Sequencing and exploitation of the genetic diversity in Vietnamese native rice lines to serve research and breeding programs

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Genetics and Breeding

Abstract

We propose to develop a modern platform for rice breeding in Vietnam focused on traits of agronomic interest. Rice is a staple food for a population of 90 million in Vietnam and it is also one of the main exporter commodities of the country. Vietnam is experiencing an exceptional growth in its economic output and population rising as a global leading agricultural country. There is, however, an increasing threat from climate change such as emerging pathogens, periods of droughts and rising sea levels. The areas under greatest risk are the deltas of the Red and Mekong rivers, which represent the major rice growing regions of Vietnam. The rapid selection of rice varieties that are tolerant and resilient to these conditions will help to mitigate some of these challenges and contribute to ensure food security in Vietnam.

The Genome Analysis Centre (TGAC) in the UK and the Agricultural Genetics Institute (AGI) in Vietnam initiated a collaboration to sequence the genome of a reduced number of Vietnamese rice varieties with the purpose to characterise the genetic variations in native lines and develop molecular markers that could be used to accelerate rice breeding.

The application of new genomics technologies to improve crop breeding is one of the priorities at the National Institute of Agricultural Botany (NIAB) at UK. The proposed project continues the partnership initiated between TGAC and AGI as a collaboration with NIAB. We aim at expanding the pilot project phase I to complete the re-sequencing of around 600 lines. We will complement the generation of these data with the development of databases and the application of bioinformatics pipelines to identify associations of alleles with specific phenotypes. We expect to characterise markers that will enable more efficient rice breeding. The application of modern technologies to rice breeding will also provide an excellent example of how these strategies could be applied to other plant species such as wheat and barley. Rice has a simple genome for which many genomics resources have been already generated and it offers an excellent model for the evaluation and assessment of new strategies for breeding that could later be applied to more complex crops. This collaboration with Vietnam will also open opportunities to work with world leading scientists with experience in rice breeding and agronomy.

Planned Impact

The proposed collaboration will support the development of a modern rice breeding platform in Vietnam that will contribute to ensuring food security in the country. The impacts on research will be delivered within the timeframe of the proposed project and continue thereafter on an international scale. There will be direct impacts on staff through training and outreach activities in bioinformatics and the deployment of modern breeding technologies. The indirect impacts, for example, on the food security agenda and the wider public will take longer.

There is a requirement for bioinformatics expertise in Vietnam, and a shortage of scientists with the required expertise in genomics, computer science and mathematics. Capacity building in bioinformatics will strengthen research into genomics globally to exploit the opportunities presented by big data but this requires good people and requires tapping into reserves of mathematicians, physicists and computer scientists internationally that we can attract to increase the pool of skilled labour Vietnam.

Publications

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Caccamo M (2017) Delving into diversity: computational key to the crops of the future in Research Features Magazine

 
Description We have generated sequencing data for ca. 10% of the rice varieties in Vietnam National rice seed bank (Earlham Institute). These datasets have been shared with our collaborators in the Agriculture Genetics Institute in Hanoi and will be used to support the characterisation of the material that in turn will improve and modernise their rice breeding pipelines. We have also analysed the data to provide a more reliable classification for the Vietnamese rice varieties (NIAB). We have generated a high-quality genetic marker set based on single nucleotide polymorphisms that has been shared with the collaborators in the project.
Exploitation Route The data have been shared with colleagues in the UK and Vietnam. It will be uploaded in open-access browsers to enhance accessibility and maximise impact.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)

 
Description The sequencing data generated by this project has been used by Vietnam National Genetic Resources organisation to classify the material in their seed banks. This material has also been used by Vietnamese breeders to improve their marker-assisted selection pipelines. We will continue to work with our collaborators in Vietnam to realise the value of the data generated by this project.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Economic

 
Title Whole-genome resequencing of 508 varieties of Vietnamese rice 
Description These lines have been selected from the Vietnamese National Genebank to show diversity within the phenotypes of interest. There are currently ~8000 accessions in the Vietnamese National Genebank, 616 of which have been selected by AGI for additional phenotyping focusing on traits of interest such as biotic and abiotic stresses and root phenotypes. From these 616, we have sequenced 508 at a coverage between 3X and 5X as part of this project 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact Contributing to identify markers suitable for Vietnamese materials and traits of agronomic importance. 
 
