Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

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Summary Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2 n = 4 x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2 n = 2 x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single‐nucleotide polymorphism ( SNP ) array for coffee trees. A total of 8580 unique and informative SNP s were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNP s (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high‐density genetic map by adding 1307 SNP markers, whereas 945 SNP s were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora‐derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high‐density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.

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Catherine Kiwuka (2020). Genetic diversity and phenotypic variation of wild, feral and cultivated Coffea canephora in relation to drought stress. PhD thesis, Wageningen University, The Netherlands, with summaries in English and Dutch, 180 pp.Coffea canephora Pierre ex A. Froehner (Robusta coffee) is an important crop sustaining millions of livelihoods in its production zone which is predominated by poor countries. Like the other commercially important coffee species, Coffea arabica, the production of Coffea canephora is threatened by the prevailing intense and frequent drought spells reported to be increasing in relation to climate change. There is thus an urgent need to develop drought resilient C. canephora cultivars especially for poor farmers who often lack irrigation options.Availability of C. canephora intraspecific diversity and occurrence of wild populations across an environmental gradient may indicate presence of valuable genetic material, which could be used directly as a new variety or as a parent in breeding climate resilient varieties. This thesis explored: (i) the genetic diversity of Ugandan Robusta coffee; (ii) linkages between allelic variation and environmental variables; (iii) phenotypic variation in drought tolerance and (iv) phenotypic plasticity to shifts in water availability and its relationship with drought tolerance.Results showed that: Uganda's C. canephora differentiates into five geographically delimited groups, and there is substantial phenotypic variation in relation to their response to water availability across locations and genetic groups but no significant phenotypic variation along the level of cultivation status. We observed a trade-off between drought tolerance and growth in ample water conditions. Drought tolerance of the genotypes was negatively associated to an index that indicated wetness of the climate at their locations suggesting some degree of local adaptation. Finally, our results also showed a negative correlation between plasticity in response to changes in water availability and drought tolerance. Generally, our study revealed the comprehensive genetic structure of Uganda's C. canephora, its differential response in to drought stress, growth-tolerance trade-off, plasticity-tolerance trade-off, the link between δ 13 C discrimination and water-use efficiency, and the probable implications of the findings to developing drought tolerant cultivars. Our findings can be used in further studies like association studies to identify putatively adapted genotypes and in breeding programs to develop climate resilient cultivars. Table of contents Chapter General introduction 1 Chapter Genetic diversity of native and cultivated Uganda's Coffea canephora 19 Pierre ex A. Froehner. A perspective into potential utilization and conservation of the diversity Chapter Intraspecific variation in growth response to drought stress across 51 geographic locations and genetic groups in Coffea canephora Pierre ex A. Froehner Chapter Phenotypic and genotypic variation in trait plastic response...

The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species' native range can provide valuable insights about habitat loss and the species' adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution | 4125 TOURNEBIZE ET al.

In-solution based capture is becoming a method of choice for sequencing targeted sequence. We assessed and optimized a capture protocol in 20 different species from 6 different plant genus using kits from 20,000 to 200,000 baits targeting from 300 to 32,000 genes. We evaluated both the effectiveness of the capture protocol and the fold enrichment in targeted sequences. We proposed a protocol with multiplexing up to 96 samples in a single hybridization and showed it was an efficient and cost-effective strategy. We also extended the use of capture to pools of 100 samples and proved the efficiency of the method to assess allele frequency. Using a set of various organisms with different genome sizes, we demonstrated a correlation between the percentage of on-target reads vs. the relative size of the targeted sequences. Altogether, we proposed methods, strategies, cost-efficient protocols and statistics to better evaluate and more effectively use hybridization capture.

Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes.To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long-lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defence pathways in coffee. Seventy-one single nucleotide polymorphisms (SNPs) were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB-like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, such as the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate-associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex situ conservation strategies are discussed.