Current Projects

Project links

Background
POPYOMICS project
TSEC-BIOSYS project
UKERC
Southampton Biomass Project
BEGIN project
POPGENICS project
EVOLTREE
Publications
Contact

Background

Increasing atmospheric carbon dioxide and depleted reserves of fossil fuels are encouraging the increased use of carbon neutral renewable fuels. The UK has a policy to increase renewable fuels from 3% to 20% by the year 2020 which is in keeping with the Kyoto commitment to reduce the 1990 CO₂ emission by 22 %. Biomass crops such as willow, poplar and the grass Miscanthus, can be used as carbon neutral, renewable fuel.

One of the strongest contenders for a potential biomass crop is Populus , and in previous experiments it has been shown that there is a correlation between leaf area and biomass in this genus. This result has prompted further investigations into understanding the genetic mechanisms controlling leaf development as well as the effects of [CO₂ ] on Populus.

The topic of leaf development has been of long- term interest to our laboratory and to date we have conducted a number of experiments in different Populus species, which are outlined below.

Large-scale changes in the agricultural landscape in the UK may be envisaged if specialist bioenergy crops are widely planted. We have become involved in work as part of the UKERC and TSEC projects that will be considering the likely environmental impacts that may arise from the large-scale planting of these crops, particularly the effects on biodiversity.

This is a European funded project involving nine European partners, initiated in November 2002.

The over-arching aim of POPYOMICS is to use the latest techniques in molecular genetic mapping, genomics and the physical sequence of poplar, as available, to define gene that determine yield and disease resistance in Populus with the aim of improving this species for growth across Europe as a bioenergy and timber crop.

The University of Southampton involvement

Workpackage 1: Genetic material and development of a European Experimental Network for poplar molecular genetics and genomics.

Four poplar mapping pedigrees were planted at three contrasting European sites in April 2003. Sites have been maintained with irrigation and pest control.

Workpackage 2: Physiological traiting For Yield

Stem, leaf and phonological traits have been measured over three growing seasons.

Work at Southampton has focussed on POP1 ( P. trichocarpa x P. deltoides F 2 pedigree) at the three sites. Biomass (ODT ha -1 yr -1 ) has been calculated for each genotype of the mapping pedigree at each site. Measures of genotype stability across sites have been calculated using Wricke's ecovalence values and additive main effects and multiplicative interaction (AMMI) model.

The average height performance of each genotype across sites plotted against the first component of the AMMI model. Sites are plotted on graph showing that the UK and French site were similar, but differed to the Italian site.

Workpackage 3: Disease resistance traits .

Rust assessments have been carried out in both lab and field experiments for POP1 and QTL for these traits are being mapped.

QTL mapped for rust traits, Uridia size, (US), Uridia number, (UN) and Latent period, (LP) scored for five strains of Melampsora larici-populina leaf discs of POP1.

Workpackage 4: Detection of QTL and development of a POPLAR consensus map .

Much work has been carried out to map QTL for the traits scored on POP1 across the three sites, using different mapping techniques. QTL have been mapped for stability parameters and mapping techniques used to identify QTL which show different effects across sites.

QTL mapped for stem traits showing both equal and unequal additive effects across the three sites.

Workpackage 5: A genomics approach to the identification and mapping of candidate genes

We have run two abiotic stress experiments on POP1 looking at the effects of acute drought stress and exposure to tropospheric ozone. Both of these stresses have mejor impacts on productivity of forests and crops worldwide and are likely to be of increasing importance in future years.

In the case of both stresses, we collected a range of phenotypic and physiological data and mapped QTL for these as well as running samples of the population grandparents and extreme F₂ individuals on microarrays. We have then been examining the co-location of expression candidate genes to genomic regions identified by QTL mapping.

TSEC-BIOSYS

A whole-systems approach to analyzing bioenergy demand and supply: mobilizing the long-term potential of bioenergy.

The government is committed to generating 15.4% of power from renewable sources by 2050. To achieve this and deliver large energy and greenhouse gas benefits, on-farm production must be efficient, based on high yielding crops delivering to required standard. Research on increasing the efficiency of primary production of viable energy crops will is a priority. A doubling of commercial yields of biomass crops (from 8 to 16 t/ha) over the next ten years. These higher yielding crops should ideally be protected using host resistance and biological techniques rather than conventional pesticides.

