Genomic approaches to sugarcane breeding
Lead Research Organisation:
EARLHAM INSTITUTE
Abstract
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Technical Summary
70% of the sugar produced globally originates from sugarcane. Sugarcane is grown in tropical ODA countries (Brazil, China, India, Colombia) and sugar production is a major component of their economies. As consequence, there are conventional sugarcane breeding programs in several countries that produce commercial varieties adapted to the local conditions. The average time to develop and release a new commercial sugarcane variety is 10 years. Implementing genomic approaches in breeding, particularly the use of marker assisted selection (MAS) and trait association through Genome Wide Association Studies (GWAS), would allow more efficient characterisation of natural and breeding populations, reducing this time. However, these techniques require genomic data and resources that do not exist in sugarcane to date. Our data and analysis will provide the breeders with the fundamental genomic resources required to start using MAS and GWAS in sugarcane breeding worldwide
Planned Impact
unavailable
Publications
De Vega J
(2019)
Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth
in PLANTS, PEOPLE, PLANET
Trujillo-Montenegro JH
(2021)
Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid.
in Frontiers in plant science
| Description | This project is an industrial collaboration with Colombian sugarcane producers. Actual sugarcane cultivars used for sucrose production result from several backcrossing cycles between S. officinarum x S. spontaneum hybrids and their ancestor S. officinarum. This has resulted in complex genomic architecture and population structure that makes tracing haplotypes very complicated. With that in mind, we sequenced the whole genome of 220 Saccharum accessions in this project. The dataset of 220 accessions includes accessions from the six Saccharum species, hybrids from several improvement programmes (mainly from the Colombian one), and samples from 28 countries. It notably contains 189 sugarcane hybrids from 18 breeding programmes in 15 countries (Australia, Barbados, Brazil, Colombia, India, Indonesia, Mauritius, Mexico, Argentina, Peru, Puerto Rico, Dominican Republic, South Africa, USA and Venezuela). All the samples were sequenced to coverage of ~2X and analysed to select a subset of 57 samples representative of the global diversity (The "global sugarcane diversity panel") that were further sequenced to coverage of ~10X. Using this new "global sugarcane diversity panel", we found two key findings: 1) We characterised the genetic diversity in elite sugarcane hybrids used for sucrose production in different countries; genetic diversity plays an essential role in the survival and adaptability of a species. We hypothesised that most actual sugarcane breeding programs rely on the intercrossing of elite cultivars that would derive from only 15-20 of these early S. officinarum x S. spontaneum hybrids. We concluded there is, indeed, a need to use novel "donor" accessions we identified as the source of diversity since the sugarcane gene-pool is pretty narrow. In other words, there is a need to bring novel material to the breeding activities to improve the adaptability of sugarcane to guarantee the sucrose's production chain under increasing global pressures such as climate change. 2) The complexity of the species has limited the generation of fundamental genomic resources. For example, the reference genome of a sugarcane genotype (a tetraploid S. spontaneum variety) was just completed in 2018. This dataset and analysis, given sugarcane's complexity and size, could only be achieved by an international collaboration. Using the great resources available at Earlham Institute in the UK, we have identified the number, pattern, and origin of these elite hybrid materials' introgressions. |
| Exploitation Route | Skills building between in our groups: A researcher from Cenicana did a 3-month internship in the Earlham Institute during 2018, which was followed by several short visits of a postdoctoral researcher from Earlham Institute to Cenicana in 2019 (interrupted in 2020, but planned for 2021). Following-up on these internships, we unsuccessfully applied for further funding (British Council's Newton Fund). Sugarcane breeders in Colombia: This project collaborates with the Colombian Sugarcane Research Centre (Cenicana). Sugarcane is one of the main cash crops in Colombia, contributing to post-conflict economic development. Our findings supported our hypothesis that sugarcane has minimal adaptability. Our results will inform and influence our Colombia partners' breeding strategy (Cenicana), for example, on the varieties that are the source of greater diversity within the collection. Sugarcane breeders in other developing countries: We have produced one of the most extensive and complex analyses and datasets for a key crop species for several developing countries. This offers an opportunity to engage with further collaborations overseas. Before that, the results would ideally need to be made available to breeders in a more practical way for them, for example, to design markers quickly. Our group is directly leveraging on this project to interact and engage with new partners working on sugarcane in Brazil, Kenya, India and China; and promoting knowledge exchange and future projects with those countries. Computational biologist: As part of this project, we improved methods for accurate diversity analysis, genome architecture profiling, and allele expression analysis in complex aneupolyploids. However, because of the limited length of the project (less than a year), we still pending to complete the dataset's computational analysis to catalogue the polyploidy, karyotypes, haplotype structure and ancestors contributions; and identify signatures of selection in the sugarcane hybrid genomes. Plant researchers: Because the sugarcane hybrids have been selected independently in different countries for the same trait, high sucrose content, this dataset is an ideal model to compare the effect of independent selection events in a polyploid system from a fundamental research point of view. The selection of different genomic regions for a single trait has been probed in simpler models, as seed size in rice. |
