Uitdagingen voor de in situ en ex situ conservatie van de genenpool van Robusta koffie (Coffea canephora) in de Democratische Republiek Congo

Food production faces significant challenges due to increasing global demand and the impacts of climate change. The growing population requires more food, while climate change introduces unpredictable weather patterns, pests, and diseases, threatening crop yields. One promising solution lies in plant breeding, particularly using crop wild relatives. These crop wild relatives, also known as CWRs, may possess usefull traits such as pest resistance and drought tolerance that are not currently present in cultivated crops. By incorporating these traits into domesticated crops, breeders can develop varieties that are more resilient to climate change and newly emerging diseases. However, crop wild relatives are themselves threatened by habitat loss, climate change, and human activities, which complicates their conservation and utilization. Two approaches can be followed to conserve CWRs: in-situ and ex-situ conservation. In-situ conservation protects the plants in their natural habitats, preserving the natural ecological interactions and evolutionary processes. However, it faces challenges like habitat loss and genetic mixing with related crops that are cultivated nearby. Ex-situ conservation involves relocating CWRs that are threatened in their natural habitat to places such as seed banks or botanical gardens. This method helps preserve genetic material, but may face difficulties with maintaining genetic diversity in the long term, and reintroducing the species into their natural habitat can be problematic because of maladaptation and increased vulnerability to pests and diseases. In-situ and ex-situ conservation are therefore complementary and must be used together to effectively preserve CWRs for future use. Coffee is the world's most popular hot beverage and a crucial export product for developing countries. The Coffea genus, belonging to the Rubiaceae family, includes 131 species, but only three are of significant economic importance. Arabica (Coffea arabica) and Robusta (Coffea canephora) dominate the market, with Arabica making up 60% and Robusta 40% of global coffee production. Coffea liberica has a market share of less that one percent and is mainly consumed locally. This thesis focuses on Robusta coffee, which is gaining popularity due to its greater disease resistance and adaptability to the changing climates. Coffea canephora is the crop wild relative of Robusta coffee. Similar to other wild relatives, C. canephora likely possesses valuable traits that could enhance coffee production, making it critical to preserve the genetic diversity of its wild populations. However, this presents challenges. Coffea canephora is native to the Congo Basin, home of the world's second-largest rainforest, which is severely threatened by human activities such as encroaching agriculture and forest degradation through logging. Little is known about the genetic diversity and population structure of wild C. canephora, complicating efforts to assess the impact of human activities on these populations and to assess its in-situ conservation status. On the other hand, also the ex-situ conservation of Robusta coffee faces challenges. A highly important centre of ex-situ conservation of Robusta coffee is the INERA Coffee Collection near Yangambi in the Democratic Republic of Congo. However, this collection has been neglected during the past decades and has never been genetically characterized, making it difficult to assess its conservation status. Therefore, to effectively protect wild C. canephora populations, the primary limiting factor is the lack of genetic knowledge. This thesis aimed to address the following questions: (i) What is the genetic population structure and genetic diversity of wild C. canephora populations in the Yangambi region of the Democratic Republic of Congo? (ii) What is the genetic diversity and structure of the INERA coffee collection in Yangambi? (iii) Is there potential genetic exchange between the cultivated material in the INERA coffee collection, local gardens, and the wild C. canephora population? To answer these questions, genetic variation in the wild C. canephora populations was quantified using Single Nucleotide Polymorphisms (SNPs) and their derived haplotypes identified through high-throughput sequencing data from Genotyping-by-Sequencing libraries. This technique was also applied to the INERA Coffee Collection, and was supplemented with data from HiPlex amplicon sequencing libraries, to assess its genetic variation. First, the genetic diversity and structure of wild C. canephora populations in the Yangambi region were investigated. This area comprised primary, secondary, and disturbed primary forest, making it an ideal location to examine the impact of forest disturbance on the genetic diversity and structure of wild C. canephora populations. Despite forest disturbance and forest regeneration, these populations maintained high genetic diversity with very limited signs of genetic erosion. Yet populations in regenerated forests exhibited lower diversity, likely due to founder effects. Overall, wild coffee population genetic structure was more influenced by geographical location than by disturbance. Next, the historically significant INERA Coffee Collection in Yangambi was genetically characterized. Using genome-wide marker sets and a multiplex amplicon sequencing assay, unique genetic fingerprints were identified and categorized into three origin groups within the collection. These genetic fingerprints did not align with the existing field plans and revealed that the origin groups had been crossbred multiple times. The findings emphasize the importance of understanding the genetic structure within a collection to enable breeders to develop well-structured breeding plans. Additionally, the multiplex amplicon marker set created for this study facilitates future genetic screening in a simple and cost-effective manner, enhancing the potential exploitation of Robusta coffee's genetic resources. Finally, we quantified potential gene flow between cultivated and wild C. canephora populations in the Yangambi region. Surprisingly, cultivated C. canephora plants were discovered within supposedly undisturbed forests, challenging the notion of their undisturbed condition. This co-occurrence of cultivated and wild individuals poses a potential threat to the genetic integrity of the wild populations. However, our observations suggest that gene flow between wild and cultivated individuals has been limited so far. Vigilant monitoring of this area is imperative to detect any alterations in gene flow dynamics to safeguard the integrity of the wild gene pool. The findings of this thesis indicate that human activities had very limited impact on the genetic diversity of the wild C. canephora population in Yangambi so far, yet vigilance is crucial as the risks persist. More specifically, the presence of cultivated genotypes within undisturbed forests may compromise the potential for conserving wild C. canephora populations in-situ in the Yangambi region. With the genetic diversity of the INERA Coffee Collection characterized and a marker set available for the identification of cultivated individuals, the future management and expansion of the coffee collection becomes feasible in a cost-effective manner. Overall, this thesis furthers our insights regarding important aspects of both in-situ and ex-situ conservation of Robusta coffee in Yangambi, with potential implications for preserving wild coffee genetic resources and enhancing coffee cultivation practices.