PEGASUS: Prediction and Exploitation of Genebank Accessions. A Study in Ugandan Sorghum
Final Report Abstract
Efficient utilisation of crop genetic resources is becoming increasingly important in order to breed sustainable, resource-efficient crops with increased productivity to feed the growing world population under fluctuating environmental constraints. Modern, high-throughput genomics methods can play a key role in characterising, evaluating and implementing plant genetic resources, however important diversity collections in developing countries often lack the resources to implement genomics tools. For example, Uganda is a major centre of diversity and domestication of sorghum, the most important cereal crop in sub-Saharan Africa and a staple food for millions of people. The Uganda national genebank harbours an extensive, unique collection of 3,333 sorghum accessions, including rare landraces and wild germplasm. These materials represent a substantial reservoir of genetic and phenotypic diversity for adaptation of sorghum crops to abiotic and biotic stress factors. However, prior to this project that diversity had not yet been systematically characterised and evaluated. Hence, this valuable crop genetic resource was not used at all so far to improve modern sorghum varieties with beneficial traits for farmers. Rapid recent advances in cost-effect genome sequencing technologies and phenotype prediction based on genome-wide DNA profiles make it theoretically possible today to generate genetic fingerprints for huge plant genebank collections even from developing countries with few resources for maintenance of plant genetic resources. In the absence of detailed information about plant traits in such collections, performance predictions based on genome profiles represent an important opportunity to preselect seed stocks which are potentially interesting for breeding from the thousands of accessions held in gene banks, and use these “genomic selected” genotypes for more detailed genetic investigations and/or breeding. In this project, the Ugandan genebank sorghum collection served as a case study for the use of “genebank genomics” to characterise valuable crop genetic resources using genome-based prediction techniques. Based on genome-wide DNA profiles of the entire collection of 3,333 seed samples, we selected a core-collection of accessions which best represents the entire genetic diversity present in the entire collection, along with a random selection of 444 accessions that were not included in the core collection. The genome data also enabled detailed classification of the 3,333 genebank accessions in regard to their racial composition and genetic diverts yin the context of a previously-genotyped global sorghum collection. This enabled us to identify genetically unique accessions from the southern highlands of Uganda which are distinct from most previously characterised sorghum collections. Despite difficulties caused by travel disruptions and lockdowns during the global Covid19 pandemic, which meant that many of the phenotypic evaluations in greenhouse and field conditions could not be completed as planned, we nevertheless collected substantial quantities of phenotype data for numerous traits of agronomic interest. These data sets were used as training and validation sets for predictions of plant performance based solely on the genome profile. The results showed that, for simply inherited traits, gnomic production enables an accurate prediction of traits of interest in non-characterised materials. Moreover, even for traits with a much more complex pattern of inheritance that are strongly impacted by environmental factors, we showed that genome-based predictions provide valuable data to preselect promising materials for breeding. For example, in a case study of interest for adapting sorghum to temperate climatic conditions in Europe, we identified previously untapped genetic diversity for adaptation to early sowing in cold, temperate growing regions of central Germany. The project presents a practical case study for management and use of valuable genebank collections in developing countries using genomic tools. It has furthermore made an important contribution to the human resource capacity of the Uganda National Genebank in plant breeding and genetics, ensuring technology and knowledge transfer to the African partner country and enabling long-term implementation of the results for African sorghum improvement. All genetic and phenotypic data associated with the Ugandan genebank sorghum collection is now freely available and breeders globally can access the seed materials associated to this material and the data within the framework of the International Treaty of the United Nations on Plant Genetic Resources for Food and Agriculture. As such the project makes an important contribution to global sorghum breeding in the face of mounting challenges to agriculture from human population growth and climate change.
Publications
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(2022) Genetic and genomic diversity in the sorghum gene bank collection of Uganda. BMC Plant Biology 22: 378
Chakrabarty S, Mufumbo R, Windpassinger S, Jordan D, Mace E, Snowdon RJ, Hathorn A
