Title Promoter Affiliations Abstract "Evolution and diversification of East African sweet potato crop wild relatives, Ipomoea L. (Convolvulaceae)." "Lars Chatrou" "Biology, Jomo Kenyatta University of Agriculture and Technology" "In Kenya, persistent drought and population increase drive up food demands, threatening food security. Advanced genomic techniques will be used to investigate the evolution and diversification of sweet potato wild relatives, with focused sampling of the understudied Eastern African species; thus, providing analytical tools for biodiversity conservation, and food security strategies in the face of climate change for the region." "The effect of crop domestication on root and rhizosphere processes." "Catherine Preece" "Plant and Ecosystems (PLECO) - Ecology in a time of change" "Crop domestication brought about many changes in the traits of plants, known as the 'domestication syndrome'. However, the impact of domestication on root processes and the rhizosphere (the soil directly surrounding the roots) remains under-studied. Root exudates and belowground volatile organic compounds (VOC) are involved in a wide range of interactions with plants and abiotic components. They also interact with rhizosphere microbes creating a specific 'rhizosphere effect' which is the difference between the rhizosphere and root-free soil in terms of the microbial community. This aspect of domestication has been overlooked and is important both for understanding the evolutionary process of domestication, and also for improving our current agricultural systems. This project aims to greatly advance our understanding of root and rhizosphere processes in crops and their wild relatives. I will focus on two root processes: (1) root exudation, which is the release of water-soluble organic compounds (including sugars, organic acids and amino acids) from the roots, and (2) root VOC emission (including monoterpenes, sesquiterpenes and isoprene). A few previous studies have demonstrated differences in root exudation and belowground VOC emission between specific wild and cultivated species, providing evidence that it is worthwhile to focus on these root traits in crop wild relatives. However, so far, there has been no systematic comparison of these processes between crops and wild plant species. This project will study, for the first time, the role of exudates, VOCs, and the rhizosphere microbiome in crop domestication. A novel greenhouse screening experiment will be established, allowing the comparison of 20 species from 10 pairs of crops and their wild relatives under controlled conditions. The hypotheses are: (1) wild relatives will have higher rates of root exudation and VOC emissions, per unit root mass, and a higher diversity of exudate compounds compared to crops; (2) crop rhizospheres will have lower diversity of microbes, compared to their wild relatives; (3) the rhizosphere effect will be explained by the quantity and composition of exudates and VOCs. Key measurements will be of root exudation quantity and composition, in situ passive sampling of belowground VOCs and DNA sequencing of rhizosphere bacteria. Result from this project will illuminate the so-far hidden domestication processes, and may guide future crop trait selection. This could include greater or more diverse exudation, or associations with beneficial soil microbes that may help maintain food production in the face of changing climate conditions and degrading soils. The requested funds will pay for the VOC and the DNA sequencing of the soil microbial community." "On a spicy journey: In search of climate resilient vanilla production systems" "Bart Muys" "Forest, Nature and Landscape, Molecular Biotechnology of Plants and Micro-organisms" "Climate change is predicted to severely affect the agricultural sector, and diversification at both crop genetic and system level will be vital in the development of climate resilient agro-systems. The tropical crop vanilla is facing a number of threats that are jeopardizing future vanilla bean supply. Being an important cash crop for many smallholder farmers around the tropics and a highly appreciated spice used in a wide range of products, there is an urgent need to enhance the resilience of the vanilla sector against projected climate change scenarios. Despite the promising role of Vanilla crop wild relatives, the wild relatives of the crop species Vanilla planifolia, in crop improvement, an in-depth evaluation and action plan to strategically integrate novel Vanilla genetics in cultivation programs with improved plant performance, especially in the face of a climate crisis, is lacking. The present project therefore aims at identifying climate resilient Vanilla species and production systems, by applying an interdisciplinary approach that combines species distribution modelling and population genetics with an experimental evaluation of species-specific stress resistance, and a participatory survey with vanilla farmers to assess the resilience of existing vanilla production systems. The results of this project will be translated into practical guidelines for the development and certification of climate-smart vanilla production systems across the Neotropics." "On a spicy journey: In search of climate resilient vanilla production systems" "Bart Muys" "Forest, Nature and Landscape" "Climate change is predicted to severely affect