Project highlights

  • Develop an evolutionary, genomic and trait framework for biodiversity in the tropical forage grass genus Urochloa
  • Integrate genomic, ecological and phylogenetic studies of the germplasm pool of the crop and wild relatives including diploid and polyploid species
  • Work within an international project involving partners in Africa and South America working towards sustainable food security in the face of climate change and biodiversity loss

Overview

More than half of the world’s agricultural land is grazing land, but tropical fodder plants receive little attention. Their relationships and biodiversity are poorly understood. The Urochloa (Brachiaria) group of African grasses were brought to South America as forages and the now domesticated forage crops are important for sustainable animal production by smallholders. Within this well-demarcated PhD project we can answer critical questions about the relationships of wild African Urochloa species to the cultivated diploids and polyploids, the processes of domestication, their biodiversity, germplasm resources (in forage crops and their wild relatives), and the occurrence of genetic bottlenecks during speciation. Previous work has shown that Urochloa brizantha, U. decumbens, U. ruziziensis and U. humidicola form a complex polyploid series of uncertain origins. Work within a Global Challenges Research Fund (GCRF NERC/BBSRC)  project (involving the three supervisory team members) has shown genome constitutions of polyploids, but we need to expand our work to unstudied related wild species, and define which species have provided donor diploid genomes. No phylogenetic reconstruction of Urochloa has been attempted, and the work will build a framework based on DNA and morphology, integrated with geographical, ecological and environmental data, allowing exploitation of genetic resources in breeding for sustainability now and under conditions of climate change, land-use pressures and biodiversity loss.

Over the last 200 years grass taxonomists at Kew have built the classification system for African grasses, and the Kew herbarium is the only comprehensive reference collection. This project will place these species in an evolutionary context, build a bridge between plant diversity research and crop science, and contribute towards developing better forage crops for sustainable agriculture. It will exploit genetic marker systems and genome-specific sequences developed at the University of Leicester, along with germplasm collections. The results will lead to measurement of biodiversity and genome compositions in the accessions, as well as defining phylogeny and taxonomic boundaries of the Urochloa species.

CENTA Flagship

This is a CENTA Flagship Project

Host

University of Leicester

Theme

  • Organisms and Ecosystems

Supervisors

Project investigator

  • Pat Heslop-Harrison, Univ Leicester
  • Maria Vorontsova, RBG Kew

 

Co-investigators

  • Paulina Tomaszewska, Univ Leicester

How to apply

Methodology

  1. Use existing DNA and RNA sequence datasets, and generate new sequences using targeted baits for taxonomically diverse genes (Angiosperms 353 gene bait system) and forage-quality related gene baits (Hanley, Pellny, Heslop-Harrison, Mitchell et al.) (20%)
  2. Phylogenomic research exploiting sequence datasets for a comparative phylogenetic analysis and reconstruction of the history of Urochloa evolution for the first time (20%)
  3. Quantify biodiversity using genes from the sequence datasets to understand within-species diversity, and make the data available to plant breeders (20%)
  4. Morphological/phenotypic trait analysis, including quantitative study of grass spikelets, leaves and ideally roots, harnessing the Kew herbarium to understand morphological diversity across space; and link data to living material and agronomic performance (including environmental-related traits), including the utility for breeding (20%)
  5. Establish the history of the genus Urochloa, identify the closest relatives of the forage crops and ancestry of polyploids, integrating morphological and molecular analyses (20%)

Training and skills

PhD work will be based at the University of Leicester (UoL) and Kew, with potential research in Africa (Madagascar/Ethiopia/South Africa) and South America (Colombia/Brazil). Students will receive training in modern quantitative taxonomic, morphological and collection methods based around RBG Kew grass taxonomy expertise; and work with wet- and dry-lab molecular biology and crop germplasm at UoL.

Both partners will provide extensive training in plant science, and have expertise in science communication (print, broadcast and social media), and international partnerships.

Skills developed are interdisciplinary and relevant to many fields in industry and academia including plant science, crop breeding, development programmes, project management, and science communication.

Partners and collaboration

This project is an equal partnership between the Genetics and Genome Biology Department, University of Leicester, and RBG Kew, building on an ongoing collaboration. Additionally, collaboration will also include CIAT (International Center for Tropical Agriculture) and the Kew-Madagascar Conservation Centre. The student will be flexibly based between the two host institutions spending approximately equal time in each, making best use of the outstanding facilities and resources at both. At UoL, supervisor PHH and PT will provide expertise in genomics, biodiversity measurement, and grass genetic improvement; supervisor MV and RBG-Kew will provide expertise on tropical grass taxonomy and collections. Both Partners have extensive collaboration with tropical partners.

