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Workshop of the Ecological Genetics Group
This workshop precedes the two day Ecological Genetics Group Annual Meeting
Phenomics and Genomics in Ecological Genetics
A Workshop Hosted by the National Phenomics Facilities
At IBERS Aberystwyth
14.00 Alan Gay, IBERS/ Johanna Breyer, Environment Systems – Remote sensing of natural plant communities in the Welsh Uplands
14.20 Steffi Carter – Phenomic variation in Succisa pratensis populations
14.40 Brian Forde, Lancaster – A novel automated microphenotyping platform for chemical genetic applications in plant ecology and biology
15.00 Gina Garson Martinez – Competition and Cooperation in Arabidopsis
15.20 Lizzy Donkin – Plant trait databases and their potential for answering ecological questions
15.40 Matt Hegarty – Applying genomics to ecology or What can I do with my DNA samples?
16.00 Rob McMahon – Genomics and Red kite populations in Wales
16.20 Afternoon Tea and refreshments
Visits / Demonstrations
Tour of Phenomics Centre (Fiona Corke)
Tour of Genomics Centre (Matt Hegarty)
Nutrient flow facility (John Doonan)
Remote sensing of natural plant communities in the Welsh Uplands
Alan Gay/ Johanna Breyer, Environmental Systems Aberystwyth
Phenomic variation in Succisa pratensis populations
Steffi Carter, IBERS Aberystwyth
As part of a conservation project by Carmarthenshire County Council to halt the decline of the marsh fritillary butterfly Euphydryas aurinia a study into populations of devil’s-bit scabious Succisa pratensis – the caterpillar’s food plant – was carried out. Seeds were collected from 24 sites in South Wales, four sites in mid-Wales and one site in Ireland and subsequently grown into plants. Variables recorded were seed count per seed head, seed weight, germination rate and seedling survival. Additionally, a total of 300 plants from 21 populations were selected to be scanned by Lemnatec RGB imaging and Phenospex PlantEye at the National Plant Phenomics Centre. Leaf area, plant height and leaf angle were recorded and compared to manual phenomic measurements as well as the data from the germination study.
A novel automated microphenotyping platform for chemical genetic applications in plant ecology and biology
Brian Forde, Lancaster University
Chemical genetics uses small molecules to perturb biological processes as a means to explore gene function. Chemical genetics offers a number of advantages over conventional genetics, most notably its ability to overcome the problem of functional redundancy that can prevent single gene mutations causing any change in phenotype. To facilitate the application of chemical genetic approaches in plants we have developed a novel high-throughput platform (the ‘Microphenotron’) that provides unprecedented insights into how small molecules affect plant growth and development. Applications of this technology include the elucidation of signalling pathways involved in root responses to edaphic signals such as water and nutrient availability.
Competition and Co-operation in Arabidopsis
Gina Garzon Martinez, IBERS Aberystwyth
Plant competition for resources, such as light, water or nutrients, is considered a complex dynamic process that has implications for the formation and diversity of plant communities and ecosystems as well as an impact in crop yield. This plant-plant interaction involves different phenotypic traits, as well as genetic and physiological mechanisms to recognize and respond to the surrounding environment. We aim to develop screens to assess the extent of natural variation in the reaction of plants to neighbours and thereby identify genomic regions associated with changes in life history traits under competitive interactions. High-throughput phenotyping approaches will be used to quantify some traits. Then, a genome wide association study (GWAS) will be performed to link the phenotype and genotype. Candidate genes associated to a specific trait would be useful to decipher gene interactions network. The study of the competitive ability of an individual would have effects in aspects of plant breeding strategies, agronomic practices and diversity and community composition.
Plant trait databases and their potential for answering ecological questions
Lizzy Donkin, IBERS Aberystwyth
Ecological databases hold a wealth of open source plant phenomic data, distribution data and details of insect-plant interactions, all of which are often under-utilised. The data has the potential to be applied to a number of ecological questions, yet issues with accessibility and data quality prevent it being used on a wider scale. Here we discuss the importance of these open source phenomic databases and caveats that apply when using data of this nature. We demonstrate how this data can be applied to ecological genetics based questions, by using mined plant trait and insect herbivore data to predict what may influence plant species spatial distribution on a range of spatial scales. Reflecting on this process we propose a framework for future ecological databases to work by, in order for data to be easily accessed and utilised by the research community.
Applying genomics to ecology or What can I do with my DNA samples?
Matt Hegarty, IBERS Aberystwyth
Next-generation sequencing (NGS) and high-throughput genotyping technologies have revolutionised the speed and power of scientific analyses in biological systems. I will talk about the technologies available and how we have been applying these to ecological experiments here at Aberystwyth and with collaborators, as well as answer any queries the audience may have regarding use of/access to the technology.
Genetics of the Red Kite in Wales – exploring the genetic architecture of an expanded relic population?
Rob McMahon, IBERS Aberystwyth
The history of the Red Kite (Milvus milvus) in the UK over the past forty years represents a conservation success story. This once widespread scavenger species was exterminated from England, Ireland and Scotland by the end of the 1870s as a consequence of human persecution and land use changes. Throughout much of the twentieth century the status of the Red Kite as a breeding British bird relied entirely on a small relic population in Wales. This population contracted to less than 10 breeding pairs in Ceredigion in the 1930s. Recovery from this low point was initially slow, despite intensive monitoring and protection, and this led to a decision to reintroduction Red Kites of non-UK origin at suitable sites across the rest of the UK. The reintroduction program started in Scotland in 1989 using imported birds from Sweden, and in the Chiltern Hills in England using initially a few birds of Swedish and Welsh origin, and subsequently mainly of nestlings sourced from North East Spain. Subsequently the success of these trial reintroductions has led to birds being released at a total of seven other sites across England, Scotland, and most recently Northern Ireland and Eire. Breeding populations have become established at all of the release sites and the UK wide population is now believed to number around 2,000 breeding pairs. The range expansions of the native and introduced populations are now starting to overlap, but genetic investigations of the process are hampered by the relative paucity of polymorphic markers in this species. We have used NGS sequencing techniques to explore the diversity within the Welsh population and to examine the temporal stability of the apparent population split observed by mini-satellite probes in the 1990s.
National Plant Phenomics Centre Tour
Fiona Corke, IBERS Aberystwyth
This automated glasshouse houses an array of conveyors and imaging facilities. The plants are imaged and watered automatically. Their growth is monitored via image analysis. Large genetically defined populations are grown under controlled conditions, allowing their response to abiotic stresses to be monitored. Stresses include drought, high temperature and nutrient levels. Plant species grown in the facility include oats, grasses, oilseed rape, wheat, maize, Miscanthus and Arabidopsis. It is the only facility of its kind in the UK.
Nutrient Flow Facility
John Doonan/Ros Mathews, IBERS, Aberystwyth
The Nutrient Flow facility is an instrumented hydroponics platform that allows screening and dynamic analysis of medium sized plant populations for ion uptake and utilisation. It has been used extensively in the breeding programs for selection of forages with improved nutrient use efficiency, with several currently commercial UK varieties having been initially identified on this platform. The platform has been used to screen for plant variation in nutrient recapture and in heavy metal tolerance and uptake. Nutrient recapture is an important trait that could be exploited to protect watercourses from agricultural fertilisers while heavy metal contamination is a widespread problem in the UK, especially in the uplands.