PhD position ‘Whole genome sequence analysis in tomato: Mechanisms of introgression breeding’
Applied Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR)
Wageningen, The Netherlands
38 hours per week
Reference number: PSG-BIOS-0001
Background: Wageningen University and Research Centre (WUR) is worldwide renowned for its research and education in the fields of life sciences, plant improvement and sustainability. Through these activities it aims to make essential contributions to the quality of life. A focus of pioneering research towards increased yields and improved quality is the genome biology of economically valuable crops such as tomato and potato.
The Plant Sciences Group of WUR has an important position in international efforts to elucidate and use the genome sequence of these crops. The Applied Bioinformatics group of the PSG participates in these efforts through next generation sequencing, genome assembly, annotation and extracting biologically relevant knowledge from such genome sequences.
WUR is also a partner in the Centre for BioSystems Genomics (CBSG2012). The CBSG and the National Institute for Plant Genome Research in Delhi, India, have received a grant from the Netherlands Organisation for Scientific Research (NWO) to start a joint research project on development and application of next generation sequencing technologies to one of CBSG’s crop targets, tomato, which is also an important crop in India.
Job description: the job concerns a PhD position in the Applied Bioinformatics group of the Plant Sciences Group of WUR. In this project, we will analyze the genomes of three tomato genotypes: two parents of the well-studied introgression line population, S. lycopersicum cv. Allround and S. pennellii LA716, and the genome of one F5 offspring line. Sequencing of these genomes will be performed in an associated project and will involve a combination of next generation sequencing technologies. Comparative bioinformatic analyses of the parent and offspring genomes will be geared towards obtaining novel insights into the molecular mechanisms underlying genetic introgression in plants. The PhD student will assemble, annotate and compare the three genome sequences with the aim to study the pattern of genome reorganization from chromosome- down to nucleotide-level detail. We will test and employ a variety of bioinformatics tools for genome assembly, annotation and whole-genome comparison, and perform SNP mining for breeding purposes.
The collaboration within this project with the National Institute for Plant Genome Research in New Delhi, India, will imply that the PhD student will spend a maximum of 2 years of the 4-year PhD study at the sister institute in India. In addition, the PhD student will actively cooperate with an Indian counterpart (PhD student) based in Delhi and working on the breeding aspects of the project. This PhD student in return will spend a maximum of 2 years in Wageningen.
Location: Wageningen, The Netherlands
What do we look for?
We are looking for an enthusiast team player with:
- an excellent academic record (MSc) in bioinformatics
- interest in genome informatics and bioinformatics for breeding
- demonstrable skills in programming (perl or python, java, R) and databases (MySQL)
- good oral and written communication skills in English
- willingness to spend several periods amounting to 2 years of the PhD period in New Delhi, India
- people skills in connection with biologists, breeders and bioinformaticians
What do we offer?
You will be part of a young, dynamic and focused applied bioinformatics group of ~15 people consisting of computational biologists and biology-oriented informaticians that focus on bioinformatics challenges in genomics. We offer a state-of-the art computational infrastructure and have close collaboration with plant biologists and breeding companies with considerable expert knowledge of the biological issues and wishes concerning the data. The position is available for 4 years, full time (38 hrs/wk), 2 years of which will be housed in New Delhi, India. The student will be part of the graduate school of Experimental Plant Sciences (EPS). The research should result in the successful defence of a PhD after 4 years. In line with the quality protocol of EPS, after 12 months and assuming progress and performance of the PhD student meets requirements the position will be continued for the full period.
Preferred starting date: as soon as possible.
Estimated maximum salary: € 2042/month in the first year, rising to € 2612/month in the fourth year (Dutch university PhD)
Need to know more?
Additional information about this project can be obtained from dr. Roeland van Ham, +31-317-481053, roeland.vanham@wur.nl <mailto:roeland.vanham@wur.nl>
How to apply?
You can apply for this job before October 1st, 2010 at http://www.wur.nl/UK/work
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