• Research group

De Vega Group

Exploring crop diversity and evolution to drive improvement

Jose de Vega

Research Fellow
Jose de Vega

Group activities.

Our group aims to increase resilience to the cascading effects of climate change on food production. Our strategy is to explore natural diversity in crops using forward genetics and newly produced genomic resources to narrow candidate loci and germplasm associated with tolerance to stress. Our research outputs allow reducing the time needed for better elite varieties to reach the farmers through accelerated screening (e.g. markers, genomic selection, etc.) and improved gene-pool (e.g. prioritise crosses, prevent bottlenecks, etc.). In short, we are a bridge between collections and breeding.

We collaborate with plant breeders, researchers and genebanks, especially from other BBSRC institutes, CGIAR centres, and developing countries. We are open to new challenges and interesting projects and collaborations, and strongly support open source principles and publicly available data. We deliver capacity building and develop genomic approaches for breeding, working with breeders to ensure that their needs are met.

A lot of our work involves studying the effect and genomic context of SNPs and CNVs, comparing the transcriptomic changes on different conditions, and describing the landscape of features of relevant genomes. We focus on developing genome-wide computational pipelines for the analysis of complex genomes and large populations in a cost-effective way.

Examples of our current projects include:

  • Understanding the adaptation of the tropical grass Brachiaria to acidic soil conditions in tropical africa and America, and collaborating with breeders to develop genomic resources. (Collaborating with IBERS, and CIAT in Colombia)
  • Studying the genomic and phenomic diversity of rice cultivars in Vietnam, and identifying key components involved in salinity tolerance. (With NIAB, and AGI in Hanoi)
  • Exploring the global genetic diversity of biomass crops Miscanthus and sugarcane, and the effect of domestication on their genomes and evolution (With IBERS, and the Colombian Sugarcane Research Centre -Cenicana- in Colombia).
  • In a recent RCUK project to Grow Research Capacity in Colombia, we are scrutinising the diversity of crops relevant for the economy of Colombia.

Our impact.

We are contributing to feeding a changing world. We aim to make farming more efficient through intensification and resilient management practices, maintaining or increasing production without compromising ecosystem services.

Our research fits into the Earlham Institute’s scientific focus on how selection and adaptation have driven the evolution of crop and the institute’s core expertise in data science and enabling technologies. We often focus on overseas collaborations and major subtropical crops, where the yield gaps are higher. We frequently implement previously tested tools and methods in new systems. Projects usually include capacity building activities to grow skills in data science, as a direct, impactful path to build research capital in emerging countries.

Publications.

A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses

Margaret Worthington, Juan Guillermo Perez, Saule Mussurova, Alexander Silva-Cordoba, Valheria Castiblanco, Juan Andres Cardoso Arango, Charlotte Jones, Narcis Fernandez-Fuentes, Leif Skot, Sarah Dyer, Joe Tohme, Federica Di Palma, Jacobo Arango, Ian Armstead, Jose J De Vega

Journal of Experimental Botany, eraa469 (2020).  https://doi.org/10.1093/jxb/eraa469

Evidence of selection, adaptation and untapped diversity in Vietnamese rice landraces

Janet Higgins, Bruno Santos, Tran Dang Khanh, Khuat Huu Trung, Tran Duy Duong, ..., Tran Dang Xuan, Anthony Hall, Sarah Dyer, Le Huy Ham, Mario Caccamo, Jose J De Vega

bioRxiv 2020.07.07.191981 (2020). https://doi.org/10.1101/2020.07.07.191981

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement

Jose J De Vega, Sarah Ayling, Matthew Hegarty, Dave Kudrna, Jose L Goicoechea, Åshild Ergon, Odd A Rognli, Charlotte Jones, Martin Swain, Rene Geurts, Chunting Lang, Klaus FX Mayer, Stephan Rössner, Steven Yates, Kathleen J Webb, Iain S Donnison, Giles ED Oldroyd, Rod A Wing, Mario Caccamo, Wayne Powell, Michael T Abberton, Leif Skøt

Scientific Reports 5, 17394 (2015). https://doi.org/10.1038/srep17394