| Sectors | Agriculture Food and Drink |
| URL | https://growcolombia.org/home/valle-del-cauca/ |
| Description | Sugar is a global industrial commodity with complex supply chains. To date, 80% of the sucrose produced globally comes from elite sugarcane hybrids, mostly grown in tropical developing countries. The project built from a collaboration with the Colombian Sugarcane Research Centre (Cenicana). Sugarcane is one of the main cash crops contributing to Colombia's post-conflict economic development after the peace agreement with the FARC in 2016 (Just months before the start of the project). Rising patterns of extreme weather are challenging food security. Climate risks to food security are more remarkable in tropical regions, drought severity in particular. For example, tropical south America experimented the most severe droughts in the last century in 2005, 2010 and 2016. This scenario with reduced water availability is particularly relevant to finding the fine-tuning between enhancing the production of food products and improving resource use efficiency and better environmental outcomes. The project's main aim was to characterise the genetic diversity in elite sugarcane hybrids used for sucrose production in different countries. We concluded there is, indeed, a need to use the "donor" accessions we identified as the source of diversity since the sugarcane gene-pool is pretty narrow. In other words, there is a need to bring novel material to the breeding activities to improve the adaptability of sugarcane to guarantee the sucrose production chain under increasing global pressures. As an example of a downstream impact, Colombian producers are testing an automatic drip irrigation system and more sustainable water management regimes that require new sugarcane varieties to maintain the yielding. Our dataset will contribute to inform this and can contribute to inform equivalent projects in the future. However, it is essential to keep in mind that farmers would be taking this development not earlier than 8-10 years from this initial investment. In addition to contributing to global food security, our project has provided direct economic benefit to the UK through guarantee the sucrose production chain, stable prices of sugar, improved quality and safety, and increased trade and exports. In the UK, 25 % of the sugar production, approximately half a million tonnes a year, comes from imported sugarcane. Several UK companies have publicly committed themselves to source their sugar from sustainable agriculture (See "Bonsucro Standards"). To date, our collaboration is active and still focused on Colombia. This collaboration between our group and the sugarcane research centre is growing as part of the Earlham Institute; further funding £6.5M RCUK-GCRF award for capacity building in Colombia. Our group in the Earlham Institute has also obtained additional funding to work in crops in Colombia, as detailed in the project's outputs list, so contributing to the bioeconomy and capacity building of Colombia. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Description | Chair GCRF CABANA's advisory board |
| Geographic Reach | South America |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Chair of the board (JDV). Advising CABANA's executive team on recommendations to accelerate the implementation of data-driven biology in the region by creating a sustainable capacity-building programme. CABANA is a capacity strengthening project for bioinformatics in Latin America by an international consortium of ten organisations. CABANA is funded by the Global Challenges Research Fund (GCRF). |
| URL | http://cabana.online |
| Description | GCRF CABANA's advisory board |
| Geographic Reach | South America |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Advising CABANA's executive team on recommendations to accelerate the implementation of data-driven biology in the region by creating a sustainable capacity-building programme. CABANA is a capacity strengthening project for bioinformatics in Latin America by an international consortium of ten organisations. CABANA is funded by the Global Challenges Research Fund (GCRF). |
| URL | http://cabana.online |
| Description | Developing capabilities in high performance digital infrastructure for data intensive scientific innovation in Colombia |
| Amount | £29,500 (GBP) |
| Funding ID | IAPP18-19\294 |
| Organisation | Royal Academy of Engineering |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 12/2020 |
| Description | GCRF-IAA |
| Amount | £15,000 (GBP) |
| Funding ID | BB/GCRF-IAA/05 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2016 |
| End | 05/2017 |
| Description | Leverage Yellow Common Bean Native Variety Liborino as a bioproduct for the sustainable and peaceful socioeconomic development of the rural communities in Colombia |
| Amount | £49,852 (GBP) |
| Funding ID | 527023146 |
| Organisation | British Council |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 10/2021 |
| Description | Meeting policy challenges for a responsible biodiversity based bio-economy in Colombia |
| Amount | £126,874 (GBP) |
| Funding ID | EP/T025026/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2020 |
| End | 05/2020 |
| Description | Preserving, Restoring and Managing Colombian Biodiversity Through Responsible Innovation |
| Amount | £5,332,079 (GBP) |
| Funding ID | BB/P028098/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 12/2020 |
| Title | Whole-genome resequencing of 220 sugarcane accessions representative of the global diversity |
