PhD Fellowship Genomics of the biomass crop Miscanthus

Genomics of the biomass crop Miscanthus: characterizing variation in the plastid genome and assessing nuclear polyploid variation

A three-year PhD fellowship funded under the Wash Fellowship Schema is available for a research project on the biomass crop plant Miscanthus. 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. The entire chloroplast genome sequence will be sequenced, partial sequences of the mitochondrial genome will be generated and chromosome number and ploidy variation recorded for the nuclear genome.

We will use DNA sequencing and bioinformatics techniques to assess the sequence information of the Miscanthus organelles. We will study their features via annotated genome diagrams and via comparisons to other grasses especially sugarcane, sorghum and maize. Structural rearrangements will be recorded and assessments made of the molecular evolution of their genes. 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. Furthermore we will use flow cytometry in conjunction with chromosome counts to assess polyploid complexes. We will determine crossability groups and gather essential
information for future ploidy manipulation.

This is a collaborative project between Teagasc Crops Research Centre Oak Park in Carlow and the Botany Department of Trinity College Dublin (TCD). The researcher will be based in Oak Park but can spend some research time at TCD. The student will receive an annual tax free stipend of €21,000 for maintenance and to cover University fees (currently €4,708 pa for EU citizens, €12,067 pa for non-EU citizens). The PhD project is funded for three years and is expected to start on 1st October 2007.

Applicants must have or expect to gain a first or upper second class or Masters degree in an area of biological sciences. Informal enquires are welcomed and further information is available from the co-supervisors (below). Applications, including a covering letter detailing research interests and aspirations, a detailed CV including names and contact details of two referees should be made to Trevor Hodkinson (hodkinst@tcd.ie; http://www.tcd.ie/Botany/staff/THodkinson.html)
or Susanne Barth (susanne.barth@teagasc.ie; http://www.teagasc.ie/oakpark/sbarth.htm) as soon as possible; the position will be open until filled.

Dr. Trevor R. Hodkinson
Botany Department
School of Natural Sciences
Trinity College Dublin
Dublin 2, Ireland
PHONE ++353 1 896 1128
FAX: +353 1 896 1147
hodkinst@tcd.ie

Dr. Susanne Barth
Teagasc
Crops Research Centre
Oak Park
Carlow, Ireland
++353 (0)599170290
++353 (0)599142423
susanne.barth@teagasc.ie