The overall objective of this interdisciplinary research is to enable the sustainable development of non-food crops as feedstocks for energy. To provide the knowledge required for development of a new competitive sector of the farming industry that can produce crops for energy whilst minimising adverse impacts on the environment and reducing chemical and energy inputs.

The project aims to protect and improve the global environment; promote sustainable, diverse and modern farming; promote sustainable management and prudent use of natural resources.

TSEC-BOSYS's objectives will be met through four strongly interdependent, interdisciplinary research themes bringing together natural and social scientists, engineers and economists. The University of Southampton is primarily involved in Theme 2

Theme 2 - Analysis of potential evolution and implications of UK biomass supply

Potential theoretical biological yields from crop systems for bioenergy production are considerably greater than those currently demonstrated on a commercial scale in the UK . Reasons for this include the use of suboptimal genotypes and/or inappropriate agronomic practices and as yet unresolved pest and disease problems.

The potential of energy crops as a source of renewable energy can only be fully realised if they are sustainable. Potential environmental impacts remain unclear and rigorous methodologies for assessing such impacts do not yet exist.

Theme 2 will focus will be on the evolution of biomass supply for bioenergy in the UK from land-use, forest and crop production perspective. It addresses opportunities, bottlenecks and limitations associated with biomass supply, and how it is influenced by social, environmental, technological and financial constraints. It will utilize experimental, modeling and analytical approaches. Future supply will be estimated using spatial and temporal models that integrate crop science, agricultural/forestry management, economic and environmental factors The emphasis is on reviewing and integrating current knowledge, filling gaps in knowledge with new research, and developing tools and recommendations for future growers, policy makers, local and central Government, investors and all those concerned with this new industry.

Work at Southampton involves:

Crop improvements - energy crop science and management

• Integrate and assess the state of current research on the underpinning science in energy crop improvement, and develop a Virtual Network for Bioenergy Crop Resources.
• Target experimental studies for ‘proof of concept' in moving from model plants to Short Rotation Coppice (SRC) crop
• Assess agronomic and silvicultural factors affecting biomass production

Productivity modeling for biomass supply from crop and forest systems

• Review current research and identify research gaps on productivity modeling for crop forest systems for bioenergy supply
• Integrate and develop models and tools for assessing the productivity of bioenergy crops in the UK for different soils and climates and in relation to future climate change scenarios . These will integrate yield, climate GIS and other UK databases

Environmental impacts of energy crop production

• Develop a synthesis of impacts of large –scale bioenergy crop production on UK biodiversity, with reference to crop, farm and UK-scale models.

Bioenergy and Environmental Sustainability

It’s a little known fact that biomass constitutes the largest source of renewable energy across Europe. On a global scale 50-60% of the energy in developing countries of Asia, and 70-90% of the energy in developing countries in Africa comes from wood or biomass, and half the world cooks with wood.

Despite this, in the UK, energy generated from biomass has remained stubbornly small, only contributing 1.5 % of electricity production and 1 % of heat.

Biomass can be defined as “Any biological mass derived from plant or animal matter. This includes material from forests, crop-derived biomass including timber crops, short rotation forestry, straw, chicken litter and waste material”.

Specialist biomass crops include fast growing grasses such a miscanthus (called elephant grass) and coppiced trees – willow and poplar. These crops may achieve phenomenal yields in ideal conditions producing in excess of 30 oven dried tonnes per hectare per year – close to the theoretical optimum.

Traditional food crops such as wheat and rape may also be used for bioenergy, producing bioethanol and biodiesel for liquid transport fuels. Biomass may also be ‘co-fired’ in traditional coal fired power stations, reducing CO₂ emissions.

It has been estimated that the UK has an available land area of 1 million hectares that could be available for non-food crops and that this could provide 8 million tonnes of energy crop.

In a recent report by the Biomass Task Force on the potential for biomass energy in the UK it was stated that:

“The potential to use biomass to reduce UK CO2 emissions is significant. But the use of biomass also contributes to other objectives notably security of energy supply and rural objectives”.

Large-scale changes in the agricultural landscape in the UK may be envisaged if specialist bioenergy crops are widely planted. UKERC we will be considering the likely environmental impacts that may arise from the large-scale planting of these crops, particularly the effects on biodiversity.

To achieve this we will be assessing and synthesising current and on-going research and participating in our own original research within the ‘Towards a sustainable energy economy’.

UKERC will act as a focus for research networking in this area both in the UK and internationally.

