceptibility in cereals will be presented.


The establishment and application of a forward genetic resource for the development of efficient breeding strategies in grass and the cereals

Julie King, Ian Armstead, John Harper, Caron James, Luned Roberts, Ann Thomas, Dagmara Gasior, Kirsten Skot, Rhys Kelly and Ian King

Crop Genomics & Biomathematics Programme, University of Aberystwyth, Aberystwyth SY23 2AX, Wales, UK

(T) +44 1970 823000, (E) juk@aber.ac.uk

Publication of the rice genome sequence has allowed an in depth analysis of genome organisation in a model monocot plant species. Comparative analysis of the rice genome with other monocot plant species has demonstrated that gene order in different monocot species has to a significant degree been maintained during evolution. SNPs derived from coding sequence from every BAC from the rice genome are being generated. The physical and genetic location of each of these SNPs will be determined via the Lolium/Festuca introgession maps. Some of the SNPs developed will be from rice sequences previously used to generate primers that have been genetically mapped in barley. Cross species markers being developed at JIC will also be introgression mapped.

Thus this work will provide a genome wide comparative analysis of gene order and distribution in rice, Lolium, wheat and barley. It will also allow grass to talk to other monocot species providing the mechanism for the amalgamation of data on the genetic control of target traits across the monocots.

We have also demonstrated that a substantial component of the coding sequences in monocots is localised proximally in regions of very low recombination frequencies. The implication of these findings is that during domestication of monocot plants, selection has concentrated on genes located in the terminal regions of chromosomes within areas of high recombination frequency. Thus a large proportion of the genetic variation available for selection of superior plant genotypes has not been exploited.


Genomes for all: the promise of next generation sequencing

Neil Hall

School of Biological Sciences, University of Liverpool, Liverpool L69 3BX, UK

(T) +44 151 795 4516, (E) n.hall@liverpool.ac.uk

Until recently, large scale genome sequencing has been the preserve of just a few centres worldwide that have large dedicated facilities. Now, a clutch of new technologies has democratised genome sequencing, enabling small labs to generate giggabases of data from a single instrument in just a few days. These technologies have suddenly made the prospect of full genome sequencing a realistic possibility for a large number of non-model species. Also, high throughput cDNA sequencing of millions of transcripts can be carried out to give highly sensitive digital transcriptomic data that can out-perform microarrays.

The University of Liverpool Advanced Genomic Facility (AGF) has recently established a sequencing service that employs 454 pyrosequencing. We are using this platform to sequence non-model genomes de novo as well as undertake cDNA sequencing and we have recently been funded to undertake an in-depth transcriptomic analysis of the circadian regulation of CAM metabolism in the non-sequenced plant Kalanchoe fedtschenkoi. Here I will highlight the relevance of this technology to the small grain community and outline recent expansion in the technology base at the AGF.


Genomic dissection of barley morphology and development: the ERA-PG BARCODE project

Arnis Druka (1), David Harrap(2) and Robbie Waugh(1)

1 - Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK

(T) +44 1382 562731, (F) +44 1382 568587 (E) arnis.druka@scri.ac.uk, robbie.waugh@scri.ac.uk

2 -KWS UK Ltd, Thriplow, Royston, Hertfordshire, UK

(T) +44 1763 207300, (F) +44 1763 207310, (E) david.harrap@kws-uk.com

The Bowman series of nearly isogenic lines (NILs) developed by Prof. J. Franckowiak contain almost all of the classically described morphological mutations in barley. The unique feature of the collection is that the original mutated donor plants have all been backcrossed into a single recurrent parent, the cultivar Bowman (generally to > BC4F3). We applied a 1536-plex SNP genotyping platform developed as part of a transatlantic collaboration (BBSRC / RERAD funded AGOUEB and USDA funded Barley CAP projects) to characterise the introgressed segments containing the mutated alleles in about 1000 of the Bowman NILs. In parallel, to facilitate rapid forward genetics-based gene isolation, we generated high density barley genetic linkage map by integrating recently developed eQTL mapping data in the barley SNP-based genetic linkage map. The SNP map was constructed by genotyping three different bi-parental DH populations with 4600 SNP markers. The integrated barley map was then anchored to the rice genome sequence. We have also developed about 200 F2 populations representing 40 different genes and alleles from the phenotypic classes such as awn development, grain size, spikelet density and the lateral spikelet development. We will present an update of the strategy and our initial results.


