RCUK-CIAT Newton Fund: Exploiting biodiversity in Brachiaria/Panicum tropical forage grasses using genetics to improve livelihoods and sustainability

Lead Research Organisation: University of Leicester
Department Name: Genetics


The overall objective is economic development in Colombia by focused, science-based exploitation of biodiversity to develop new varieties of tropical forage grasses (Brachiaria and Panicum species and hybrids) to meet needs of small and medium scale farmers, and defined goals of environmental sustainability. The following objectives will generate underpinning knowledge for this aim:

- Identify ploidy of accessions to identify appropriate parents for breeding at diploid and polyploid levels across the germplasm collection for Brachiaria; development of genome-specific probes from NGS data to identify the genomic composition of polyploids and hybrids
- Identification of candidate genes implicated in determining forage quality (eg digestibility, lipid content to reduce enteric methane emissions) leading to an atlas of the allelic diversity; Gain improved knowledge of apomixis, its genes and seed production for exploitation in breeding
- RNA-seq from 30 to 40 accessions of both genera to prioritize candidate genes for breeding, building towards a pan-genome defining variation across the genera. Analyse RNA-seq data for evidence of genome interactions and differential gene expression in hybrids
- Define pull from improvements in environmental and sustainability requirements (GHG, soils/erosion, water, nutrient cycling) from forage crops; Define economic pull for defined forage grass improved characters from farmers and breeders in Colombia; Measure the economic value of traits and market sizes for improved Brachiaria seed; define measures for environmental benefits.
- Make RNAi and CRISPR-CAS9 constructs designed to modify candidate genes to improve forage quality
- Plan second and third years programme based on results
- Outputs and capacity building: Training of CIAT staff and students in UK to raise technical skills and experience; allow UK participants to gain international experience at CIAT; Prepare publications, blogs, website for farmers, policy makers, public, hold a workshop to disseminate results.

Planned Impact

ODA objectives will be developed alongside scientific aims as we (a) build a research and innovation partnership to support economic development and environmental sustainability, and (b) develop in-country research and innovation capacity for long-term sustainable growth in the post-conflict environment.
Forage grass production is critical to the livelihoods of the small and medium size farmer in tropical Colombia, with great potential to increase livestock production with low inputs, but faces major current- erosion, disease, water - and future - climate change, new diseases - challenges. Small-scale farmers have limited resources, making genetic improvement a key approach. In addition to genomics and bioinformatics, we use UK expertise in the target traits to address the scientific and crop improvement problems. We will provide training to support transfer of technology and expertise to enable implementation via staff exchanges (particularly staff and students from Colombia learning technology in the UK by undertaking research under the supervision of the UK Investigators and their research groups), collaboration and free exchange of data.
The project addresses official development assistance, ODA, objectives through its applied and scientific aims. All work is focused to support economic development and welfare, and our programme includes developing research and innovation capacity to enable long-term sustainable growth in Colombia, an OECD Development Assistance Committee "Upper Middle Income Country" with particular challenges in livestock areas, with most opportunities to benefit in the post-conflict environment, but much poverty among the rural population of farmers and labourers. Economic development and improved welfare (including their health and education opportunities) at the farmer level comes from improved crops. Even 'standing still' in terms of crop production is an enormous challenge. New disease types (biotic stress) are continuously attacking existing crop varieties, while the increasing lack of fresh water and climate change (abiotic stress) threaten current yields, and cannot be met with the unsustainable options of more land, water, crop protection chemicals and fertilizer. Indeed, national policy is to reduce the area of agriculture though sustainable intensification, leaving land spared for biodiversity. Changing farming practices threaten the environment and the social structure. By delivering understanding and approaches with appropriate training and development, our programme builds strongly on world-class strength in UK technical knowledge in genomics and bioinformatics, including germplasm, breeding, and having a pathway for delivery to breeders and farmers, identifying and meeting their challenges. We have shown how groups work together already, and embedded within our programme are management, training at various levels (where our UK Universities are all ranked among the best), dissemination and public accessibility of data, policy impacts, the importance of health and safety in the workplace, and ethical issues.

Success is measured by 1) identifying trait genes and their allelic diversity for exploitation in breeding programmes; 2) identifying genomes in polyploids and defining the ways they may be brought together to generate resilient, seed-producing, hybrids; 3) identifying traits for introduction into forage grasses with economic and sustainability advantages; 4) having a pathway for release of varieties using germplasm and new breeding approaches.

Colombian farms are formally defined as Small (1 to 50 cattle) and Medium (51-250 cattle) (National definition by FEDEGAN); these sizes of producers are open to increased production. For economic work in CIAT, we will consider trying to find a UK PhD student who would be interested in adding a case study of Colombian livestock agriculture to their project likely to be based on an African system, spending 2 up to 6 months in CIAT.
Description The Brachiaria tropical forage grasses have many genomes involved in their ancestry. We have developed genome-specific probes that enable us to determine the various genomes, and reveal those present in polyploids species and accessions, showing their ancestry and evolution, as well as aspects of repetitive DNA sequence evolution. The results are also helping resolve taxonomy in the group (Urochloa, Brachiaria, Panicum, Megathyrsus).

RNA-seq was completed on 108 samples using diverse germplasm from the international collection at CIAT. Most of the 700Gb of sequence is now on a public database. We have analysed population structure and diversity by species and genome (STRUCTURE, optimizing for large datasets). This showed (K=6 above), two clear ancestries for Brachiaria brizantha and B. decumbens, and one for B. ruziziensis. About two accessions in each species are probably misidentified.

