Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia / Diversidad genética y estructura del hongo de la roya del café Hemileia vastatrix en diferentes sistemas de manejo del café en Etiopía

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.(AU)

Assessment of farmers' knowledge and perceptions of coffee yield reduction due to weeds and their management in Ethiopia.

The home of Coffea arabica is in Ethiopia, where it has high genetic diversity and suitable growing conditions; unfortunately, the national average yields of coffee remain low due to no technical advancements and diverse, complex biotic and abiotic constraints. Hence, this study was conducted in eight major coffee-growing zones of Ethiopia to assess farmers' knowledge and perceptions of coffee yield reduction due to weeds and the farmers' weed control practices. A purposive and random sampling technique was used to generate primary data from coffee growers (N = 320) using a semi-structured questionnaire. Quantitative data were analyzed using a three-stage nested design, and the dependent and independent variables data were subjected to canonical correlation analysis. This study revealed variation in coffee yield (t ha-1) among the assessed areas based on farmers' knowledge of estimating coffee yield. The average yield level ha-1 was very low (0.37 t ha-1) and different among the surveyed areas. The average coffee yield gap as compared to the current national level (0.64 t ha-1) was observed to be 42%, and this low yield was highly correlated with weed infestation (r = 0.879) and type of weeds r = -0.528). This investigation indicated a single factor or association of different factors contributing to the low yield level of coffee in the study areas. Thus, it is concluded that predictor variables accounting for the low yield levels need to be considered when planning future strategies to attain the yield potential of C. arabica in Ethiopia.

Purdue improved crop storage bag for kocho fermentation; Ethiopian traditional fermented food from Enset (Ensete ventricosum).

Enset (Ensete ventricosm) is a multipurpose crop serving millions of Ethiopians as an alternative food source. However, the traditional kocho preparation is labor-intensive and results in poor quality. This study evaluated Purdue improved crop storage (PICS) bag as an alternative to an underground pit for kocho fermentation. The experiment was arranged in a factorial design with two fermentation systems (underground pit and PICS bag) and three fermentation times (30, 45 & 60 days) with 5 replications. Physico-chemical, proximate composition, microbial, and sensory evaluations of kocho were conducted following standard procedures. The results have revealed that protein and moisture contents were increased with fermentation time while crude fiber, carbohydrate, and total energy were decreased regardless of fermentation systems. The microbial results have demonstrated a reduction with extended fermentation but no significant difference between PICS and the underground pit. The sensory results have shown that PICS bag-fermented kocho has better overall sensory acceptability regardless of fermentation time. Generally, PICS bag-fermented kocho for 60 days has shown overall better kocho quality. The finding revealed that PICS bags could be used as an alternative to the traditional underground pit for better kocho quality. Further validation of the PICS bag as a fermentation container with various enset varieties and seasons with extended fermentation time is needed.

Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia.

Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.

Contrasting coffee leaf rust epidemics between forest coffee and semi-forest coffee agroforestry systems in SW-Ethiopia.

Ethiopian Arabica coffee is produced in different agroforestry systems which differ in forest management intensity. In forest coffee systems (FC), coffee shrubs grow naturally in the understory of Afromontane forests with little human intervention, whereas in semi-forest coffee systems (SFC) thinning of the canopy and removal of the understory is applied. Coffee leaf rust (CLR) disease is a growing concern for coffee agroforestry, but to what extent infection pressure is affected by management intensity is poorly known. Here we assessed CLR infection through time across FC and SFC systems in SW-Ethiopia. CLR infection was significantly higher for SFC, with a gradual reduction of this difference during the beginning of dry season (November) through main rainy season of (July). Our findings also demonstrated that CLR infections were significantly lower in the FC system as compared to SFC system in both years 2015/16 and 2020/21. The higher CLR infection was partly explained by lower crown cover and higher human impact. We expect that reduced wind speed and droplet penetration under closed canopies and reduced human-facilitated spore dispersal are the dominating mechanisms behind lower CLR infection in FC systems, yet lower coffee density in FC may also play a role. Overall, our results indicate that although higher management intensity still generally results in higher total yields per hectare, proportionally larger losses due to CLR infection can be expected. Therefore, introducing more coffee genetic diversity, screening resistant coffee varieties and increasing canopy cover in the SFC will mitigate the CLR disease pressure and guarantee the sustainability of higher yields of the system in the future. Also, lower yields in the FC will be rewarded through providing price premiums so that farmers instantly get a higher price for their lower yield, guaranteeing livelihoods.

