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SEERAD Programme of Agricultural, Biological and Related Research 2002-2003

THEME 2: PLANT SCIENCE

SUMMARY OF COSTS:

THEME 2: PLANT SCIENCE

All human activities on this planet depend on the ability of plants to capture the sun's energy and turn it into food, biomass and oxygen, the substrates for human and animal life. In addition, plants are the dominating features of the natural landscape, providing an environment which is valued by the public. In order to produce food and biomass from our crops most efficiently and at the same time to conserve the natural diversity of plant life, it is necessary to understand how plants function and how they interact with other organisms, including other plants.

Theme 2 describes a programme of basic and strategic plant science, which is internationally relevant. This includes work on the mandate crops (potatoes, spring barley and soft fruit), which are of particular importance to Scotland, and in addition, a programme of classical systematics research, which is undertaken on specimens collected mainly on overseas expeditions. The plant science research in Theme 2 complements and informs other parts of the SEERAD research programme, most notably the root microbiology work listed in Theme 1 (Soil, Water and Environment), and the farming systems and floristics/ecosystem studies in Theme 5 (Systems and Socio-Economics).

Plant science research in Theme 2 aims ultimately to understand processes which limit sustainable crop production in Scotland. Much of the research described is multidisciplinary, gaining added value through the combination of different skills. For example, genetic and pathological approaches are combined to identify new sources of resistance from the germplasm collections, which can be subsequently utilised for breeding improved varieties. In many cases, SEERAD-funded research is also vertically integrated, linking theoretical studies whose outputs will be of long-term value with strategic science, which in turn can be of direct relevance to Scottish farmers and growers. In some cases this integration is achieved through joint funding, for example, with the levy bodies. Conventional genetical approaches are also now being enhanced by the application of new genomics and functional genomics technologies, which use high-throughput analyses to provide detailed information on global gene expression and function. This aspect now includes the genomic sequencing of a key bacterial pathogen of potatoes, Erwinia carotovora, to obtain the complete DNA blueprint.

Theme 2 also includes botanical systematics research, undertaken by the Royal Botanic Garden, Edinburgh (RBGE), which aims to document and interpret global plant and fungal diversity. Much of this work is undertaken on specimens obtained from overseas, and focuses in particular on plant and fungal species found in the Far East (China and Bhutan), the Arabian Peninsula and parts of South America (Brazil and Peru). SEERAD sponsors the RBGE under The National Heritage (Scotland) Act 1985.

This theme is organised in four sections, which range from the study of the genetic material itself (2.1) through studies looking at the function of plants (2.2) and natural plant products (2.3) to the investigation of pests and pathogens and their interaction with plants (2.4).

The plant science research programme is relevant to several key end-use sectors. Research on the control of pests and diseases will ultimately deliver improved, sustainable methods of pest and disease control, and is highly relevant to both sustainable agriculture and environmental end-users. Much of this research underpins the needs of seed potato growers and the policy requirements arising from the operation of the Scottish Seed Potato Classification and Certification Schemes. For example, the plant pathology research focuses in particular on pests and pathogens affecting potato production ( Phytophthora, Spongospora, Erwinia and potato cyst nematode (PCN)). Research on germplasm collections, which helps to preserve and utilise biodiversity, is relevant to environmental interests. Research into genetics and breeding is relevant to sustainable agriculture and environment end-users. In addition, some of the newer molecular, genomic and biotechnological approaches are relevant to both bioindustry and to sustainable agriculture. The Plant Science domain also contributes to nutrition and human health interests and to the food end use, with research on antioxidants, free radicals and functional foods.

2.1 Systematics and Genetics

The SEERAD-funded Systematics and Genetics programme is one of underpinning research aimed at understanding genetic relationships and evolutionary processes in plants and fungi. The development and exploitation of the botanical germplasm collections is central to much of the research activity covered in this theme. On the botanical side, some of the systematics research at the Royal Botanic Garden Edinburgh forms part of Britain's obligation to develop and fulfil international policy requirements (e.g. the Convention on Biological Diversity: Rio, 1992). On the crop side, genetics research focuses on characterising and utilising crop-based germplasm collections for the mandate crops, potato, spring barley and soft fruit ( Ribes and Rubus). In this case, a key research aim is to understand the heritability of key genes and traits of agronomic importance. A second aim is to identify molecular markers which are increasingly being used in crop breeding programmes.

2.1.1 Angiosperm Systematics

SEERAD-funded systematics research focuses on a number of temperate and tropical plant genera, including primitive legumes, rhododendrons and orchids. Classical methods for species differentiation and identification which rely on the identification of morphological characters are being expanded by newer methods of molecular taxonomy which examine differences in DNA sequence. These are enabling technologies that help researchers to understand how species have evolved from one another (the process of speciation) and how key biological processes such as floral development have evolved. The knowledge generated by this research will help explain species diversity and will inform conservation policies thus leading to the development of appropriate strategies for the sustainable management of genetic resources in Scotland and overseas. One fairly new area of activity which is partly covered here and partly in Theme 5, is the investigation of the evolution of species-rich tropical forest biodiversity. This research looks at the effects of population size on the maintenance of genetic variability, and should lead to sustainable agroforestry systems in South America, which utilise native vegetation. The research listed here under Theme 2.1.1 is closely related to other parts of the SEERAD-funded programme of research, most notably the floristics and the conservation work listed in Theme 5.

