| Project title |
Investigating variation of disease resistance and wood formation genes in willow |
| Summary |
The proposal aims to characterise native species of willow through DNA sequencing to assess the levels and the nature of natural polymorphism within the species and populations studied. Importantly, they will be assessed for
variation in specific genes known to confer tolerance to biotic agents (fungi and pests) as well as genes that affect dry matter and wood density. Efforts will concentrate on Salix viminalis since commercial varieties are available for this species. Willows and poplars (Populus) are closely related (Salicaceae
family). Several important genes affecting disease resistance and wood formation are well characterized in poplar and will have homologs in willow. We propose to examine these genes in native willows and compare them to commercial cultivars.
Material showing greater gene diversity for a target region such as disease resistance will identify germplasm with potential value for further breeding work.
The project is a collaboration between Trinity College Dublin (TCD), Teagasc and the National Botanic Gardens Glasnevin. It will be jointly supervised by Dr Gerry Douglas (Teagasc
(Kinsealy; www.teagasc.ie) and Dr Colin Kelleher (www.botanicgardens.ie). |
| Funding Agency |
Teagasc |
| Programme |
PhD |
| Type of Project |
Research |
| Date from |
Oct 09 |
| Date to |
Oct 12 |
| Person Months |
36 |
|
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| Project title |
Hybrid alien ash: Fraxinus excelsior × F. angustifolia in ireland and its potential for interbreeding with native ash |
| Summary |
In collaboration with Dr Gerry Douglas, Teagasc Research Centre, Kinsealy and Juan F. Fernández, Natalie Frascaria-Lacoste, Université Paris 11 Sud. Personnel: Ms. Muriel Thomasset. Ash is an important hardwood species for farm forestry in Ireland. From 1992, substantial grants for planting hardwoods were made available which resulted in plant shortages. Ash plants and seeds were imported to fill requirements and many of the resulting plantations have developed poorly with bad stem-form, vigour, unusual morphology, and canker. Some of these problems may be due to the unintentional importation of hybrid ash which occurs naturally in some parts of Europe and is derived from F. excelsior × F. angustifolia; some could be F. angustifolia. In other cases, poor performance may be due to using provenances which are unsuited to Irish growing conditions. There is a lack of understanding of hybrid ash in general, the scale its occurrence, and its potential to interbreed with native ash. The potential of hybrid ash to interbreed with indigenous ash in Ireland, would lead to ‘genetic pollution’ of indigenous ash.The overall aim of this project is to carry out a set of morphological, physiological and molecular tests which can confirm the hybrid nature of ash growing in plantations where growth is poor and hybridity is suspected. Trees which are confirmed as hybrids may be identified and removed whereas those confirmed as ‘pure’ F. excelsior will be retained. The flowering time of suspected hybrid material will be monitored and compared to native ash to determine if the flowering periods overlap and if hybridization is theoretically likely or possible. Similarly, the viability and germination of seeds and pollen from suspect plantations will be determined and the progeny characterized. |
| Funding Agency |
Teagasc Walsh Fellowship/COFORD |
| Programme |
PhD |
| Type of Project |
|
| Date from |
Oct 07 |
| Date to |
Oct 10 |
| Person Months |
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| Project title |
Genomics of the biomass crop Miscanthus: characterizing organelle genomes and assessing nuclear polyploid variation |
| Summary |
In collaboration with Susanne Barth, Teagasc, Oak Park. Personnel: Mariateressa de Cesare. Miscanthus species are perennial, C4 grasses capable of tremendous biomass growth under a wide range of climatic conditions. Attention has focussed on biomass crops because of the need for alternative energy sources for sustainable living. Very few Miscanthus genotypes have been assessed for their biomass potential but work is underway to develop new genotypes. The overall aim of this project is to gather essential genomic information required for plant breeding in this poorly understood genus. The focus will be on the characterization of the nuclear and cytoplasmic gene pools.
Little is known about the cytoplasmic genomes (chloroplast and mitochondrial) of Miscanthus or of their variation. We will assess the cytoplasmic gene pools available for breeding by developing and applying molecular markers (including but not exclusively SSR variants) suitable for rapid screening of diversity. We will quantify diversity, group haplotypes and study infra-generic variation. We will also assess if cpDNA and mtDNA are maternally inherited in Miscanthus.
Miscanthus species form a polyploid complex including several other genera (including Saccharum). For polyploid complex assessment we will use chromosome counts in conjunction with flow cytometry. The aim is to study nuclear DNA content and ploidy variation in the breeding genepools and to compare these to the assessments of plastid genome variation. We will determine crossability groups and gather essential information for future ploidy manipulation.
|
| Funding Agency |
Teagasc Walsh Fellowship |
| Programme |
|
| Type of Project |
PhD |
| Date from |
Oct 07 |
| Date to |
Oct 10 |
| Person Months |
|
|
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| Project title |
Characterisation of lignin and cellulose formation genes in biomass and energy grasses (Poaceae) |
| Summary |
Co-supervised by Susanne Barth. Collaborators Nicolas Salamin & Elizabeth Kellogg.