Waking dormant germplasm at the John Innes Centre

Simon Griffiths

John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

(T) +44 1603 450611, (F) +44 1603 450045, (E) simon.griffiths@bbsrc.ac.uk

In recent years plant genomics has moved very quickly. Examples of this progress include:

. The availability of sequenced genomes for rice and Brachypodium.

. Low cost parallel genotyping platforms.

. The emerging physical maps of wheat and barley.

In this presentation I will describe how these new resources allow us to revisit historical wheat germplasm at the John Innes Centre to answer questions that were left hanging when classical genetic approaches had been exhausted. This includes the use of precise genetic stocks, segregating populations, near isogenic lines, mutant populations, and landrace collections.


Whole genome profiling of small grain cereals using Diversity Arrays Technology

Eric Huttner

Triticarte and Diversity Arrays Technology, Yarralumla, ACT 2600, Australia

(T) +61 262 818 514, (F) +61 262 818 533, (E) e.huttner@DiversityArrays.com

Marker-assisted selection has been successful at improving plant breeding efficiency for genetically simple traits, using traditionally monoplex or low multiplex assays. There is now an increasing need for high-density genome profiles. They provide breeders with a tool for dealing with complex multigenic traits, or to select for multiple traits simultaneously. At the same time, increasing the scope of genetic diversity available to the breeders is necessary in many species to ensure continuous genetic progress. High density genome profiles are critical tools for breeding strategies relying on an expanded germplasm base.

For many crops, only limited molecular information has been produced and the resources available for developing molecular markers are limited by the low margin of most agricultural activities. Diversity Arrays Technology (DArT) whole genome profiles can be developed rapidly, at low cost, without sequence information. Triticarte now provides DArT whole-genome profiles for wheat and barley. Data production and utilisation of these profiles will be presented. I will also describe DArT arrays for most of the other small grain cereals. These arrays have been developed by Diversity Arrays Technology Pty Limited and are becoming available for genotyping services during the year 2008.

Plant Breeding Institute, Cambridge, 1948-87


Wheat breeding legacy, a genetic pool or puddle?

John Bingham

Hereward Barn, Mattishall Burgh, Dereham, Norfolk, NR20 3QZ, UK

(T) +44 1362 858354, (E) johnbingham@btinternet.com

The Institute, founded in 1912, moved from the University to Trumpington in 1955. In 1956 Little Joss, released 1910, Yeoman 1916, Squarehead's Master 13/4 1930, and Holdfast 1936, were still on the NIAB Recommended List but the market was dominated by the French variety Cappelle-Desprez.

The physiology department was not established until 1971, so for some years breeders undertook their own investigations, leading in 1969 to a physiological model for yield which has withstood the operational test of time. Parental genotypes were widely sourced, mainly from continental Europe, Mexico and Chile, but, apart from Holdfast and Hybrid 46, none from the UK. Thus there was a large element of adaptation to climate which gave yield increases much greater then expected.

Selection for bread-making quality in general met objectives set by the industry, with advice from the Chorleywood Flour Milling and Baking Research Association, development of the SDS sedimentation test and the use of HMW glutenin subunits for selection. However, stacking of such genes gave doughs which were too tough and may have led to the dispersion of minor genes.

Overall, the most intransigent problem was with new physiologic races of foliar diseases, possibly because major genes masked more durable resistances. Resistance to eyespot, derived from Aegilops ventricosa, is a good example of the use of alien species despite a good many years taken to eliminate a linked yield penalty.

