Contemporary Approaches to Improve the Conservation of Endangered Horticultural and Orphaned Food Security Crops

Climate change and urbanization have destroyed many urban green spaces and native habitats that support climate-adapted endangered ornamental plants and orphan food security crops. To further our understanding of the impact of habitat loss on native plants, my objectives were to: 1) characterized the microbiome of Helianthus verticillatus Small, an endangered ornamental sunflower native to the U.S.A. and 2) evaluated the population diversity and spatial structure of Coleus rotundifolius Poir (Coleus rotundifolius), a potential underutilized food security crop mainly cultivated on a small scale in Sub-Saharan Africa and Southeast Asia. The plant microbiome can buffer against anthropogenic disturbances and plant disease outbreaks that threaten the sustainability of endangered ornamental plant production in urban landscapes. However, we have a limited understanding of how ornamental plant microbiome assemblages, including the understudied flower microbiome, vary across local geographical scales and how environmental factors, such as soil physicochemical properties, drive local variation. To address this knowledge gap, we used amplicon sequencing to characterize the composition of archaeal/bacterial and fungal communities associated with the above and below-ground sections of a genetically uniform H. verticillatus cultivar ‘Denita’s Autumn Sunshine’ at three urban monitoring sites in Knoxville, Tennessee, U.S.A. Additionally, we used a culture-dependent approach to characterize the fungal communities within the leaves of H. verticillatus. Soil physicochemical properties largely explained differences in belowground microbial assembly across three sites than the various plant parts. Additionally, microbial communities associated with flower buds overlapped across sites compared to other plant tissues, indicating conserved microbial assemblages of plant reproductive organs. Most of the culturable endophytes isolated from leaves of H. verticillatus were classified as plant pathogens. For my second objective, we characterized the genetic diversity and spatial structure of Frafra potato accessions collected from Ghana and Burkina Faso using the OmeSeq quantitative reduced representation sequencing approach. We utilized a non-reference approach to identify single nucleotide polymorphisms in the Frafra potato populations. We identified low genetic variation, high inbreeding coefficient, low genetic differentiation, and weak population structure. Our findings highlight the need for improved genomic resources of orphan crops, which will provide a better resolution to delineate its population diversity.