Further details

Please visit the University of Leicester website for application guidance:

https://le.ac.uk/study/research-degrees/funded-opportunities/centa-phd-studentships


This is a CENTA Flagship Project

These have been selected because the project meets specific characteristics such as CASE support, collaboration with our CENTA high-level end-users, diversity of the supervisory team, career development of the supervisory team, collaboration with one of our Research Centre Partners (BGS, CEH, NCEO, NCAS) or student co-designed project. These characteristics are a CENTA priority. Studentships associated with Flagship projects will be provided exactly the same level of support as all other studentships.

Possible timeline

Year 1

Using 200 (Leicester germplasm material) and up to 25 (Kew herbarium) accessions, extract DNA for baiting and sequencing. Develop numerical taxonomy framework based on herbarium specimens. Collect data on geographical ranges of the species. Grow selection of seedlings and plants for chromosomal and genome-composition analysis, and for hybridization.

Year 2

Bioinformatic and phylogenetic analysis of DNA sequence and morphological (phenotypic) trait data. Field collection of new materials (if possible); reconstruction of polyploid origins. Correlate genetic diversity with geographical range (environment), test genome sweeps in “domesticated” lines, and measure levels of diversity.

Year 3

Using data on diversity in the accessions obtained in the first two years, with data on the phylogenetic and ecological profiles and traits, the PhD will establish a phylogeny of the genus, and identify the nature of and approaches to utilization of the biodiversity identified in germplasm. Experimental work will be conducted as necessary to fill in gaps and test hypotheses.

Further reading

Besnard, G., Christin, P.-A., Malé, P.-J.G., Lhuillier, E., Lauzeral, C., Coissac, E., Vorontsova, M.S. (2014) From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition. Journal of Experimental Botany 65(22):6711-6721

Clayton, W.D, Vorontsova, M.S., Harman, K.T. & Williamson, H. 2017. GrassBase – The Online World Grass Flora (http://www.kew.org/data/grassbase/index.html). Updated annually.

Corrêa, C.T.R., Bonetti, N.G.Z., Barrios, S.C.L., do Valle, C.B., Torres, G.A., Techio, V.H. (2020) GISH-based comparative genomic analysis in Urochloa P. Beauv. Molecular Biology Reports 47: 887-896

Hanley, S., Pellny, T., de Vega, J., Castiblanco, V., Arango, J., Eastmond, P., Heslop-Harrison, J.S., Mitchell, R. (in preparation) Allele mining in diverse accessions of Urochloa spp. tropical grasses to improve forage quality and reduce environmental impact

Heslop-Harrison, J.S. (2019) Using genome diversity for the environment, livelihoods and tropical grasslands. Available at: https://www.botany.one/2019/01/using-genome-diversity-for-the-environment-livelihoods-and-tropical-grasslands/

Keller-Grein, G., Maass, B.L., Hanson, J. (1996) Natural variation in Brachiaria and existing germplasm collections. In: JW Miles, Maass BL, CB do Valle (eds.) Brachiaria: biology, agronomy, and improvement. CIAT, Columbia, pp 16-39

Pessoa-Filho, M., Martins, A.M., Ferreira, M.E. (2017) Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. BMC Genomics 18: 516

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 Res 23: 571-582

Tomaszewska, P., Vorontsova, M.S., Renvoize, S., Ficinski, S., Tohme, J., Schwarzacher, T., Castiblanco, V., de Vega, J., Mitchell, R., Heslop-Harrison, J.S. (in preparation) Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and ancestral evolution in Urochloa (Brachiaria) species using repetitive sequences and molecular cytogenetic data

Vorontsova, M.S., Clayton, D. and Simon, B.K., 2015. Grassroots e-floras in the Poaceae: growing GrassBase and GrassWorld. PhytoKeys 48: 73-84

COVID-19

Much work involves bioinformatic analysis of DNA sequences, potentially carried out remotely using home-based computers and remote servers. With availability of some sequence data already, the project can work with these. Especially if additional species (genera) were introduced to the project, there is additional data available on NCBI Genbank and SRA Sequence Read Archive. Outsourced DNA sequencing requires only limited lab-time. The RBG Kew herbarium is a COVID-19 secure workplace; the student will be assigned to a separate herbarium bay. Fieldwork is desirable but not essential as the supervisors have already made multiple visits for trials and collections.