Using genome diversity for the environment, livelihoods and tropical grasslands

Pat Heslop-Harrison (with collaborators listed below) examines why it's not just humans that need better crops.

Tropical grassland grazing by cattle provides food for millions of people, and livelihoods for huge numbers of farmers and smallholders in developing countries. Pasture and rangelands have a profound influence on the environment. As the dominant vegetation over much of the world’s land, covering areas from floodplains to high uplands, grasslands are some of the most environmentally important and sensitive vegetation types. Grasslands are grazed by animals used for human food, and are often unsuitable for other agriculture so, despite the recent call from the Intergovernmental Panel on Climate Change for people to eat less meat, animal production on grasslands will remain important for economies and food supply for the foreseeable future. Furthermore, grazing is often critical to maintaining landscapes and maximizing grassland biodiversity. Grasslands provide ecosystem services such as stabilizing soil, preventing erosion, and purifying and slowing the flow of water. It is vital that grasslands are as productive and environmentally sustainable as possible. Farming must be efficient to minimise land use while ensuring reliable food production and maintaining livelihoods in a changing climate.

Forage grass flower
Forage grass flower, Brachiaria. Photo: Pat Heslop-Harrison.

Even small improvements in the performance of pasture by genetic improvement of grasses can deliver both economic and environmental benefits, whether through the impact of the grasses themselves, including the reduction in use of herbicide, pesticide and fertilizer, or through reducing pressure to increase farmed areas. Better grazing can reduce the need for growing field crops, about a third of which are fed to animals. Improvement of grasses can come from exploiting genetic biodiversity, finding and bringing together traits of ecological benefit and increased productivity. Our research project involves a partnership between CIAT (The International Center for Tropical Agriculture) based in Colombia, and the UK institutions, University of Leicester, Rothamsted Research, Earlham Institute and the Centre for Ecology & Hydrology. We are taking a three-pronged approach to improving tropical forage grasses, with a focus on the Panicum and Brachiaria (Urochloa) genera: we are measuring the genetic diversity present in the species; identifying critical traits related to environment, productivity, and the rural economy; and developing improved approaches for breeding and selection, to identify the best characters that will improve grass varieties for farmers.

As well as productivity and disease resistance, we are looking at the importance and genetic basis of a range of characters related to the environment and sustainability. Our work is of global importance but in the short-term will help the world-class grass breeding programme at CIAT. Traits to be investigated include genetic characteristics related to soil nitrification, drought resistance, waterlogging tolerance, allelopathy (how plants compete with neighbours using their own chemicals), and insect resistances (particularly to the sap-sucking spittlebug). We will also look at grass genetics related to grazing animals such as leaf lipid content, which affects cow methane (greenhouse gas) emissions, and cell wall modifications affecting digestibility. Traits such as grass productivity and digestibility determine how many cattle the pasture can support, and increased production reduces pressure to convert biodiverse natural habitats such as forests to farmland. Our project will also provide an analysis of reasons why farmers do not use improved grass seed; this analysis will provide key information to ensure the best use of the knowledge gained during the project to support future grass breeding efforts at CIAT. This project, therefore, helps economic development by improving livelihoods and the environment for farmers and wider communities.

CIAT has one of the most comprehensive genebanks of the tropical forage grasses, and these germplasm resources are central to finding new and useful characters to exploit. These resources are available for the benefit of the world. Since the Nobel Prize winning work of Norman Borlaug at CIAT’s sister institute, CIMMYT (International Maize and Wheat Improvement Center) based in Mexico, we have seen the positive global impact of genetic improvement. In our project, we have measured the diversity of all the genes in more than 10% of the germplasm collection. This huge amount of data – well over 500 billion DNA bases –was released publically in January 2019 (http://www.ncbi.nlm.nih.gov/bioproject/513453). Another challenge is working out which plants have the potential to be crossed together for breeding and the next phase of the project we will use modern techniques to work out which are the best grasses that can used for breeding programs. We will use information about the grass genes to develop a genotyping ‘platform’ which will speed up the methods for choosing plants to act as parents for producing improved varieties. Genotyping platform technology is revolutionising plant breeding and our project will enable us to apply genotyping and molecular assisted breeding technology to tropical forage grasses.