Privatisation in 1987 led to a network of breeding programmes across Europe, ideally suited to utilising that gene pool for yield, for which it still appears to be substantial, and adapting to moderate climate change as it develops. Marker assisted selection is becoming widely used by breeders, so public sector research is this gene pool should target the difficult problems, particularly disease resistance and grain quality.

However, the greatest public sector input should be directed to sourcing �new genes beyond the breeder's pool, both hexaploid varieties and alien species. GM should also be intensified, initially where it could be of benefit to environmental factors, like resistance to aphids, BYDV and take-all, and hopefully leading on to major physiological advances. All such projects should finish with transfer to a high yielding variety, so that the benefits can be accurately judged.



Impacts of abiotic stress on growth and functioning of cereals: a whole plant perspective

William J. Davies

Lancaster Environment Centre, University of Lancaster, Lancaster LA1 4YQ, UK

(T) 44 1524 510203, (E) w.davies@lancaster.ac.uk

Soil drying limits plant productivity through an impact on both gas exchange and plant development. This limitation will be analysed as a function of the impact of drought on the components of the Passioura identity. We will focus on the influence of chemical and hydraulic signals on harvest index, biomass/water ratio and total water use, and argue that these signals integrate the impact of climatic and edaphic influences on plant growth and functioning.

This paper addresses the regulation of growth and functioning under drought and considers prospects for sustaining yielding via manipulation of signalling cascades, with emphasis on the impact of modified fluxes of C and N and of the plant growth regulators abscisic acid (ABA) and the ethylene precursor ACC (1-aminocyclopropane-carboxylic acid). ACC signalling, which can have an influence on leaf and root growth and functioning in drying soil can be manipulated if we use genotypes with altered ACC status. In addition, rhizosphere flora can play an important role in soil to plant signalling under drought and bacteria containing the enzyme ACC deaminase and utilizing ACC as an N source, can be shown to modify the sensitivity to soil drying of root and leaf growth and functioning. Root and shoot growth of plants in drying soil as well as seed yield, seed number and seed nitrogen accumulation can be sustained as a result of the activity of particular bacteria in the rhizosphere.

The paper shows how low technology management solutions may be deployed to sustain plant growth and development by manipulating the plant's stress signalling cascades.


Resource use efficiency in barley

Philip J. White

Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK

(T) +44 1382 560043, (F) +44 1382 562426, (E) philip.white@scri.ac.uk

Several concerns have led to pressures to reduce N fertilizer inputs in crop production. The price of mineral fertilizers is increasing dramatically. The production of nitrogenous fertilizers using the Haber-Bosch process consumes considerable quantities of fossil fuels, corresponding to GHG emissions of 6.69 kg CO2 per kg N. The application of N fertilizers can result in nitrate leaching from agricultural land, which can impact water quality adversely, especially in nitrogen vulnerable zones. Strategies to improve the nitrogen use efficiency (NUE) of crops will, therefore, be important in the near future.

Several (interrelated) definitions of NUE have been proposed. The agronomic objective is to maintain (or improve) crop yield and quality, whilst reducing the amount of N fertilizer applied. This can be achieved either by improving the acquisition of fertilizer N by crops and/or by increasing their N content to yield ratio (i.e. their N utilization efficiency) when grown with reduced N supply. There is genetic variation in both the acquisition and physiological utilization of N among barley varieties. This presentation will review current and historical research to identify the genetic determinants of NUE in barley and the traits associated with the efficient use of N fertilizers in barley production.


Dissecting processes involved in NUE using integrated 'omics approaches

Jonathan Howarth, Jane Ward, Michael Beale, Peter Barraclough and Malcolm Hawkesford, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK

(T) +44 1582 763133, (F) +44 1582 763010, (E) jonathan.howarth@bbsrc.ac.uk

Wheat is the major arable crop grown in the UK with 15 million tonnes produced annually supplying 85% of the country's requirement for milling, bread making and animal feeds. Grain quality depends on nutrient availability throughout the development of the crop and particularly the internal remobilisation of nutrient resources to the seed during grain development.

