Digital Cassava Genebank - Phase 1
Lead Research Organisation:
National Institute of Agricultural Botany
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
1) Elucidate the genetic makeup of the global cassava collection held at the CIAT genebank.
Genotyping-by-sequencing data from the DArT-seq platform will be available for 4,000 genebank
accessions by the end of 2016. We will analyse these data to reveal the genetic relationships
between these accessions and to provide a molecular framework for trait-association studies.
2) Assemble and deploy a foundational suite of software tools for a Digital Cassava Genebank. We
will deploy the Germinate data warehouse and associated software tools for storing passport,
characterisation, and GBS data, linked to Digital Object Identifiers (DOI) of genebank accessions
where available. We will develop pilot software that enables Germinate to communicate with, and
automatically upload data from GRIN-Global.
3) Whole-genome sequence a group of high-value accessions. We will sequence a set of frequentlyused
cassava accessions, assemble reads, call variants and deploy appropriate browsing tools.
4) Capacity building and scientific exchanges. Two research staff from CIAT will visit NIAB and SRUC
for training in quantitative genetics and bioinformatics applications. Two PDRAs from SRUC and NIAB
will visit CIAT to take stock of passport and characterization data to be uploaded to Germinate and
to demonstrate the approaches and results from the GBS data analyses.
Genotyping-by-sequencing data from the DArT-seq platform will be available for 4,000 genebank
accessions by the end of 2016. We will analyse these data to reveal the genetic relationships
between these accessions and to provide a molecular framework for trait-association studies.
2) Assemble and deploy a foundational suite of software tools for a Digital Cassava Genebank. We
will deploy the Germinate data warehouse and associated software tools for storing passport,
characterisation, and GBS data, linked to Digital Object Identifiers (DOI) of genebank accessions
where available. We will develop pilot software that enables Germinate to communicate with, and
automatically upload data from GRIN-Global.
3) Whole-genome sequence a group of high-value accessions. We will sequence a set of frequentlyused
cassava accessions, assemble reads, call variants and deploy appropriate browsing tools.
4) Capacity building and scientific exchanges. Two research staff from CIAT will visit NIAB and SRUC
for training in quantitative genetics and bioinformatics applications. Two PDRAs from SRUC and NIAB
will visit CIAT to take stock of passport and characterization data to be uploaded to Germinate and
to demonstrate the approaches and results from the GBS data analyses.
Planned Impact
unavailable
People |
ORCID iD |
| Sarah Dyer (Principal Investigator) | |
| David Marshall (Co-Investigator) |
| Description | We have explored the genetic diversity of 3,977 accessions (64%) of CIAT's cassava collection of 6,155 accessions. We have developed a collaboration with IITA to extend this analysis to jointly explore and compare both cassava collections held at CIAT and IITA, to understand the relatedness of the accessions and of the collections. |
| Exploitation Route | These data will allow the cassava genebank managers to better understand and maintain the collections in light of genetic redundancy between accessions within and across collections, safety backups, prioritisation for sample cryopreservation and definition of core subsets. These data will also allow better use of the genebank materials for researchers and breeders as we have a greater understanding of the genetic diversity available for use, and the genotypic data can be used for association analyses by genebank users. |
| Sectors | Agriculture Food and Drink |
| Description | The genotyping data is available to help genebank managers (a) identify and eventually remove genetically redundant accessions, (b) prioritise accessions for cryopreservation, (c) identify a robust and informative marker subset to incorporate genetic-identity testing in genebank workflows, and (d) select materials of interest for users e.g. researchers and breeders. |
| First Year Of Impact | 2017 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Title | Cassava Germinate instance |
| Description | Germinate is a generic plant genetic resources database which offers facilities to store both standard collection information and passport data along with more advanced data types such as phenotypic and genotypic data. An instance has been installed and populated at CIAT for testing purposes. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | This model has allowed CIAT to gain experience installing and populating the database for cassava, and is helping them to evaluate the use of this resource for both cassava and CIAT's other mandate crops. |
| Title | DArT genotyping data |
| Description | We have performed quality control and analyses of DArT genotyping data from CIAT's cassava collection for 3,977 accessions |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | We have shared this resource with researchers at CIAT and IITA. A collaboration has been developed to jointly analyse this data set and a similar data set produced by IITA, including a collection from East Africa. |
| Title | Manihot esculenta draft genome assemblies |