Description Agriculture Genetic Institute - Hanoi - Vietnam 
Organisation Agriculture Genetics Institute
Country Viet Nam 
Sector Charity/Non Profit 
PI Contribution DNA sequencing data and bioinformatics analysis of the diversity rice studies. We have also trained our collaborators in the use of advanced bioinformatics approaches.
Collaborator Contribution Contribute with DNA materials, phenotyping data and breeding experience in rice.
Impact Completion of the fist DNA sequencing data for native Vietnam lines (it was recognise by the Vietnamese government with a special award). Successful submission to the Newton programme.
Start Year 2011
 
Description Bioinformatics for Breeding 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The practical course featured a collection of methods and bioinformatics tools fundamental for modern breeding, especially for crops. Next generation sequencing (NGS) has made large collections of open-source diversity genomic data possible, such as SNPs, that can be used as molecular markers for breeding. Combined with phenotypes, genome-wide association studies provide breeders with an understanding of the molecular basis of complex traits. Content: SNP calling/discovery and SNPs effects and context; NGS techniques for genotyping; Genetic markers, linkage analysis, and genetic maps; High-throughput phenotyping and image analysis; Association mapping (GWAS); Genome-wide predictions, modelling and simulations; Genomic selection.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/bioinformatics-breeding
 
Description Bioinformatics workshop in Hanoi 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Training workshops to build bioinformatics capacity, using rice as a model, held at AGI in Hanoi in June 2016. Developing the bioinformatics capacity in Vietnam will allow research institutes to take advantage of the developments in genomics, and apply them to rice breeding to help maintain productivity in the face of changing climates, and potentially develop new higher value rice varieties for the global market.
Year(s) Of Engagement Activity 2016
 
Description Genome Informatics 2018 - Genome Campus - Cambridge - September 2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited speaker at the Genome Informatics meeting in 2018. This is the most prominent annual bioinformatics conference. The session on Complex Genomes was initiated with this presentation.
Year(s) Of Engagement Activity 2018
URL https://coursesandconferences.wellcomegenomecampus.org/our-events/genome-informatics-2018/
 
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 Invited Speaker at the 10-year celebration of the Centre of Excellence in Genomics (ICRISAT, India) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 10-year anniversary of the Centre of Excellence in Genomics. This event congregated researchers and industry stakeholders from across the globe working in crop genomics.
Year(s) Of Engagement Activity 2017
URL http://www.icrisat.org/celebrating-a-decade-of-genomic-advances-in-agriculture/?utm_content=buffer55...
 
Description Key Note Speaker at VIII Argentinian Bioinformatics and Computational Biology Congress 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Key note speaker - meeting was followed by a number projects to apply for GCRF funding to work with researchers in Latin America
Year(s) Of Engagement Activity 2017
URL http://ufq.unq.edu.ar/8cab2c/
 
Description Launch of the Newton-funded sustainable rice programme. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact The BBSRC organised a workshop at IRRI (The Philippines) to launch the Sustainable Rice Programme supported by the Newton fund.
Year(s) Of Engagement Activity 2017
URL http://www.bbsrc.ac.uk/news/food-security/2017/170106-pr-over-6m-newton-fund-investment-in-research-...
 
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 NIAB Director's day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I presented at the NIAB Director day - the focus of the presentation was on describing the application of new technologies to agriculture. I engaged with a diverse audience - explaining the advantages that new technologies could bring to agronomical practices.
Year(s) Of Engagement Activity 2017
 
Description Poster Day at NIAB 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Poster Day - NIAB - this event is attended by postgraduate, researchers and relevant industry partners.
Year(s) Of Engagement Activity 2018
 
Description Poster Presentation - Analysis of a Large Collection of Vietnamese Native Rice Lines Reveals Novel Genomics Variants - PAG 2019 
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 Poster presentation at the Plant and Animal Genomes in January 2019. Te poster was presented in the rice section maximising the opportunity to engage and discuss the work of the project with the community.
Year(s) Of Engagement Activity 2018,2019
URL https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/36001
 
Description Poster Presentation - NIAB Poster Day - February 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Presentation of the Vietnam Rice Project in annual NIAB Poster Day.
Year(s) Of Engagement Activity 2019
 
Description Poster day at NIAB 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact We presented a poster with a summary of the current status of the project at NIAB's poster day on 8 February 2017.
Year(s) Of Engagement Activity 2017
 
Description Poster presentation at the Plant and Animal Genomes 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We presented a poster at the Plant and Animal Genomes meeting in 2018. A number of opportunities for collaboration emerged from this event.
Year(s) Of Engagement Activity 2018
URL http://www.intlpag.org
 
Description Sustainable Rice Initiative - dissemination workshop - Newton Fund and BBSRC - Bangkok - January 2019 
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 Sustainable Rice initiative from Newton Fund organised a three events with all the funded projects. The presentation summarised the results of the project and set out the benefits of the research.
Year(s) Of Engagement Activity 2019
 
Description Training in bioinformatics delivered in Vietnam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Training workshop in bioinformatics delivered to breeders and scientist at AGI (Hanoi, Vietnam). The workshop was held over 4 days covering aspects of genomics data, diversity analysis and advances topics such as imputation.
Year(s) Of Engagement Activity 2016
 
Description Uniqueness amongst the Indica and Japonica subpopulations within a diverse collection of Vietnamese Rice 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation and discussion with rice breeding and researchers during the quadrennial Rice International Congress in Singapore.
Year(s) Of Engagement Activity 2018
 
Description Unravelling the Diversity of Native Rice in Vietnam for Future Climatic Scenarios 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Talk and discussion with the members of the International Rice Informatics Consortium (IRIC-IRRI) during PAG XXVII
Year(s) Of Engagement Activity 2019