Aim

• to provide the U.K biomass industry with a supply of genetically improved poplar material suitable for Short Rotation Coppice (SRC).

Objectives

• to select for yield and disease resistance in S.R.C.
• to understand the physiological basis of high yield and to define a S.R.C. ideotype
• to map physiological traits for yield on a molecular genetic linkage map
• to develop the concept of Marker Assisted Selection (M.A.S.) for long term accelerated breeding
• to provide the underpinning science to develop breeding activity for Populus in the U.K
• to assess the suitability of current poplar material in the UK, Belgium, France, Italy and the U.S.
• to use the findings from the project to make a new poplar collection for the U.K.
  

Scientific Approach
Overall biomass is affected by many traits, such as stem growth rate, leaf area, stem diameter, so it is necessary to first identify which traits are important to biomass yield, or to identify an “Ideotype” which can be defined as a plant model that will produce high yield in a given environment. Most of the traits affecting biomass are controlled by interactions between the environment and a number of genes with relatively small effect. Traits that have a continuous variation and are controlled by many genes are described as quantitative, and the region of genome that contains the gene is called a quantitative trait locus (QTL). This complicates breeding programmes as it is necessary to identify the genes for the traits of interest before incorporating them into commercial poplar through selective breeding.

The traits effecting biomass can be studied by investigating the association between the quantitative trait and molecular markers of known position in the genome, i.e. QTL mapping. The associated molecular markers can then be identified and selected for in breeding programmes to produce individuals with the advantageous traits. This is known as Marker Aided Selected (MAS). Studies have shown that MAS can reduce the number of generations required in breeding programmes.

We are investigating the link between yield and QTL using a pedigree of trees imported from the USA – ‘family 331’. An experiment was planted in 2000 at a site in Hampshire and will be studied throughout the project. Details of this family may be sound at http://www.soton.ac.uk/~popyomic.

Preliminary investigations have already identified QTL linked to some yield traits.

Objectives

• to compare the locations of robust yield QTL in poplar with identified QTL in willow
• to improve the molecular genetic map of poplar
• to identify and map gene sequences as candidates for yield traits
• to detect candidate genes in the newly released poplar genome
• to confirm associations between candidate genes and QTL

Scientific Approach
A large number of genes have now been functionally characterized in model plant species like Populus. It is thought there is a high degree of synteny between the genomes of poplar and willow. A search of public databases will identify genes playing a key role in yield traits of interest in willow. New and interesting gene targets will be identified using poplar microarrays. The genetic maps of both willow and poplar will be improved by locating markers and comparing maps. Robust QTL identified in poplar will be compared with QTL in willow.

We have conducted substantial literature based searches to produce an extensive list of candidate genes thought to be involved in leaf development. We have also successfully used cDNA microarrays in leaf development experiments on a natural population of Populus nigra , which has highlighted some further possible candidate genes. We are currently also using this linkage disequilibrium study population for SNP detection in the candidate genes of interest for leaf development.

The current focus on the effects of climate change has inspired interest in alterative forms of energy such as biomass crops. One of the strongest contenders for a potential biomass crop is Populus, and in previous experiments it has been shown that there is a correlation between leaf area and biomass in this genus. This result has prompted further investigations into understanding the genetic mechanisms controlling leaf development as well as the effects of [CO₂ ] on Populus.

The topic of leaf development has been of long- term interest to our laboratory and to date we have conducted a number of experiments in different Populus species, which are outlined here.

Objective: Understanding the responses to predicted future [CO₂ ]

One of the leaf development experiments that has been completed to date has involved work at the EUROFACE site, whereby P.x euramericana was exposed to elevated CO₂ levels. This work was conducted in collaboration with UPSC ( link- and link to base- where the results are available??) and the University of Tuscia , Viterbo and the results of the study have been published.

A second experiment has involved work at the Bangor FACE site. In this experiment the parents ( P. trichocarpa and P. deltoides ) of the pedigree mapping population, Family 331, were exposed to elevated [CO₂ ]. Whilst this study was mainly based upon understanding the physiological differences in the two species under ambient and elevated [CO₂ ], we are also interested in changes occurring at the transcript level. This part of the project is still ongoing.

As well as understanding anatomical and physiological changes, we are also interested in understanding the underlying genetic basis of leaf development, using techniques including cDNA microarrays and real-time RT-PCR. We are currently using such transcriptomic techniques in combination with proteomic studies to understand the changes that occur in the leaf profiles of Family 331, in response to elevated CO₂ levels.

