Trans-national Infrastructure for Plant Genomic Science

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

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.

Publications

10 25 50
 
Description This research supported the development of a big data infrastructure for plant genomics in partnership with a large European consortium.
Exploitation Route The plant genomics infrastructure provide the foundations for research and science development in plant science. The platform and data infrastructure are open and were developed using open source software.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment

URL http://www.transplantdb.eu
 
Description Invited Speaker - DBT's Smart Agriculture Conclave - New Delhi (India) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Department of Biotechnology (India) organised a conclave to discuss opportunities for the implementation of smart agriculture using modern digital approaches. The application of standards for phenotyping technologies was a key aspect of the meeting.
Year(s) Of Engagement Activity 2017
URL http://www.dbtindia.nic.in/dbts-smart-agriculture-conclave/#
 
Description Invited Speaker at XI National Symposium of Biotechnology (RedBio) Argentina 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to present at RedBio 2017 in Argentina. This was followed up with an opportunity to apply for BBSRC GCRF funding to establish a collaboration with the potato research group at INTA Argentina which has been successful.
Year(s) Of Engagement Activity 2017
URL http://www.redbioargentina.org.ar/simposio-2017-bahia-blanca/
 
Description Myanmar - Green Fruits Dedicated Workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The Workshop, dedicated to Green Fruits in Green Horticulture, was organized in the context of (the ASEAN Institute for Green Economy, AIGE Component on Increasing and Improving Green and Blue Productivity and Sustainability The Dedicated Workshop was forward looking, taking into account fast emerging and converging regional and international trends on the imperative need for green and clean economy, articulated and adopted in an increasing number of national, regional and international for.
Year(s) Of Engagement Activity 2018
URL http://geggmyanmar.org/green-fruits-dedicated-workshop-report/
 
Description Presentation in the 4th Plant Genomics Congress (May 2016) - London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented about the tools developed within TransPlant and about the Ash Tree genome project.
Year(s) Of Engagement Activity 2016
 
Description Workshop on Plant Genomics Resources 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact A workshop on plant genomics resources organised in the Universidad Nacional del Comahue (San Antonio Oeste, Argentina) - 29 March 2016
Year(s) Of Engagement Activity 2016