As Dr Ruben Echeverria, Director General of CIAT, has written, “Livestock provides much of the protein needed for the balanced nutrition of the world’s population and is an important part of the economy in rural areas. At the same time, it is usually associated with environmental problems such as deforestation and high emissions of greenhouse gases. We believe that sustainable intensification of livestock production will reduce the environmental impact while responding to the requirements of protein food of a growing population worldwide.” Professor Alison Goodall, Head of Department of Genetics and Genome Biology in the University of Leicester, UK, adds “The proposed research aligns strongly with the major themes of food security and research that supports the economic development of developing countries, generating solutions to global challenges through world-class research and impact activities.”

Breeding better crops is a long-term undertaking, and CIAT already has breeding pipelines for tropical forage grasses. Our project is designed to supplement and accelerate breeding by exploiting wide biodiversity and the latest cost-efficient, genomic technologies, leading via improvements in forage grasses, to increased food security, reduction of rural poverty, and efficient, sustainable use of land as pasture.

Acknowledgements

This research is funded by the UK Biotechnology and Biological Sciences Research Council through the RCUK-CIAT Newton-Caldas Fund Sustainable Tropical Agricultural Systems Programme pump-priming award “Exploiting biodiversity in Brachiaria/Panicum tropical forage grasses using genetics to improve livelihoods and sustainability” BB/R022828/1.

The project is a collaboration between co-PIs Dr Rowan Mitchell (Rothamsted Research), Dr Jill Thompson (Centre for Ecology & Hydrology CEH), Dr Jose de Vega (Earlham Institute) and Pat Heslop-Harrison (University of Leicester) with particular contributions to the research from Dr Paulina Tomazewska (Leicester) and Dr Till Pellny (Rothamsted). The partners from CIAT involved in the research are Dr Michael Peters, Dr Valheria Castiblanco, Dr Jacobo Arango, Dr Stefan Burkart, Dr Lou Verchot, Dr Joe Tohme, and Dr Juan Andres Cardoso.

Further reading

Alix, K., Gérard, P. R., Schwarzacher, T., & Heslop-Harrison, J. S. (Pat). (2017). Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. Annals of Botany, 120(2), 183–194. https://doi.org/10.1093/aob/mcx079

Buckley, H. L., Case, B. S., Zimmerman, J. K., Thompson, J., Myers, J. A., & Ellison, A. M. (2016). Using codispersion analysis to quantify and understand spatial patterns in species-environment relationships. New Phytologist, 211(2), 735–749. https://doi.org/10.1111/nph.13934

De Souza, W. R., Martins, P. K., Freeman, J., Pellny, T. K., Michaelson, L. V., Sampaio, B. L., … Molinari, H. B. C. (2018). Suppression of a single BAHD gene in Setaria viridis
causes large, stable decreases in cell wall feruloylation and increases biomass digestibility. New Phytologist, 218(1), 81–93. https://doi.org/10.1111/nph.14970

Hogan, J. A., Zimmerman, J. K., Uriarte, M., Turner, B. L., & Thompson, J. (2016). Land-use history augments environment-plant community relationship strength in a Puerto Rican wet forest. Journal of Ecology, 104(5), 1466–1477. https://doi.org/10.1111/1365-2745.12608

Hyde, L. S., Pellny, T. K., Freeman, J., Michaelson, L. V., Simister, R., McQueen-Mason, S. J., & Mitchell, R. A. C. (2018). Response of cell-wall composition and RNA-seq transcriptome to methyl-jasmonate in Brachypodium distachyon callus. Planta, 248(5), 1213–1229. https://doi.org/10.1007/s00425-018-2968-9

Kosina, R., & Tomaszewska, P. (2015). Variability of breeding system, caryopsis microstructure and germination in annual and perennial species of the genus Brachypodium P. Beauv. Genetic Resources and Crop Evolution, 63(6), 1003–1021. https://doi.org/10.1007/s10722-015-0297-4

Santos, F. C., Guyot, R., do Valle, C. B., Chiari, L., Techio, V. H., Heslop-Harrison, P., & Vanzela, A. L. L. (2015). Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses. Chromosome Research, 23(3), 571–582. https://doi.org/10.1007/s10577-015-9492-6

Worthington, M., Heffelfinger, C., Bernal, D., Quintero, C., Zapata, Y. P., Perez, J. G., … Tohme, J. (2016). A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens. Genetics, 203(3), 1117–1132. https://doi.org/10.1534/genetics.116.190314