| Description | We used whole genome sequencing to develop draft genomic assemblies for 25 diverse accessions of Manihot esculenta from CIAT's genebank |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | These assemblies have allowed us to explore the diversity between 25 different domesticated cassava genomes. |
| Description | IITA |
| Organisation | International Institute of Tropical Agriculture |
| Country | Nigeria |
| Sector | Charity/Non Profit |
| PI Contribution | We are providing bioinformatics expertise with genomic and genotyping data. |
| Collaborator Contribution | Our partners are providing expertise and access to data and Manihot samples |
| Impact | This collaboration resulted in a month long visit of an IITA researcher to NIAB-EMR to perform joint-analyses on cassava genotyping data. In addition a pump-priming award has been made to develop a capture for Manihot sequences. |
| Start Year | 2019 |
| Description | SRUC |
| Organisation | Scotland's Rural College |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have contributed bioinformatics analyses such as performing data QC, diversity analyses and genome assemblies for the cassava DArT and whole genome data. |
| Collaborator Contribution | SRUC have provided software development, training and support setting up a Germinate instance for our collaborators in CIAT's genebank, |
| Impact | - Training in Germinate software/database for CIAT researcher as part of Digital Cassava Genebank project - Test instance of Germinate installed and populated with cassava data at CIAT |
| Start Year | 2017 |
| Description | Argentinean cassava workshop December 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented this project at a Cassava workshop with Argentinean academics and industry linked to cassava production, held as a side meeting of the Argentinean Conference on Bioinformatics and Computational Biology. The workshop included round table group discussions to identify opportunities and threats for cassava production in Argentina. |
| Year(s) Of Engagement Activity | 2017 |
| Description | CIAT visit 2018 |
| 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 | We met with CIAT's genebank staff, trials staff and breeders to promote awareness of the resources being developed and ensure user engagement through a series of small meetings |
| Year(s) Of Engagement Activity | 2018 |
| Description | Divseek meeting flash presentation Jan 2018 |
| 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 | A flash presentation was given during the annual DivSeek meeting in Jan 2018, San Diego describing the Digital Cassava Genebank. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Divseek workshop presentation PAG 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A presentation was given within the DivSeek workshop describing the Digital Cassava Genebank project and highlighting best practices for large-scale genotyping projects for germplasm collections. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/31138 |
| Description | EBI visit |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | We hosted a visit from EMBL-EBI Strategic Partnership Office to explore opportunities to collaborate within the AgriTech sector |
| Year(s) Of Engagement Activity | 2018 |
| Description | Grand Challenges meeting |
| 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 | I was invited to attend the Crop Research workshop at the Bill & Melinda Gates Foundation Grand Challenges meeting where I presented the project and contributed to discussions. |
| Year(s) Of Engagement Activity | 2017 |
| Description | PHG meeting at Cornell |
| 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 | A Post-graduate researcher from NIAB and a staff member from CIAT visited Cornell and took part in a workshop on the Practical Haplotype Graph (PHG), helping to generate a PHG for cassava |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation PAG 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Plant and Animal Genome conference in San Diego in January 2018 which has more than 3000 attendees, presenting the resources developed within this project. The poster was displayed within the 'cassava' section which facilitated engagement with cassava researchers from around the world. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/29997 |
| Description | Press Release Cassava projects |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | We made a press release announcing the project via institute websites and social media. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.niab.com/news-views/news/news-boosting-breeding-of-carbohydrate-heavyweight-cassava |
| Description | Press Release NIAB-IITA cassava joint analysis |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We released a news item describing the collaboration via institute website and social media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.emr.ac.uk/news-articles/exploration-of-the-global-diversity-of-cassava-manihot-esculenta-... |
| Description | Visit to NRI |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented the research to a multi-disciplinary group of researchers from the Natural Resources Institute to raise awareness of our research and identify areas of potential collaboration across disciplines |
| Year(s) Of Engagement Activity | 2018 |