Evaluation of the herbicidal potential of some fungal species against Bidens pilosa, the coffee farming weeds.

Weeds are the most productive limiting factor, especially in organic farming systems where the uses of synthetic herbicides are not allowed due to their negative impacts. Hence, synthetic herbicides need to be replaced with biological herbicides for weed management. Thus, the present study was designed to evaluate the herbicidal activity of conidia suspensions from Aspergillus niger, Trichoderma asperlium, Trichoderma atroviride, Trichoderma hamatum, Trichoderma harzanium, Trichoderma longibrachatum and Trichoderma viride against Bidens pilosa weed via a series of laboratory and lath-house conditions that laid out in a CRD and RCBD, respectively, with three replications for each bioassay. The results revealed that all fungi, except T. longibrachatum, had significantly reduced seed germination as well as early growth of the target weed compared to the untreated control. The inhibitory effects were measured to be varied among the types of conidia suspensions of fungal species and their level of concentration. The highest rate of inhibition was observed for conidia suspension from A. niger which suppressed with the maximum seed germination inhibitory level (65%) over control. Likewise, the plumule and radicle growth length of the target weed also significantly inhibited by the tested fungi (ranging from 10 to 85% and 34 to 97%) compared to the control, respectively. Based on their efficacy in the laboratory bioassay, the herbicidal potential of selected fungi was further evaluated in pot experiments. In contrarily to laboratory observations, the effect of different fungal conidia suspensions on various growth parameters of the targeted weed was insignificant in the lath-house experiments. In conclusion, the application of A. niger displayed some potential green light to be investigated as a biocontrol agent with promising retarding in the germination and early growth of B. pilosa. Hence, we recommend further investigation of those fungi under field conditions on different coffee weed species.

Fragmentation and management of Ethiopian moist evergreen forest drive compositional shifts of insect communities visiting wild Arabica coffee flowers.

Coffea arabica is an indigenous understorey shrub of the moist evergreen Afromontane forest of SW Ethiopia. Coffee cultivation here occurs under different forest management intensities, ranging from almost no intervention in the 'forest coffee' system to far-reaching interventions that include the removal of competing shrubs and selective thinning of the upper canopy in the 'semi-forest coffee' system. We investigated whether increasing forest management intensity and fragmentation result in impacts upon potential coffee pollination services through examining shifts in insect communities that visit coffee flowers. Overall, we netted 2,976 insect individuals on C. arabica flowers, belonging to sixteen taxonomic groups, comprising 10 insect orders. Taxonomic richness of the flower-visiting insects significantly decreased and pollinator community changed with increasing forest management intensity and fragmentation. The relative abundance of honey bees significantly increased with increasing forest management intensity and fragmentation, likely resulting from the introduction of bee hives in the most intensively managed forests. The impoverishment of the insect communities through increased forest management intensity and fragmentation potentially decreases the resilience of the coffee production system as pollination increasingly relies on honey bees alone. This may negatively affect coffee productivity in the long term as global pollination services by managed honey bees are expected to decline under current climate change scenarios. Coffee agroforestry management practices should urgently integrate pollinator conservation measures.

Genetic variation and risks of introgression in the wild Coffea arabica gene pool in south-western Ethiopian montane rainforests.

The montane rainforests of SW Ethiopia are the primary centre of diversity of Coffea arabica and the origin of all Arabica coffee cultivated worldwide. This wild gene pool is potentially threatened by forest fragmentation and degradation, and by introgressive hybridization with locally improved coffee varieties. We genotyped 703 coffee shrubs from unmanaged and managed coffee populations, using 24 microsatellite loci. Additionally, we genotyped 90 individuals representing 23 Ethiopian cultivars resistant to coffee berry disease (CBD). We determined population genetic diversity, genetic structure, and admixture of cultivar alleles in the in situ gene pool. We found strong genetic differentiation between managed and unmanaged coffee populations, but without significant differences in within-population genetic diversity. The widespread planting of coffee seedlings including CBD-resistant cultivars most likely offsets losses of genetic variation attributable to genetic drift and inbreeding. Mixing cultivars with original coffee genotypes, however, leaves ample opportunity for hybridization and replacement of the original coffee gene pool, which already shows signs of admixture. In situ conservation of the wild gene pool of C. arabica must therefore focus on limiting coffee production in the remaining wild populations, as intensification threatens the genetic integrity of the gene pool by exposing wild genotypes to cultivars.