Sequencing and exploitation of the genetic diversity in Vietnamese native rice lines to serve research and breeding programs
Lead Research Organisation:
National Institute 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.
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.
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
Trung KH
(2017)
Whole Genome Sequencing Reveals the Islands of Novel Polymorphisms in Two Native Aromatic Japonica Rice Landraces from Vietnam.
in Genome biology and evolution
Caccamo M
(2017)
Delving into diversity: computational key to the crops of the future
in Research Features Magazine
Carballo J
(2021)
Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula.
in Plants (Basel, Switzerland)
Higgins J
(2021)
Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.
in Rice (New York, N.Y.)
Higgins J
(2022)
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.
in Evolutionary applications
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. The genetic variation data have supported the classification of the native Vietnamese varieties in a putative novel phylogenetic group. In turn, this finding will support a better understanding of the recent history of rice varieties in Vietnam. |
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. The novel phylogenetic classification of the native Vietnamese varieties has also supported the work of the international rice community and also informed recent sequencing work. |
First Year Of Impact | 2017 |
Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software) |
Impact Types | Economic,Policy & public services |
Title | PRJEB36631: Whole-genome resequencing of 612 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. Deposit at NCBI's SRA under accession number PRJEB36631. |
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 | Proyecto Omicas / Omics project |
Organisation | Pontifical Xavierian University |
Country | Colombia |
Sector | Academic/University |
PI Contribution | Participation as an associated collaborator. The research program optimization Multiscale In-silico Agricultural Crops Sustainable (omics) is the winner of the second round of Colombia Science in focus Food which seeks, through seven projects, develop and implement strategies science and technology to improve agricultural varieties with the aim of contributing to food security and sustainable production worldwide . |
Collaborator Contribution | Omic is made up of researchers, undergraduate and graduate students , and support staff from 16 institutions, including institutions are higher education (IES) accredited, national and international, IES national non - accredited, international research centers in agriculture and domestic enterprises in the industrial sector, with the Pontificia Universidad Javeriana Cali anchor entity . |
Impact | This is a multidisciplinary project that involves collaborators working on genetics, genomics, bioinformatics, agriculture, phenotyping and social sciences. The Colombian government is also directly engaging with the collaborators. |
Start Year | 2019 |
Description | 'New' rice varieties offer potential for greater crop resilience |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Public/other audiences |
Results and Impact | https://www.agri-tech-e.co.uk/new-rice-varieties-offer-potential-for-greater-crop-resilience/ |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.agri-tech-e.co.uk/new-rice-varieties-offer-potential-for-greater-crop-resilience/ |
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 | Breeding crop with a higher resilience to climate change: finding novel rice diversity in Vietnam to help breeding resistant varieties |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Agri Tech East. 2021. Webminar. |
Year(s) Of Engagement Activity | 2021 |
Description | Conference Oral Presentation: Genomic regions and candidate genes selected during the breeding of rice in Vietnam |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Monogram 2022, Leeds. |
Year(s) Of Engagement Activity | 2022 |
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 | Kick off event of the Omics Project - key note speaker |
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 at the Omicas project kick-off workshop in Cali (Colombia) |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.omicas.co/noticias/recomendaciones-y-agenda-del-taller-anual-omicas |
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 | Local Rice Varieties in Vietnam Could be Used to Breed Improved Climate-Resilient Crops |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | https://www.azocleantech.com/news.aspx?newsID=29646 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.azocleantech.com/news.aspx?newsID=29646 |
Description | Local rice varieties in Vietnam could be used to help breed improved crops with a higher resilience to climate change, according to a new study published in Rice. |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | https://www.seedquest.com/news.php?type=news&id_article=129197 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.seedquest.com/news.php?type=news&id_article=129197 |
Description | Local rice varieties in Vietnam could be used to help breed improved crops with higher resilience to climate change, according to a new study. Researchers are aiming to identify varieties that can survive an increasingly unpredictable climate. |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | https://www.sciencedaily.com/releases/2021/06/210615132132.htm |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.sciencedaily.com/releases/2021/06/210615132132.htm |
Description | London Embassy of Vietnam |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Policymakers/politicians |
Results and Impact | Meeting with the First Secretary (Mr. PQ Hung) from the London Embassy of Vietnam |
