Cutting-edge genomics to unravel the evolutionary history of minor crops

  • Hanin Ahmed

Student thesis: Doctoral Thesis


Humanity faces the grand challenge of having to produce nutritious food for a growing global population. Genomics has provided powerful tools to accelerate crop improvement. In particular, genomics facilitates the diversification of agriculture, allowing to ‘tap’ into genetic diversity that has been lost during domestication and modern breeding. This PhD dissertation aims to utilize recent advances in DNA sequencing technologies to establish high-quality genomic resources for two minor cereal crops; fonio millet and einkorn wheat. Fonio is a drought-tolerant, fast-maturing cereal crop native to West Africa and adapted to nutrient-poor and sandy soils. This minor crop holds the potential for sustainable grain production in desert environments. In chapter 2, we present a chromosome-scale reference assembly of a tetraploid fonio accession. In addition, we re-sequenced 183 wild and cultivated fonio accession covering a wide geographic range. We found that fonio genetic diversity is shaped by geography, climate, and ethnolinguistic factors, reflecting the high cultural value of fonio across West Africa. We identified two genes associated with seed size and shattering that are under selection and might serve as direct targets for rapid fonio improvement by genome editing or chemical mutagenesis. The second crop investigated in this dissertation is einkorn (Triticum monococcum), a diploid relative of modern pasta and bread wheats. Einkorn can serve as a reservoir to increase the genetic diversity of bread and pasta wheat cultivars. In chapter 3, we generated highly contiguous chromosome-scale assemblies of one wild and one domesticated einkorn accession using PacBio circular consensus sequencing. The high contiguity of the assemblies enabled us to resolve a magabase-sized tandem duplication and to study centromere structure. Our results show that einkorn centromeres are highly dynamic, including ancient and recent centromere shifts caused by inversions. We also re-sequenced 219 wild and domesticated einkorn accessions, which unraveled the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions following domestication. Taken together, this dissertation provides valuable insights into the evolutionary history of minor cereal crops while establishing genomics resources for crop improvement.
Date of AwardNov 2022
Original languageEnglish (US)
Awarding Institution
  • Biological, Environmental Sciences and Engineering
SupervisorSimon Krattinger (Supervisor)

Cite this