| Description | Whole-genome resequencing of 220 sugarcane accessions representative of the global diversity. The dataset includes 15 S. officinarum, 7 S. barberi from 3 subspecies, 5 S. sinense from 2 subspecies, 1 S. spontaneum, and 3 Erianthus genotypes. These include 2 samples from Papua New Guinea and 1 from India, hypothetical centers of origin of the species. The dataset also includes 189 sugarcane hybrids from breeding programmes in 15 countries: Australia, Barbados, Brazil, Colombia, India, Indonesia, Mauritius, Mexico, Argentina, Peru, Puerto Rico, Dominican Republic, South Africa, USA and Venezuela. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | 57 samples sequenced to a coverage of ~10X for genome composition analysis. All 220 samples sequenced to a coverage of ~2X for population structure analysis. The data has been shared with the Colombian sugarcane breeding institute, that is making (confidential) use of the data for breeding. |
| Description | Colombian Sugarcane Research Centre (CENICANA) |
| Organisation | Colombian Sugarcane Research Center |
| Country | Colombia |
| Sector | Public |
| PI Contribution | We have sequenced and analysed a collection of sugarcane accessions from around the world from samples provided by different collaborators, but specially from the Colombian Sugarcane Research Centre (CENICANA). |
| Collaborator Contribution | Provided sugarcane accessions, including elite varieties they have breeded during the last 10 years. |
| Impact | Dataset comprising 220 sugarcane whole-genomes |
| Start Year | 2017 |
| Description | University of Los Andes, Universy del Rosario and Earlham Institute (RAEng partnership) |
| Organisation | Del Rosario University |
| Country | Colombia |
| Sector | Academic/University |
| PI Contribution | This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng. |
| Collaborator Contribution | This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng. |
| Impact | two training workshops held at Uniandes campus in 2019 one Data Science summer school in 2020 |
| Start Year | 2020 |
| Description | University of Los Andes, Universy del Rosario and Earlham Institute (RAEng partnership) |
| Organisation | University of the Andes |
| Country | Colombia |
| Sector | Academic/University |
| PI Contribution | This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng. |
| Collaborator Contribution | This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng. |
| Impact | two training workshops held at Uniandes campus in 2019 one Data Science summer school in 2020 |
| Start Year | 2020 |
| Description | Visiting researcher at Cenicaña (Dr Nasmille L Larke-Mejia) |
| Organisation | Centro de Investigación de la Caña de Azúcar de Colombia |
| Country | Colombia |
| Sector | Charity/Non Profit |
| PI Contribution | As a postdoctoral researcher for the GROW Colombia project, I will be analysing the sequence data of the experiment. This collaboration began in 2019 with the planning of the experiment, the fieldwork was done in 2020 and we will analyse the sequence in 2021. |
| Collaborator Contribution | Our Colombian collaborators have engaged and contributed to the experimental plan, search for the appropriate sampling sites, search of other national collaborators to work with to achieve the objectives of the project. Because of COVID we were not able to travel to Colombia to do some of the field work in April and September 2020. Our collaborators have been proactive in looking for solutions, looking for people inside the organization that could do all the sampling and doing the essential lab work and DNA extractions. |
| Impact | Application for further funding with the Newton Fund (unsuccessful) |
| Start Year | 2019 |
| Description | 'Soil health for the future' blog for the Society for Applied Microbiology |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | Blog written for the 'Plant microbe interactions' conference organized by the Society for Applied Microbiology. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://sfam.org.uk/resource/soil-health-for-the-future.html |
| Description | EI Innovate Day 3: Accelerating plant breeding with next generation genetics, genomics, and epigenetics. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Assessing crop diversity and metagenomics as a resource for breeders - crop diversity; how we link genebanks with crop improvement |
| Year(s) Of Engagement Activity | 2020 |
| Description | How to communicate science on climate change? ¿Cómo comunicar la ciencia del cambio climático? |
| 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 | Media (as a channel to the public) |
| Results and Impact | De Vega J,Arango J,Fog L,Calzadilla L; Virtual Press Conference. British Council Colombia. Bogota, 2021. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Orphan Crops: the neglected side of food security & 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 | Blog interview to PI and PD working on this project about their work on orphan crops, and the importance of research about orphan crops. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/orphan-crops-neglected-side-food-security-climate-change |
| Description | Virtual Summer school in HPC, and bio and data sciences in Colombia |
| 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 activity consisted of five days of cutting-edge training on core skills for HPC, data science and data analytics delivered through the videoconference tool "Zoom" and targeted to Colombian researchers. Our Summer School provided a unique opportunity to attend state-of-the-art training delivered by world-leading academics and industry partners from around the globe, practising hands-on exercises lead by renowned experts, and networking with peers in an invaluable forum for knowledge exchange. The event had 35 attendants, split almost equally between students vs. graduate/senior/technical staff. As in the previous event, we observed under-representation of female participants and speakers (4/16, 25%) despite our effort to invite female speakers. In our future planning, we need to more energetically tackle the historical female representation in the computational and data sciences. We decided to add a cheap registration fee (£35) to prevent the no-show problem we had observed in other events, but we waive the fees for several students when requested. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://cybercolombia.org/summer-school-2020/ |