We have used Rothamsted's Broadbalk resource, WGIN field experiments and a custom designed 6-variety nitrogen trial to study the genetic and metabolic processes of nutrient remobilisation during wheat grain-filling and the effects of varying fertiliser application. Leaf and grain tissues were sampled weekly during the grain-filling period. At this time, protein, carbohydrates and cell components in vegetative tissues are broken down and exported to developing grain tissues. N-deficiency adversely affects these processes and consequently grain quality. Affymetrix, metabolomics and chemical analyses were used to study gene expression in leaves and the principal metabolite pools in the leaf and grain tissues in N-deficient wheat crops. Combined studies have highlighted varietal differences in the timing and strategy of nitrogen remobilisation and identified potential global regulators of senescence and remobilisation processes.


The nitrogen economy of wheat grown under field conditions

John Foulkes(1), John Snape(2), Jacques Le Gouis(3), Pierre Martre(3), Simon Griffiths (2), Vincent Allard (3) and Mikhail Semenov (4)

1 - University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK

(T) +44 159 516024, (F) +44 159 516060, (E) john.foulkes@nottingham.ac.uk

2 - John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

3 - INRA Clermont-Ferrand UMR GDEC, Domaine de Crouel, 63039 Clermond-Ferrand, France

4 - Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK

Current work with nitrogen-use efficiency (NUE: grain yield per unit available N, from the soil and/or fertilizer) in wheat is discussed. To lower N fertilizer requirements and increase grain protein concentration stability through breeding, altering the partitioning of N between plant organs (leaf, stem and ear) could be easier than altering single metabolic processes such as photosynthesis. Current research is testing how components of the N in wheat canopies (leaf, stem and ear) respond to changes in crop N supply and whether there is identifiable genetic variation in canopy N storage in adapted wheat germplasm. Leaf laminae have been found to need levels of N per unit green area of 1-2 g m-2 for photosynthetic requirements depending on light intensity. Analysis of UK wheat canopies has shown that leaf laminae tend to match these levels, but has also found substantial additional N in the stem. Decreasing the concentration of N in the stems may offer an avenue for improving crop photo-assimilation per unit canopy N hence lowering fertilizer requirements in feed varieties. Alternatively increasing the concentration of "photosynthetic" N in the leaf laminae at flowering may be a mechanism to achieve high grain protein content at high yields in bread-making wheats. Current BBSRC-INRA funded research is quantifying the genetic variation in (1) N storage capacity of stem and leaves, affecting rate of leaf senescence during grain filling, and (2) the rate and the amount of N re-translocated to the grains and their correlations with NUE in adapted UK and French varieties. This analysis will help us to understand the synergies and trade-offs between traits and the likely G x E, hence to jointly optimise traits in new N-efficient plant types. The objectives are to provide breeders with selection tools to lower fertilizer N requirements below current recommendations whilst conserving yield and/or end-use quality. Current work is underway which identifies target genes for such improvement.


Establishing durum wheat adaptations to drought using multidisciplinary genetic and physiological approaches

Dimah Habash

Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK

(T) +44 1582 763133, (F) +44 1582 763010, (E) dimah.habash@bbsrc.ac.uk

Durum wheat is one of the most widely cultivated crops in the Mediterranean basin. It is mainly grown under rain-fed conditions characterised by drought and thus water is a major determinant of growth and final yield. Molecular genetics and genomic tools offer the breeders and the scientific community new opportunities to identify allelic variation, study candidate genes and select loci defining responses and yield adaptation to drought.