Ploidy analysis of 362 accessions is complete, with a number now karyotyped. Little link of diversity with ploidy (2x, 4x, 6x) was found.

Allele mining of RNAseq for alleles related to cell was composition, digestibility and lipid content of forage grasses has revealed many relevant variants which will be useful for breeding.

Enormous sequence diversity is present in this collection compared to other crop species. The remarkable variation we have revealed in the germplasm suggests presence of appropriate natural variants for many candidate genes.
Exploitation Route The measurement of ploidy of the majority of the accessions in the CIAT (internationally available) germplasm collection enables rational design of within-ploidy crosses and inter-ploidy crosses to make new hybrids to enter into plant breeding trials. Diploids with promising phenotypic characteristics (eg resistances to biotic or abiotic stresses) could be subjected to ploidy duplications.

The determination of the nature of the diploid genomes, and development of a probe toolkit, complements the ploidy measurements to enable design of optimal combinations of parents to bring together in new hybrids for development of novel germplasm for farmers.

The diversity measurements made with RNA-seq are important to help enrich the diversity of breeding populations. With the ability for discovery of useful alleles, valuable combinations can be suggested for breeding targets, and the data are highly valuable to support decision making in breeding programs.

The genome-composition and RNA-seq data are immediately applicable for development of a platform for genomic breeding (or marker assisted selection), which can be applied by international organizations (eg CIAT), national breeding programmes, and commercial breeders. The results are valuable to forage breeders throughout the tropics and sub-tropics in Asia, Africa and South America.
Sectors Agriculture, Food and Drink,Environment

Description Measurements of ploidy of germplasm collection are now being integrated into the international breeding programme for tropical forage grasses at CIAT. The genome specific sequences are being used to define a robust taxonomy and phylogeny of Brachiaria/Urochloa/Panicum group of grasses. The markers developed are being used to identify unknown accessions where morphological characters are unclear. Alleles from the RNA seq are being investigated as targets for breeding and for genome editing in appropriate lines.
First Year Of Impact 2020
Sector Agriculture, Food and Drink,Environment,Other
Impact Types Societal,Economic,Policy & public services

Description H2020-MSCA-IF-2018
Amount € 212,000 (EUR)
Funding ID H2020-MSCA-IF-2018 (H2020-MSCA-IF-2018) Proposal: 844564 - OCHRE 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 06/2019 
End 06/2021
Description Newton Award: Comparing alternative technologies for genetic improvement of digestibility of Brazilian grass crops
Amount £8,225 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 03/2019
Title Genome-specific markers for polyploid tropical forage grasses 
Description Using DNA sequences, major DNA motifs specific to particular diploid genomes have been identified. Used with in situ hybridization to chromosome preparations, or in sequence bioinformatic analysis, these enable identification of the genomes in diploid grasses, and the nature of the ancestral genomes present in the polyploid accessions. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? No  
Impact Now being used to refine the taxonomy and phylogeny of the Brachiaria forage grasses; also being incorporated into breeding programmes with knowledge of genome composition. 
Title Brachiaria and environment reference library 
Description An endnote database has been created to store a reference library for published papers that deal with Brachiaria grasses and their environmental impact. These published papers are being used to extract information and write a review. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? No  
Impact No results currently available. Reference database is currently available to project team members and will be available to the wider community on publication of the review. 
Title Tropical forage grasses RNAseq 
Description RNAseq paired end reads (800 GByte) from 104 accessions (genotypes) of Center for Tropical Agriculture (CIAT) gene bank collection. The data is deposited in NCBI Bioproject Accession: PRJNA513453 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact This represents a major resource that will be exploited for many years by CIAT tropical grass breeding program, 
URL http://www.ncbi.nlm.nih.gov/bioproject/513453
Description BBC Radio Leicester discussion 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Pat Heslop-Harrison has a c. 15 minute discussion on the lunchtime/drivetime BBC Radio Leicester weekday programme. Forage grass breeding was discussed in UK and international contexts on 10 January 2019.
Year(s) Of Engagement Activity 2019
URL https://www.bbc.co.uk/radioleicester
Description Blog post 
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 A blog post for the CIAT audience was written by Pat Heslop-Harrison with all the other participants in the project: "Using genome diversity for the environment, livelihoods and tropical grasslands". (A slightly modified post, for a different audience, was posted on Botany.One).
Year(s) Of Engagement Activity 2019
URL https://blog.ciat.cgiar.org/using-genome-diversity-for-the-environment-livelihoods-and-tropical-gras...
Description Blog post - Botany.One 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A blog post for the Botany.One blog audience was written by Pat Heslop-Harrison with all the other participants in the project: "Using genome diversity for the environment, livelihoods and tropical grasslands". (A slightly modified post, for a different audience, was posted on the CIAT website). Botany One is ranked as the top botany website and blog for botanists and plant scientists (https://blog.feedspot.com/botany_blogs/), and the best blog for botany students.
Year(s) Of Engagement Activity 2019
URL https://www.botany.one/2019/01/using-genome-diversity-for-the-environment-livelihoods-and-tropical-g...
Description Presentation and discussion with seed technical working group 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Invited presentation to Herbage Seed Technical Working Group Meeting 2019

Presented potential for our plant science to feed into genetic improvement of pasture grasses
Year(s) Of Engagement Activity 2019