Developing a natural variation platform for pest-resistant cassava breeding

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

Abstract

Cassava (Manihot esculenta) is the third most important source of calories in the tropics and a key staple for millions in Africa, Asia and Latin America. Predictions of rising temperatures linked to climate change favour the productivity of cassava, a crop that performs well under stressful growing conditions linked to drought and high temperatures. However, cassava is susceptible to a number of pests and diseases, and projections of movement of cassava pests linked to climate change predict substantial yield losses. As such, cassava breeders are prioritising traits linked to pest and disease resistance within their breeding programmes. Within Latin America, the largest pest and disease threats to cassava production are whitefly, cassava frogskin disease and bacterial blight. Bacterial blight is also prevalent throughout cassava growing regions in Africa and Asia. These can cause yield losses of 76-92%.

We can explore cassava's wild relatives to introduce novel disease resistance traits through conventional or molecular breeding techniques. Crop wild relatives have been used in wheat, rice, tomato, potato, sunflower and other crops to provide sources of novel resistance to pests and diseases. The Genetic Resources Program (GRP, genebank) at the International Center for Tropical Agriculture (CIAT) in Colombia currently houses ~4,900 accessions of cassava and its wild relatives. The mission of genebanks includes the conservation of materials, but also aims to make the material available for use. However having limited information for the vast majority of accessions makes it difficult for users, or even genebank managers, to select materials that may contain useful properties for breeding.

Through sequencing the genomes of cassava wild relatives we will reveal the genetic diversity of their resistance genes. In addition we will check the performance of these species against whitefly, cassava frogskin disease and bacterial blight. We will also develop novel tools to explore these datasets, making it easier for breeders to choose which wild materials to include in their programs. All the information generated through this project will be made publicly available for breeders and researchers to access via the GRP portal.

Breeders tend to be cautious about including wild materials into their breeding programs as wild species bring a mixture of desirable and undesirable characteristics into the offspring. Breeding is a slow process, and removing the undesirable traits can take many generations. Therefore, having more information about the physical and genetic characteristics of these wild species will help breeders to make the most appropriate choices of plants to use and encourage the inclusion of wild relatives to provide novel sources of pest and disease resistance into cassava.

CIAT has centres in Colombia and Vietnam, with researchers working in 53 countries worldwide. Having novel sources of pest resistance will benefit cassava breeders and growers in many countries, however we will target breeders in Colombia, Brazil, Vietnam, Cambodia and Lao People's Democratic Republic. Through the reduction of losses due to pests and diseases, this project will contribute to sustainable agriculture and increasing the resilience of food systems to climatic variability.

Technical Summary

We will explore wild relatives of cassava (Manihot esculenta) to identify novel sources of disease resistance. The Genetic Resources Program (GRP, genebank) at the International Center for Tropical Agriculture (CIAT) in Colombia currently houses ~4,900 accessions of cassava and its wild relatives. We will phenotype 100 accessions from 30 wild Manihot species for resistance to whitefly (Aleurotrachelus socialis), cassava frogskin disease (a complex of virus and phytoplasma infections) and bacterial blight (Xanthomonas axonopodis pv. Manihotis). These can cause yield losses of 76-92%.

The existing cassava reference genome remains fragmented, as such we will sequence the same accession (AM560-2) using PacBio (30x). We will assemble these long reads and integrate with the existing reference and genetic map data. We will transfer the existing annotation and reannotate the R-genes. In addition we will sequence the 100 accessions of wild Manihot (Illumina 20x) and call variants with respect to the improved reference. Unaligned reads will be assembled to produce species-specific contigs. We will also develop novel tools and visualisations, making it easier for breeders to explore these datasets and choose which wild materials to include in their programs. All the information generated through this project will be made available publicly for breeders and researchers to access via the GRP portal.

CIAT has centres in Colombia and Vietnam, with researchers working in 53 countries worldwide. Having novel sources of pest resistance will benefit cassava breeders and growers in many countries, however we will promote our new resources to breeders in Colombia, Brazil, Vietnam, Cambodia and Lao People's Democratic Republic, using CIAT's existing extension networks.

Planned Impact

Cassava (Manihot esculenta) is a globally important crop and a key staple for millions in Africa, Asia and Latin America; it is often grown under harsh conditions and in poor soil where other crops would fail. Cassava's roots and leaves are consumed as food, and cassava also has important uses for bioenergy and the production of industrial starch. Improving the disease resistance of cassava varieties will reduce yield losses globally, improving the welfare of communities dependent on this staple crop.