Grasses have received considerable attention as a source of woody biomass for bioenergy production to provide alternatives to fossil fuels. Potential bioenergy grasses include Miscanthus, maize, switchgrass and several woody bamboos. Most grasses are herbaceous but some subfamilies have evolved woodiness. Bamboos (subfamily Bambusoideae) have evolved a woody character via enhancement of the lignocellulosic component of vascular tissue, especially vessels. Reeds (e.g. Arundo, Phragmites, subfamily Arundinoideae) and Panicoideae (e.g. Saccharum, Miscanthus, Panicum) have also evolved this trait. It is not known if they have achieved this via alternative biosynthetic paths/genes. Grass cell walls differ from other angiosperms in their major structural polysaccharides, pectins, proteins and phenolic compounds. Recent advances in genomics have revealed cellulose synthase‐like (Csl) gene families (unique to grasses) and the CslF gene (unique to Poales, the order to which the grass family belongs). An understanding of how these gene families and lignocellulosic biosynthesis evolved in grasses is key to improving the processing quality of grasses for bioenergy and the manipulation of the genes in future biotechnology and plant breeding. Objectives and methodology: 1) Investigate, via a candidate gene approach, the evolution of genes known to be of importance for woodiness in grasses (e.g. cellulose synthase genes, Cesl, a highly expressed gene family in developing vascular fibres, including CslF, and monolignol biosynthesis genes. 2) Investigate the effects of woodiness on grass evolution (e.g. investigate, using diversification statistics and molecular dating, whether woodiness was a significant key innovation for speciation in the groups that have evolved it).
|
| Funding Agency |
HEA PRTLI 5 |
| Programme |
Earth and Natural Sciences, ENS |
| Type of Project |
Structured PhD |
| Date from |
Sept 2011 |
| Date to |
Sept 2015 |
| Person Months |
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|
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| Project title |
Phylogenetics of paclitaxel biosynthesis genes in Taxus baccata, Taxus hybrids and allies |
| Summary |
Taxus baccata (the Irish Yew) produces a natural diterpenoid commonly known as Taxol that is an effective chemotherapeutic agent against a wide range of tumors especially ovarian, breast and lung cancers. With recent advances in molecular biology, the entire taxol biosynthetic pathway has been elucidated and many of its genes have been characterised. We plan to study molecular variation in these genes to establish differences between species including hybrids and their know parents so that associations can be discovered between paclitaxel production and DNA sequence polymorphism. The primary aim is to discover which genes are most important for paclitaxel production in Taxus baccata and discover variation in these genes.
Co-supervisor James Carolan. Collaborator Ingrid Hook. |
| Funding Agency |
TCD |
| Programme |
Part-time study |
| Type of Project |
MSc |
| Date from |
Sept 2011 |
| Date to |
|
| Person Months |
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Grass Phylogeny Working Group II: Aliscioni S, Bell HL, Besnard G, Christin PA, Columbus JT, Duvall MR, Edwards EJ, Giussani L, Hasenstab-Lehman K, Hilu KW, Hodkinson TR, Ingram AL, Kellogg EA, Mashayekhi S, Morrone O, Osborne CP,Salamin N, Schaefer H, Spriggs E, Smith SA, Zuloaga F, New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins, New Phytologist, 193, 2012, p304 - 312
DOI |
Hodkinson, TR, Jones, MB, Waldren S, Parnell, JAN, Climate Change, Ecology and Systematics. The Systematics Association Special Series Volume 78, Cambridge University Press, 2011, 524 + IXpp
Url |
Delętre M, McKey DB, Hodkinson TR, Marriage exchanges, seed exchanges, and the dynamics of manioc diversity, Proceedings of the National Academy of Sciences USA, 108, (45), 2011, p18249-18254
Url
DOI |
Integrating ecology and systematics in climate change research in, editor(s)Hodkinson, TR, Jones, MB, Waldren S, Parnell, JAN , Climate Change Ecology and Systematics, Systematics Association Special Series Volume 78, Cambridge, Cambridge University Press, 2011, pp3 - 43, [Hodkinson, TR]
Url |
Bouchenak-Khelladi Y, Verboom, GA, Savolainen, V, Hodkinson, TR, Biogeography of the Grasses (Poaceae): a Phylogenetic Approach to reveal Evolutionary History in Geographical Space and Geological Time, Botanical Journal of the Linnean Society, 162, 2010, p543 - 557 Alt. Url
DOI |
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