The EUFVI TRITIMED project http://www.rothamsted.bbsrc.ac.uk/cpi/mers/dh.html integrates quantitative genetics, crop physiology, transcriptome and biochemical network studies to identify loci controlling wheat responses and growth under drought. A mapping population of durum wheat from two breeding lines, Lahn (high yield potential) x Cham1 (drought adaptation) was studied in different field environments in Syria, Tunisia, Morocco, Spain and Italy. Quantitative trait loci for yield, yield components, plant development, photosynthetic and physiological traits are established from over 30 field trials. GxE interactions will be explored to screen for loci particular to each environment and to identify ideotypes. Individuals showing stability of yield under drought were selected for transcriptome studies under controlled environment and field conditions. Pathway and network analysis of global gene expression using ONDEX is uncovering metabolic pathways involved in early and late responses to water stress in top performing germplasm.

The project ultimately aims to deliver new molecular markers to enable marker assisted breeding for optimal plant response and yield stability under drought in wheat.



Improving the content and composition of dietary fibre in wheat

Gilles Charmet

INRA-UBP, F63100 Clermont-Ferrand, France

(T) +33 4 73 62 43 09, (F) +33 4 73 62 44 53, (E) gilles.charmet@clermont.inra.fr

The HEALTHGRAIN programme, module 2 is aimed at estimating genetic variation in wheat collection and developing breeding tools for variety improvement. Content and composition in dietary fibre were measured in the HG core wheat collection, made of 150 lines of worldwide origin (most from Europe). A wide range of variation was found, and multi-site trials are being carried out to estimate GxE interactions and heritability. From literature, it is known that arabinoxylan content and induced viscosity are highly heritable. This was verified by studying a recombinant doubled haploid population in several environments. A molecular map build with SSR and DArTs markers enabled us to identify a new major QTL on chromosome 6B (r2#50%)

While this major QTL is being fine mapped using a larger population, a candidate gene approach has been used by sequencing genes coding for key enzymes of the AX metabolism in the HG collection. In the 34 genes studies so far, we have found 81 SNP in 15 genes, out of which six were significantly associated with either AX content, A/X ratio or xylanase activity. Specific markers tagging the best alleles are thus available for use in breeding programmes. Gene identification for the major QTL may hopefully be achieved in 2008.


Forage and bioenergy quality traits in grasses

Iain Donnison

Institute of Grassland & Environmental Research, Plas Gogerddan, Aberystwyth SY23 3EB, Wales, UK

(T) +44 1970 823092, (F) +44 1970 823242, (E) iain.donnison@bbsrc.ac.uk

Biomass from forage and energy grasses can provide a renewable source of meat, milk, and wool, or power, heat, transport fuels and platform chemicals, respectively. Whilst in forage grasses some improvements have been made, the potential of energy grasses is limited because plant varieties have not yet been selected for this purpose. There are distinct challenges to determine and improve quality traits which increase ultimate energy yield but experience from forage crops can help. Energy grasses offer the potential to be utilised through either thermal or biological conversion methods with the route chosen being largely determined by the calorific value, moisture content and the ratio of soluble to structural carbohydrates. Plant chemical composition underlies these characteristics, for example whichever way grass feedstocks are converted the major determinates of energy are lignin, cell wall phenolics and the soluble and cell wall carbohydrates. These components affect the efficiency of the energy conversion process to meat, milk, wool, energy, platform chemicals and the end quality of certain liquid fuels such as pyrolysis oils. To associate phenotype to genotype for such underlying chemical composition, it is necessary to develop both DNA based molecular markers and high throughput methods for compositional analysis. The genetic resources available in forage and energy grasses are limited in comparison with several model grasses and for some traits it may be appropriate to work initially on a model and then translate this research back to the forage or bioenergy crop. However not all traits will be present in the model, and so genetic and genomic resources are and will have to be developed in the crops themselves. High throughput calibration models have also been developed using near infrared reflectance spectroscopy (NIRS) and Fourier trans-form infrared spectroscopy (FTIR) in the mid-infrared spectral range that allow accurate predictions of a number of composition traits including lignin, cellulose and hemicellulose contents in several forage and energy grasses. These calibrations have allowed a comparison of chemical composition from different grass genotypes, species and environments. Tools and genetic resources for the optimisation of biomass as forage and energy feedstocks are therefore being developed to enable association of phenotype with genotype.