2.1.2 Non-Angiosperm Systematics

Systematics research is also undertaken on lower and non-flowering plants such as algae, lichens and bryophytes. The research aims to use taxonomic and systematic approaches to understand the biodiversity of these organisms, many of which have become widely used as bioindicators of various environmental features such as atmospheric pollution, water quality and climate change. Diatoms form one important focus of this programme, and research aims to identify species and, perhaps more importantly, to development a fundamental understanding of the actual process of speciation in diatoms. Recent developments have included the application of image analysis for automatic diatom identification (ADIAC).

2.1.3 Evolution & Exploitation of Genetic Resources

A second major thrust of the SEERAD-funded genetics research, is the characterisation and utilisation of the germplasm collections for the mandate crops (potatoes, spring barley and soft fruit). The largest of these collections is the expanded Commonwealth Potato Collection (CPC) which includes Professor Hawkes' Birmingham Potato Collection (BPC). This combined collection, which is maintained as a potato spindle tuber viroid (PSTV)-free seed collection, contains just under 1500 accessions, representing 83 species, including many wild, diploid species of potato collected in South America, which should provide many useful traits for deployment by potato breeders. Research described here links very closely to research under plant pathology in Theme 2.3. Examples of useful traits currently being studied are novel sources of host resistance to the white form of potato cyst nematode (PCN) Globodera pallida and to bacterial and fungal pathogens that infect potatoes. Agricultural practices often involve the use of chemical inputs to control pests and diseases and these practices are not always sustainable. If new resistance genes can be identified and used in breeding programmes then there will be less need for chemical inputs and input costs for crop production will decrease. Other genes being targeted are those controlling product quality such as improved colour, flavour and texture. These features are now being demanded by retailers, processors and consumers. The soft fruit germplasm collections include 300 Rubus (raspberry) and 500 Ribes (blackcurrant) accessions, and these accessions are again stored as high health, pathogen-tested stocks. Recently modern molecular-based techniques have been introduced into the research programme to complement older approaches to genetic characterisation. Again understanding the genetic variation contained in this unique germplasm collection and determining how this genetic variation is linked to fruit quality is a key aim of the soft fruit research programme. Some of this work on potato and soft fruit genetics links to complementary research listed under Theme 2.2.2, where biochemical characterisations of the same material is being undertaken. This section also includes research on more applied aspects such as the use of cereal mixtures. In this approach a number of cereal varieties are mixed before sowing in contrast to sowing monocultures of just one cereal variety. This technique aims to broaden the genetic base within a crop therefore making it more resilient to attack from the environment and pests and pathogens. The biological mechanisms underlying this behaviour is not yet understood and are being studied in this research. Finally this section contains collaborative research between the Scottish Crop Research Institute (SCRI) and the Royal Botanic Garden Edinburgh (RBGE), to evaluate the potential of modern molecular marker technology as a research tool for conservation biology.

2.1.4 Plant Genomics

Genomics and functional genomics has become a significant component of the plant genetics programme. Research activity is most advanced in the diploid species barley, where a comprehensive molecular marker map of the barley genome has already been prepared and is currently being added to with Expressed Sequence Tag (EST) information. SEERAD is participating in the BBSRC Investigating Gene Function (IGF) Initiative by co-funding work to develop a UK cereal transcriptome resource which involves a collaboration between the Scottish Crop Research Institute (SCRI), the John Innes Centre (JIC) and IACR-Long Ashton. Within this consortium, SCRI's role is to develop a barley transcriptome resources and a barley mutant library. Also included in this Theme are new studies where genomics approaches are being applied to understand the genetic control of barley root growth and how root structure influences the local soil environment. Genomics research on the tetraploid potato species is technically more difficult to undertake and the current programme focuses on one specific linkage group (linkage group V) which is known to contain many desirable quantitative trait loci (QTL). A pathogenomics programme has been commissioned and focuses on two pathogens infecting potato the fungus Phytophthora infestans and a bacterium, Erwinia carotovora and is covered under theme 2.4.1.

2.1.5 Bioinformatics

The genomics research programme is underpinned by a programme of bioinformatics, which stores, annotates and analyses the data coming from the genomics research. This data can be in the form of molecular marker locations, chromosomal locations of QTL (for example resistance genes), or gene (or EST) DNA sequences. A new introduction is the development of computational biology expertise where bioinformatics and other computer-based techniques are being used for knowledge-based "dry science", or in silico approaches to biological research. Bioinformatics skills are also being used to capture information from systematics research in the Prometheus project.

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