Year(s) Of Engagement Activity | 2019 |
Description | Meeting of the UK Rice Research Consortium |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | NIAB is now member of the UK Rice Research Consortium - discussion of future collaborations were discuss in detail. |
Year(s) Of Engagement Activity | 2019 |
URL | http://ukrrc.org |
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 | Presentation as part of Agri-tech week |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | Scientist from Norwich Research Park came together to discuss the research surrounding crop/soil health studies. The event was advertised in the Eastern Daily press and the audience included people from the general public, researchers and farmers/industry around East Anglia. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.edp24.co.uk/news/business/agri-tech-week-norwich-research-park-6415196 |
Description | Presentation at Monogram 2019 - rice and other grasses |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation to the Monogram event of the progress of the Vietnam rice project. Following this event we met with the Ensembl plant team to discuss how to integrate rice data in the genome browsers. |
Year(s) Of Engagement Activity | 2019 |
URL | http://www.monogram.ac.uk/MgNW2019.php |
Description | Researchers Report Resequenced Vietnamese Rice Genome |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=18856 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=18856 |
Description | Rice varieties could sustain crop supplies facing climate change |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | https://phys.org/news/2021-06-rice-varieties-sustain-crop-climate.html |
Year(s) Of Engagement Activity | 2021 |
URL | https://phys.org/news/2021-06-rice-varieties-sustain-crop-climate.html |
Description | Selective sweeps during domestication and adaptation of rice subpopulations within a diverse collection of Vietnamese Rice (3rd UK Plant Evolution Meeting ) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Presented by Janet Higgins at the 3rd UK Plant Evolution Meeting on 4th Apr 2019 |
Year(s) Of Engagement Activity | 2019 |
Description | Software Carpentry 18-21 January 2021 |
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 | This workshop is designed to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. Following discussions with trainers and review of the feedback from the first online iteration of this workshop in June 2020, the programme was redeveloped to run over the course of four, shorter days (10:00-15:00). This allowed for the short tutorials to continue as before, but with more time allowed for the hands-on practical exercises with which they alternated. Lessons included: using the shell to do more in less time; automating tasks and pipelines; writing structured programs; using Git to manage and share information; how (and how much) to test programs. In particular, there was more time to spend on the breakout groups for the Git collaboration lessons, and for Python tutorials. Attendees were predominantly UK residents (88%) and all were from academic institutions, with the majority from our local community across the Norwich Research Park (94%). 100% of delegates rated the course as very good or excellent and agreed or strongly agreed that trainers were knowledgeable and approachable. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.earlham.ac.uk/software-carpentry-virtual-workshop-2021 |
Description | Software Carpentry 30 June-02 July 2020 (Virtual) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | This workshop is designed to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. In this three-day bootcamp, short tutorials will alternate with hands-on practical exercises. Lessons included: using the shell to do more in less time; automating tasks and pipelines; writing structured programs; using Git to manage and share information; how (and how much) to test programs. Usually this syllabus is taught over two days, for this online only iteration we opted to run this as a three-day programme with shorter days (10:00-15:00). Attendees were all UK residents and from academic institutions, with the majority from our local community across the Norwich Research Park. 100% of delegates rated the course as very good or excellent and agreed or strongly agreed that trainers were knowledgeable and approachable. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.earlham.ac.uk/software-carpentry-2020 |
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 | UK Rice Research Network Early Career Researcher Meeting |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Study participants or study members |
Results and Impact | Networking for early career UK rice researchers |
Year(s) Of Engagement Activity | 2020 |
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 |
Description | Untapped rice varieties could sustain crop supplies in face of climate change |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | https://scienmag.com/untapped-rice-varieties-could-sustain-crop-supplies-in-face-of-climate-change/ |
Year(s) Of Engagement Activity | 2021 |
URL | https://scienmag.com/untapped-rice-varieties-could-sustain-crop-supplies-in-face-of-climate-change/ |
Description | Untapped rice varieties could sustain crop supplies in face of climate change |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | https://www.eurekalert.org/news-releases/484861 |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.eurekalert.org/news-releases/484861 |
Description | Visit and presentation to the Bioscience Division at UCL |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | This visit was focused on exploring potential collaborations between UCL and NIAB. We are currently discussing a joint appointment and pursuing PhD funding opportunities. |
Year(s) Of Engagement Activity | 2020 |