African Plant Genomics

Patience Chatukuta

The African Plant Genomics group uses a genome-centred approach to study the diversity of under-researched subsistence crops in southern Africa together with scientists based on the African continent. The insights from our research will inform the conservation and improvement of these crops. Working with horned melon (Cucumis metuliferus) as our model crop, we study its genomic and phenotypic diversity and the basis of its resistance to root-knot nematode disease. We are also examining whether an understanding of its agronomically valuable traits can be exploited for other crops.

Using herbarium specimens together with digitisation, AI-assisted data analysis and geospatial technologies, we determine the distribution of and assess the threats to the conservation of African crop wild relatives.

Our work extends to applied functional genomics, specifically by exploring DNA-free genome editing and single activating RNAs to improve regeneration of recalcitrant plants by targeting transcription factors.

Our fields of interest are:

• Plant population diversity
• Plant-pathogen interactions
• Crop conservation and improvement

 

Horned melon diversity

We want to identify the genetic loci associated with important phenotypes and are thus candidate targets for agronomic improvement of horned melon. We are planning to generate a whole-genome assembly annotated with full-length cDNA information. We have initiated studies of genomic and phenotypic diversity in horned melon accessions from Zimbabwe, Zambia, Botswana, Malawi, South Africa, and Mozambique. In this collaborative project with the University of Zimbabwe, we will conduct regional germplasm sampling, field surveys, comprehensive phenotyping, resequencing, and genome-wide association studies.

Root-knot nematode interactions

Horned melon is resistant to root-knot nematode, which causes economically significant yield losses in cultivated cucumber, melon and watermelon, all susceptible to root-knot nematodes. We will study what the transcriptomic response of horned melon to the nematode Meloidogyne incognita can reveal about the genetic basis of resistance to root-knot disease. Apart from gene expression levels, we will also test changes in transcript isoforms when different accessions of horned melon are exposed to root-knot nematodes. This is a collaborative project with the University of Zimbabwe.

Biodiversity conservation

Crop wild relatives (CWRs) is a term for undomesticated wild species that are genetically close enough to modern crop cultivars to be used as genetic resources for crop trait improvements. We are using herbarium specimens to describe CWR distribution in Zimbabwe, aiming to ameliorate threats to CWR conservation. With our collaborators we are creating and analyzing digital images of the CWR complement of the Zimbabwe National Herbarium, creating a national CWR priority list, and identifying threats to and making recommendations for the conservation of priority CWRs to the relevant stakeholders. Together with the herbarium, we combine digital imaging with AI-assisted transcription and data validation, geo-spatial surveying, and field surveying. Digital curation of specimens will facilitate herbarium specimen-linked gene bank creation and the use of DNA from herbarium specimens for a range of genomics applications, including predictions of responses to a changing climate.

Crop improvement through DNA-free genome editing

Cassava (Manihot esculenta) is Africa's third most important staple source of carbohydrates, but efforts to improve it have been hampered by its recalcitrance to transformation and regeneration. The BABY BOOM gene is well known for boosting regeneration in many species. We are attempting to transiently alter BABY BOOM expression levels by targeting the promoter and dCas9 activation to enable efficient regeneration in this species. We combine tissue culture, transient protoplast transformation, DNA-free genome editing with Cas9 RNPs, and high-throughput amplicon sequencing to develop a scalable protocol for improving the regeneration of cassava from protoplasts using new genomic technologies.