the agricultural sector, and diversification at both crop genetic and system level is vital in the development of climate resilient agro-systems. The tropical cash crop vanilla is facing a number of threats that are jeopardizing its future supply. Being an important crop for many smallholder farmers around the tropics and a highly appreciated spice used in a range of products, there is an urgent need to enhance the resilience of the vanilla sector against projected climate change effects. The present project therefore aims at identifying climate resilient vanilla genotypes and agroforestry systems, by applying an interdisciplinary approach that combines distribution modelling with an experimental evaluation of species-specific stress resistance, and a participatory resilience assessment of existing vanilla production systems. The results of this project will be translated into practical guidelines for the development and certification of climate resilient vanilla production systems across the Neotropics." "Exploring the potential of a newly discovered Arabidopsis gene as a molecular trait in banana for increasing resistance against fungal disease" "Bruno Cammue" "Centre of Microbial and Plant Genetics, Division of Crop Biotechnics" "Banana (Musa spp.) is one of the major crops globally, as it is an essential food source for millions of people as well as an important export product for many (sub)tropical countries. Banana production is threatened by diverse abiotic (e.g. drought, soil salinity, temperature extremes) and biotic (e.g. diseases) factors. Of relevance for this study are the two most important fungal diseases in banana; Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), and black Sigatoka, caused by Mycosphaerella fijiensis. Various approaches have been used to manage these fungal diseases, including cultural measures (e.g. removing infected materials, crop rotations), chemical and biological control agent applications, and growing resistant cultivars. Banana resistant cultivars can be generated either by conventional breeding to exploit pre-existing resistant traits in wild banana or by genetic modifications using molecular traits from banana itself or other species. Conventional breeding is hampered by very low fertility or sterility of commercial banana cultivars, making genetic modifications the most viable strategy to develop resistant banana against these fungal diseases. When this study was started, a banana genome sequence had not yet been released. Therefore, we opted for identification and isolation of molecular traits against these fungal diseases in other plant species, more specifically the model plant Arabidopsis thaliana. Through screening of activation-tagging mutants, the E3 ubiquitin ligase AtSFO1 was isolated as a potential positive regulator of the sensitivity of Arabidopsis thaliana to Foc.To gain insight into the role of AtSFO1 in plant immunity, several molecular aspects of AtSFO1 have been studied, including protein structure, ubiquitination, tissue-specific expression, subcellular localization, and expression analysis upon treatment with defense-related phytohormones In addition, we identified the banana ortholog of AtSFO1, namely MusaSFO1. Expression analysis of MusaSFO1 in banana plants infected with Mycosphaerella fijiensis showed that MusaSFO1 expression was induced in the resistant cultivar ‘Tuu Gia’ and down-regulated in the susceptible cultivar ‘Williams’. Therefore, transgenic MusaSFO1-overexpressing banana plants were generated and subjected to disease assays with Mycosphaerella fijiensis using a leaf disk bioassay.Since AtSFO1 has E3 Ub ligase activity, we further investigated which proteins in Arabidopsis are targeted for degradation. LSU1 (response to Low Sulfur 1), a protein with an unknown function and 14-3-3κ, a regulator of various biological processes in plants, were identified as interaction partners of AtSFO1 through a yeast-two-hybrid screening. Using a transient Arabidopsis leaf mesophyll protoplast system, in vivo interactions of AtSFO1-LSU1 and AtSFO1-14-3-3κ could be confirmed. However, up to now it remains uncertain whether LSU1 and 14-3-3κ are direct targets of AtSFO1 and additional experiments are needed. After further characterization of LSU1 and 14-3-3κ, including protein structure, tissue-specific expression and subcellular localization, overexpression plants of LSU1 and 14-3-3κ were challenged with Foc tropical race 4 to investigate their role in the defense response of Arabidopsis. Based on these data, a role for LSU1 and 14-3-3κ as negative regulators of defense response against Foc TR4 in Arabidopsis thaliana could be suggested.A next approach of generating transgenic banana against fungal diseases is to exploit banana endogenous molecular traits, particularly with the release of the banana sequenced genome. To study gene function, a gene silencing strategy (e.g. RNAi-induced gene silencing) is necessary. However, RNAi-induced gene silencing has not been demonstrated in banana. Therefore, using embryogenic cell suspension transformed with β-glucuronidase (GUS) as a model system, we assessed silencing of gusAINT using different intron-spliced hairpin RNA constructs. The results demonstrated that RNAi-induced gene silencing works in banana. In the future, the RNAi system can be applied to silence banana gene(s) for studying their functions in banana."