Award details

Trans-national Infrastructure for Plant Genomic Science

Reference	BBS/E/T/000GP006
Principal Investigator / Supervisor	Professor Mario Caccamo
Co-Investigators / Co-Supervisors	Dr Sarah Dyer, Dr David Swarbreck
Institution	Earlham Institute
Department	Earlham Institute Department
Funding type	Research
Value (£)	280,706
Status	Completed
Type	Institute Project
Start date	01/09/2011
End date	31/08/2015
Duration	47 months

Abstract

Food and energy security are major challenges facing humanity in the coming decades. The falling costs of nucleotide sequencing are opening up significant opportunities for crop improvement through plant breeding and increased understanding of plant biology; in particular through interpreting the growing volume of plant genomics data in the context of phenotype. However, at present, there is no adequate infrastructure for plant genomic data. TransPLANT will develop a new infrastructure for this data, leveraging the experience of medical informatics while addressing the particular challenges and opportunities of plant genomics. TGAC will lead the work package on the implementation of resource-intensive algorithms for plant genomics data. This will include the evaluation of current resource-intensive algorithms for plants genomics data; building a network of developers with expertise in algorithms for plant genomics; and the implementation of novel algorithmic solutions for concrete challenges in large plant genomes. One focus will be on the evaluation and development of strategies for plant genome sequencing and assembly. The aim being to develop guidelines for genome sequencing and assembly strategies taking into account the characteristics of the genome in question, including the presence of repeats, heterozygosity and polyploidy. Other tasks include the evaluation and development of data structures for algorithm optimisation; testing methods, tools and pipelines for gene and repeat annotation; and development of tools for the enablement of virtual plant breeding.

Summary

unavailable

Committee	Not funded via Committee
Research Topics	Crop Science, Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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