Professor Trevor Hodkinson

• Zhao, D., Parnell, J.A.N., Hodkinson, T.R., Typification of names in the genus Camellia (Theaceae), Phytotaxa, 292, 2017, p171 - 179Journal Article, 2017
• Pornpongrungrueng, P., Parnell, J.A.N., Hodkinson, T. & Chantaraonthai, P. , Phyllanthus kaweesakii (Phyllanthaceae), a new species from Thailand., Botany, 95, 2017, p567 - 577Journal Article, 2017, DOI
• Zhao, D., Parnell, J.A.N. & Hodkinson, T. R., Names of Assam tea: Their priority, typification and nomenclatural notes. , Taxon, 66, 2017, p1447 - 1455Journal Article, 2017, DOI
• Sirimongkol, S., Parnell, J.A.N., Hodkinson, T, Middleton, D.J. & Puglisi, C. , Five new species of Henckelia (Gesneriaceae) from Myanmar and Thailand. , Thai Forest Bulletin, 47, 2019, p38 - 54Journal Article, 2019, DOI
• T R. Hodkinson, F. M. Doohan, M. J. Saunders and B. R. Murphy, Endophytes for a growing world. , Cambridge University Press, 2019, 1 - 420ppBook, 2019, URL
• Zhao, D., Parnell, J.A.N. & Hodkinson, T.R., Typification of names in Camellia (Theaceae), III., Phytotaxa, 415, 2019, p298 - 300Journal Article, 2019
• Pornpongrungrueng, P., Chantaranothai, P., Parnell, J.A.N. & Hodkinson, T.R. , Two new species of Phyllanthus (Phyllanthaceae) from Thailand., Phytokeys, 136, 2019, p35 - 44Journal Article, 2019
• Hodkinson, TR, Waldren S, Parnell, JAN, Kelleher, CT, Salamin, K, Salamin, N, DNA banking for plant breeding, biotechnology and biodiversity evaluation, Journal of Plant Research, 120, (1), 2007, p17 - 29Journal Article, 2007, DOI
• Sungkaew, S., Teerwatananon, A., Parnell, J.A.N., Dransfield, S., Stapleton, C.M.A. & Hodkinson, T. , Dendrocalamus khoonmengii, a new bamboo species (Poaceae: Bambusoideae) from Peninsular Thailand., Thai Forest Bulletin, 35, 2007, p98 - 102Journal Article, 2007, URL
• Jones E, Simpson DA, Hodkinson TR, Chase MW, Parnell, JAN, The Juncaeae-Cyperaceae interface: a combined plastid sequence analysis, Aliso, 23, 2007, p55 - 61Journal Article, 2007, URL
• Hodkinson, T.R., Jones, M.B., Waldren, S. & Parnell, J.A.N., Climate Change, Ecology and Systematics, Cambridge, Cambridge University Press, 2011, 1 - 524ppBook, 2011
• Jones MB, Finnan J, Hodkinson TR, Morphological and physiological traits for higher biomass production in perennial rhizomatous grasses grown on marginal land, GCB Bioenergy, 7, 2014, p375-385Journal Article, 2014, DOI , URL
• Hodkinson TR, Klaas M, Jones MB, Prickett R, Barth S, Miscanthus: a case study for the utilization of natural genetic variation, Plant Genetic Resources: Characterization and Utilization, 13, 2015, p219-237Journal Article, 2015, DOI

My laboratory is currently used by seven postgraduate students with research mainly focussed in fields known as molecular systematics, genetic resource characterisation and population genetics. I have specialist knowledge of the grass family and of forest tree genetics. I collaborate with a number of national (Department of Agriculture, Teagasc) and international institutions (Royal Botanic Gardens, Kew, UK; University of Lausanne).

• Title

  GrassMargins
  Summary

  As part of an EU FP7 funded project called GrassMargins, this project is collecting novel germplasm of Dactylis, Festuca, Phalaris and Miscanthus in Europe and Asia. We are also collating existing geographical and ecological data on the species and their close relatives. When this is complete we will construct ecological niche models and model biogeography to help predict the areas with highest potential for production of each of the crops. Once these factors have been identified breeders will be able to better select germplasm for development of new varieties especially for growth in marginal habitats that are less suited to conventional agriculture. We also conducting diversity and phylogeographic studies of the target grasses using molecular markers. PhD student: Ruby Prickett. Co-supervisor: Prof. Mike Jones. http://www.grassmargins.eu
  Funding Agency

  EU
  Date From

  October 2011
  Date To

  September 2015
• 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. PhD student: Aude Perdereau. The project is a collaboration between Trinity College Dublin (TCD), Teagasc and the National Botanic Gardens Glasnevin. It is jointly supervised by Dr Gerry Douglas (Teagasc (Kinsealy; www.teagasc.ie) and Dr Colin Kelleher (www.botanicgardens.ie).
  Funding Agency

  Teagasc
  Date From

  Oct 09
  Date To

  Sept 13
• Title

  Characterisation of lignin and cellulose formation genes in biomass and energy grasses (Poaceae)
  Summary

  PhD Student: Vishnu Mohanan. 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
  Date From

  Sept 2011
  Date To

  Sept 2015
• Title

  Genotypic and phenotypic assessment of forage quality in Lolium in the age of large-scale, inexpensive genotyping
  Summary

  With the rapid advances in genotyping offered by next generation sequencing (NGS) we are at a stage in forage grass breeding where the major limiting step in linkage mapping/association mapping is likely to be phenotypic (observable characteristics) and not genotypic characterization. Thus, the collection of high-quality phenotypes will be crucial for mapping studies. Forage quality and digestibility of Lolium perenne (perennial ryegrass) is related to biomass accumulation, flowering time and lignocellulosic content. This project will combine phenotypic and genotypic studies on a diverse set of Lolium accessions to specifically assess the genetic control of these traits. Forage quality traits examined will include lignocellulose content and composition, flowering time, re-heading, biomass accumulation, and tillering capacity. We will combine this with an examination of variation in candidate genes relating to these traits using DNA sequencing and association mapping using high-density single nucleotide polymorphism (SNP) data and genic SNPs. Many of these genes are well studied in cereals and hence these genome resources can be applied to Lolium
  Funding Agency

  Teagasc
  Date From

  2013
  Date To

  2017
• 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. PhD student Patricia Coughlan. Co-supervisor James Carolan. Collaborator Ingrid Hook.
  Funding Agency

  TCD
  Date From

  Sept 2011
• Title

  Isolation of low temperature tolerant beneficial fungal root endophytes of crops
  Summary

  There is an increasing chemical load on the environment, partly due to high agri-chemical inputs. More sustainable methods that would reduce chemical use, while still maintaining crop performance, are needed. Bio-control and bio-fertilisation methods are often longer lasting than chemical applications in their effects, can reduce labour time, and are also generally more environmentally friendly. A group of endophytic root fungi in the Sebacinales order have recently been shown to increase yield, enhance stress tolerance and induce pathogen resistance in many crop plants. This research will investigate the natural occurrence, diversity and efficacy of Sebacinalean and other fungal root endophytes in a variety of Irish plant species. Competent fungal strains suitable for Irish conditions could be used in various forms for crop inoculation. Irish agriculture could significantly benefit from any positive outcomes from this research, with potential reductions in fungicide, pesticide and fertiliser use. Future global warming may result in altered Irish crop growing conditions, and this area of research could therefore become increasingly relevant. PhD Student: Brian Murphy. Co-supervised by Fiona Doohan (UCD).
  Funding Agency

  TCD
  Date From

  Oct 2012
  Date To

  Sept 2015