EVOLTREE

(2006-2010) This Network of Excellence will kick-off in January 2006, EVOLTREE – The Evolution of Trees as Drivers of Terrestrial biodiversity. This is a new project with 25 partners from 15 countries. We aim to overcome fragmentation in ecosystem genomics researched linked to understanding biodiversity in past present and future climates. We will restructure European research in this area, spread a high level of excellence and improve training and mobility – more In January 2006. Southampton is a full partner in this project and member of the Network executive Committee.

Publications

Presentations at Scientific Meetings

G Taylor et al. POPYOMICS: a project linking physiology, molecular genetics and genomics. Presented at the Plant, Animal & Microbe Genome Conference San Diego, California USA 12-16th Jan 2002

G Taylor, R Ferris, KM Robinson & AM Rae. QTL for leaf cell and stomatal traits in elevated CO₂ in Populus. Can we move to candidate genes? Poster presented at the Society of Experimental Biology Annual General Meeting 8-12th April 2002.

AM Rae, KM Robison & G. Taylor. The Ideotype for short rotation coppice poplar: QTL mapping in poplar for short rotation coppice. Paper presented at the third International Poplar Symposium in Uppsala 26-30th Aug 2002.

G Taylor, W Boerjan, M Villar, R Ceulemans, M Steenackers, G Scarascia-Mugnozza, F Martin, S Jansson, M Morgante, P Gustaffson. POPYOMICS: A project linking physiology, molecular genetics and genomics in Populus to understand and improve yield and quality for biomass and timber poduction across Europe. Poster presented at the third International Poplar Symposium in Uppsala 26-30th Aug 2002.

G Taylor. Global gene expression of a poplar forest following lon-term adaptation to future CO2 concentration. Plant and Animal Genome XI San Diego USA 11-15 January 2003.

AM Rae, MM Sewell, KM Robinson & G Taylor. Energy from trees? QTL discovery in biomass poplar grown in short rotation. Paper presented at the Societ of Experimental Biology Annual General Meeting, Southampton UK, 31 March- 4 April 2003.

AM Rae, MM Sewell, KM Robinson & G Taylor. QTL discovery in biomass poplar grown in short rotation Poster presented at Tree Biotechnology 2 Conference, Umea, Sweden 7- 12 June 2003.

G Taylor. Research support for developing short rotation coppice (SRC) poplar. Conference on Renewable Industrial Materials and Bioenergy, Warwick, UK. 16- 17 June 2003.

AM Rae & G taylor. Mapping QTL. Presentation at Popyomics QTL Mapping Meeting , Udine, Italy. 11- 12 August 2003

Publications

G Taylor, KP Beckett, SM Bunn, KM Robinson & AM Rae (2001). Identifying QTL for yield in UK biomass poplar. Aspects of Applied Biology. 65 173-182.

G Taylor. Poplar: Arabidopsis for Forest Science. Do we need a model tree? Annals of Botany. In press.

R Ferris, L Long, SM Bunn, HD Bradshaw, AM Rae & G Taylor (2002). Leaf stomatal density and index: the identification of putative QTL in relation to elevated CO₂ in poplar. Tree Physiology. 22 633-640.

G Taylor, PJ Tricker, FZ Zhang, VJ Aloston, E Kuzminsky (2002). Spatial and temporal effects of free air CO₂ enrichment (POPFACE) on leaf growth, cell expansion and production in a closed canopy of Populus. Plant Physiology (In Press)

S Wulschleger, S Jansson & G Taylor (2002). Genomics and forest biology – Populus emerges as the perennial favorite. The Plant Cell (In Press)

AM Rae, KM Robinson, NR Street & G Taylor (2004). Morphological and Physiological Traits Influencing Biomass Productivity in Short Rotation Coppice Poplar. Canadian Journalk of Forest Research. In press.

SM Bunn, AM Rae, CS Herbert & G Taylor. Leaf-level productivity traits in Populus grown in short rotation coppice for biomass energy. Submitted to Forestry.

Contact

Gail Taylor
University of Southampton
School of Biological Sciences
Bassett Crescent East
Southampton
SO16 7PX

g.taylor@soton.ac.uk
tel:0044(0)2380592335
fax: 0044(0)2380594269
cell: 0044(0)7885031007