The direct beneficiaries from this project will be cassava researchers and (pre)breeders, as they will be able to make genomically and phenotypically informed wide crosses using cassava wild relatives. Cassava pre-breeders will have genomic information for 30 Manihot species and their phenotypes in response to three pests/diseases (whitefly, cassava frogskin disease and bacterial blight) to help make informed breeding decisions about the inclusion of wild materials. Breeders will be able to take advantage of novel sources of pest and disease resistance for their breeding programmes, and improved varieties will benefit farmers and consumers through a more predictable supply. CIAT's genebank will also benefit from the inclusion of additional genomic and phenotypic information, and novel query tools and visualisations, encouraging the use of their materials for breeding projects.

Indirect beneficiaries include researchers in other crops, as this approach may serve as an exemplar. Also genebanks for other species could benefit from the adoption of the query tools and visualisations which we will develop.

In the long term, cassava-growing regions will benefit as they face fewer losses associated with pests/disease, in particular in Latin America and South East Asia (e.g. Colombia, Brazil, Vietnam, Cambodia and Lao People's Democratic Republic). Increased yield of cassava will improve food security and public health in the face of climate change. Reduced dependency on pesticides will also provide environmental benefits.

This programme will generate new opportunities for collaborative work between NIAB and CIAT. The proposed work will directly impact the local UK community with the generation of new jobs in the field of computational biology. This collaboration will contribute to reinforce the UK's leadership in bioinformatics and genomics, translating this expertise into the breeding of a tropical crop and having a positive impact on the global economy.

Publications

10 25 50
 
Description We have generated draft genome assemblies for 100 wild relatives of cassava from across 22 species. We have developed a resource cataloging the genetic differences between these species and individuals. We have also contributed data to the development of an improved cassava reference genome for the research community. We have contributed to software improvements for the Cassava Genome Hub. We have assessed a number of these wild relatives for their response to white fly and cassava frogskin disease.
Exploitation Route Researchers and breeders will be able to explore the genetic and phenotypic data to identify accessions of interest for incorporation into their programmes
Sectors Agriculture, Food and Drink

 
Description The Hi-C data has been incorporated into the latest version of the cassava genome which is currently being finalised for public release. The improved genome will be available for use in modern breeding approaches such as genomic selection.
First Year Of Impact 2019
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Capture development and deployment to detect sequences enhancing geminivirus symptoms in cassava and its wild relatives
Amount £9,260 (GBP)
Organisation National Institute of Agronomy and Botany (NIAB) 
Sector Academic/University
Country United Kingdom
Start 09/2020 
End 04/2021
 
Title Hi-C for cassava reference 
Description We contributed long-read PacBio and Dovetail Hi-C data to develop an improved reference genome assembly for cassava with collaborators at DOE's Joint Genome Institute. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact The validation of the new reference assembly is ongoing at JGI 
 
Title Manihot draft genome assemblies 
Description We used whole genome sequencing to develop draft genomic assemblies for 100 accessions from 22 wild Manihot species 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact We have identified genetic variations between these samples and species. \we have shared this data with researchers at CIAT for joint validation. 
 
Description CIAT, cassava program and genebank 
Organisation CGIAR
Department International Center for Tropical Agriculture
Country Colombia 
Sector Charity/Non Profit 
PI Contribution We are providing bioinformatics and genomics expertise. We are working to improve the cassava reference genome.
Collaborator Contribution CIAT are providing access to cassava wild relative's materials and their associated information, performing DNA extractions and phenotyping for biotic stresses. It also provides expertise in cassava biology, access to screen houses, lab equipment and staff time.
Impact We have generated PacBio and Hi-C sequence data for the cassava reference accession AM560-2, extracted DNA from 100 cassava wild accessions for whole genome sequencing and multiplied and screened cassava wild relative accessions for phenotypic evaluations to different biotic stresses. The collaboration is multi-disciplinary involving bioinformatics and plant biology.
Start Year 2017
 
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 NCSU 
Organisation North Carolina State University
Country United States 
Sector Academic/University 
PI Contribution We have been contributing to analysis of Manihot genomic sequences.
Collaborator Contribution Our partners at NCSU have provided access to Manihot samples and information.
Impact This collaboration resulted in a successful pump-priming application to develop a hybrid capture for Manihot sequences.
Start Year 2019
 
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 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 Bellagio blog 
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 We communicated the activities and the impact of the outcome of the project in a blog
Year(s) Of Engagement Activity 2018
URL https://blog.ciat.cgiar.org/in-bellagio-experts-devise-a-global-system-to-stop-crop-diseases-in-thei...
 
Description CIAT - Cassava genomics workshop 
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 I chaired and ran the workshop at CIAT (Colombia) to mark the completion of the genomics work of the project. The workshop attract the attention of collaborators and the wider cassava genomics community.
Year(s) Of Engagement Activity 2019
 
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 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 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 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 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 Genome conference in San Diego in January 2019 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 2019
URL https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/35968
 
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 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