The genetic control of key quality traits in wheat-based bakery products

Sam Millar (CCFRA) and John Snape (JIC)

Campden & Chorleywood Food Research Association (CCFRA), Chipping Campden, Glos, UK

(T) +44 1386 842157, (F) +44 1386 842150, (E) s.millar@campden.co.uk

Project partners: CCFRA, John Innes Centre, ADM Milling Ltd, Allied Technical Centre Ltd, Defra, Federation of Bakers, Heygates Ltd, HGCA, National Association of British & Irish Millers (nabim), Nickerson - Advanta UK Ltd, RAGT Seeds Ltd, RHM Technology - Premier Foods Group Ltd, Rothamsted Research, Smiths Flour Mills, Syngenta Seeds Ltd, University of East Anglia

The wheat supply chain in the UK has seen significant changes in the last 40 years with a move from a market dependent on imports to one where the majority of wheat for a range of uses is home-grown. During this period, improvements in varieties have been seen through enhanced understanding of the genetic control of key quality parameters such as wheat hardness and protein quality. More recent advances in plant breeding have allowed better targeting of traits of interest through the use of molecular markers. The work reported here was generated through a unique project1 in which a number of genetic links to processing quality in wheat have been established for the first time.

Three doubled haploid populations were developed and comprehensively genotyped. Each population (~100 lines) was grown for processing over two harvest years, 2005 and 2006. Each of the lines for each harvest year was milled and baked to give four products: Chorleywood Bread Process (CBP) white bread, CBP wholemeal bread, no time dough (Spiral) white bread and puff pastry. A number of objective methods for assessing key parameters of baked product quality were validated including measures of physical size, internal structure by image analysis (C-Cell), crumb texture and colour. Measures of functionality were then used to discover new quantitative trait loci (QTL) for wheat processing quality.

A total of 606 QTL across all three populations were identified. A significant proportion of the QTL were stable across both growing seasons with a number for key measures of bakery performance such as crumb structure being found across the three populations. These QTL represent new targets for the plant breeders involved in the consortium and are now being used to generate better and more consistent processing quality in UK wheat. This unique project has provided wheat breeders with targets for specific end-uses, will lead to growers and processors having wheat better-adapted for their needs and the cereal science community with a major advance in the understanding of genetic controls on wheat quality


Development of barley cultivars with altered starch properties

Kay Denyer (1), Alison M. Smith (1), Sylviane Comparot(1), Thomas Howard (1), Wayne Powell(2), Andy Greenland(2) and Fiona Leigh(2)

1 - John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK

(T) +44 1603 450000, (F) +44 1603 450045, (E) kay.denyer@bbsrc.ac.uk

2 - National Institute of Agricultural Botany, Huntingdon Road, Cambridge CB3 0LE, UK

The properties of the starch in cereal seeds are likely to influence profoundly the baking quality of flour, the quality of malt for brewing, the efficiency of conversion to ethanol, the health-promoting properties of derived food products and the industrial value of extracted starch. Most commercial cultivars of wheat and barley have very similar starches. However, worldwide collections of barley contain lines with starches that differ radically from those of commercial cultivars in many respects, including granule size, gelatinisation temperature, paste- and gel-forming abilities and digestibility. This variation could be used to breed improved varieties of wheat and barley for various food and industrial purposes, but it is not presently being exploited. This is because most of the potentially interesting lines are unsuitable for UK agriculture and because in most cases, the genes responsible for the variation in starch properties have not yet been identified. There has been no systematic effort to evaluate functionality of the flour and starch from these lines, or to introduce these characters into UK lines that could be taken forward into breeding programmes.

We have set up a project (the Smart Carbohydrate Centre) to overcome these problems. We will collect and characterise barley and wheat lines with altered starch, and provide information on starch properties to a consortium of end users. The consortium encompasses plant breeding, farming, food, milling, brewing, distilling and bioethanol. For starches that interest members of the consortium, the relevant genes will be identified and moved into pre-breeding lines that can be bulked up under UK agricultural conditions. Samples of starch or seeds for testing will be provided to members of the consortium. We hope to reach this point in three years. Lines that look commercially interesting at this stage will be fast-tracked into commercial breeding programmes, in close association with the relevant end-users.


Changes in the mineral composition of wheat grain

Steve McGrath, Mingsheng Fan, Jackie Stroud and Fangjie Zhao

Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK

(T) +44 1582 763133, (F) +1582 469036, (E) steve.mcgrath@bbsrc.ac.uk

The project reported seeks to answer the question: is the nutrient composition of bread-making wheat (Triticum aestivum L) grain changing? We made measurements of mineral concentrations in grain using sensitive multi-element ICP-MS instrumentation on two types of samples. The first consists of survey samples representative of wheat growing areas of Britain and the second the long-term Broadbalk experiment at Rothamsted.

The national survey samples were collected in 1982, 1992 and 1998 and archived at Rothamsted. Concentrations of Se concentrations were low and of concern in terms of animal and human nutrition. The means and distributions of Se concentrations in the three sample years were similar, with mean grain concentrations of 0.025, 0.033 and 0.025mg kg-1 dry weight respectively. No long-term changes in the distribution of wheat Se concentrations were found over the 17 year period. The daily UK dietary contribution of Se from wheat-based products was estimated and the daily intake was calculated to be 6.4 ƒÊg Se, around one-tenth of the UK recommended intake values. Progress on fortification of wheat with Se will be presented.

From the Broadbalk experiment we have grain samples grown on the same field over the last 150 years and we chose treatments that have changed little over the whole period. Again, Se concentrations were low, and shown to be depressed by a) S from fertilisers and manures and b) atmospheric S inputs. However, in this time course it was also apparent that the concentrations of zinc, iron, copper and magnesium remained stable between until 1967, but since then have decreased significantly, which coincided with the introduction of semi-dwarf, high-yielding cultivars. In comparison, their concentrations in soil have either increased or remained stable. Similar decreasing trends were observed in different treatments receiving no fertilizers, inorganic fertilizers or organic manure. Multiple regression analysis showed that both increasing yield and harvest index were highly significant factors that explained the downward trend in grain mineral concentration.


Improving wheat for human nutrition: the EU HEALTHGRAIN Programme

Peter Shewry, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK

(T) 01582 763133, (F) 01582 763010, (E) peter.shewry@bbsrc.ac.uk

The HEALTHGRAIN programme is supported by the European Union as part of the 6th Framework Programme. It is a five year programme (2005-2010) with a total budget of .16m, including .10.8m from the EU. A total of 43 partners come from 15 countries and include 11 companies. In addition, over 50 companies and other organisations have joined an Industrial Platform. The project aims to improve the health of consumers by reducing the risk of diseases associated with the metabolic syndrome, including type 2 diabetes and obesity, by increasing consumption of whole grain products. Five modules cover aspects of consumer research, grain improvement and biotechnology, technology and processing, nutrition and metabolism and dissemination and technology transfer.

The grain improvement and biotechnology model aims to identify or generate novel sources of variation in bioactive components and to develop tools which can be used to select for higher levels of these components in breeding programmes. It has carried out an extensive diversity screen of over 200 cereal lines (including 150 wheats) which have been analysed for dietary fibre components, phenolics, tocols, sterols, alkylresorcinols and folates. In addition, novel variation is being generated using mutagenesis, transgenesis and introgression of genes from exotic germplasm.

Finally, a suite of high tech "omic" technologies have been developed which will be used as a basis for developing a simplified "toolkit" suitable for use in breeding programmes.