Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred similar to 30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
Rice production is highly susceptible to various pathogens, including Rhizoctonia solani, Curvularia lunata, and Epicoccum rostratum, which are major threats in Asia. Exploring biological control methods using endophytic bacteria offers promising opportunities to enhance rice resilience against these lethal diseases. Using 16S RNA sequencing, we identified four endophytic isolates of Bacillus spp. from rice roots, stems, and leaves. We evaluated the antagonistic activity of these endophytic bacterial isolates against rice pathogens both in vitro and in vivo. These isolates inhibited the growth of C. lunata by 82 %, R. solani by 79 %, and E. rostratum by 88 % in vitro. The detached leaf assay for sheath blight (ShB) disease severity in strains ranged from 10.4 % to 73.3 %. In vivo results showed that B. amyloliquefaciens (R-19) exhibited the lowest disease intensity at 7.2 % and the highest disease suppression at 78.8 %. The fungicide propiconazole at 0.1 % treatment showed the lowest disease intensity of 7.7 % and the highest disease suppression of 73.4 %, compared to the infected control. Besides biocontrol efficacy, endophytic isolates enhance plant growth parameters, including shoot height, root length, fresh and dry weights, number of tillers, and grains per tiller. Plant hormones abscisic acid (ABA) and gibberellic acids (GA3) increased by 35 % and 53 %, respectively, due to B. subtilis (R-20) and B. amyloliquefaciens (R-19), while flavonoid and indole acetic acid (IAA) concentrations surged by 30%-80 %. Similarly, chlorophyll (a, b), carotenoids, antioxidant enzymatic activity, phenolic content, carbohydrates, and proline contents were higher compared to the control. This study provides a foundation for future studies on novel and eco-friendly biocontrol agents. In addition, our study recommends the integration of endophytic bacteria into sustainable agriculture for enhancing rice production and reducing disease impacts.
Sweetpotato is climate smart crop, grown with limited external inputs (fertilisers, pesticides, less labour) making it an attractive crop for resource-constrained smallholder farmers. It is also a major cash and food crop for many countries in sub-Saharan Africa. However, adoption of the high yielding and nutritious improved varieties has been disappointingly low. This study uses qualitative methods to explore the barriers and enablers of farmer varietal replacement and adoption. Unlike the extant quantitative studies that identify the determinants of adoption, we delve deeper into understanding the reasons for or against the preference for specific varieties. We used a rich set of information collected via focus group discussions which explore why farmers prefer certain varieties over others and how they perceive the new improved varieties from the national breeding programs. Doing so enabled us to unravel specific traits or trait combinations that farmers seek and identify those that they perceive needing improvement. We find that the most preferred traits were ‘yield’ and ‘good taste’. Implying that the neglect of sensory attributes by breeders contributes to the low adoption of improved sweetpotato varieties. Moreover, we find that altruism among the respondents plays an important role in farmer use of, and sharing of information about improved sweetpotato varieties. Women and men farmers obtained most of their information from neighbours, NGOs and radios. For women, the most important source of planting materials doubled as their most important source of information. Thus, concerted efforts to minimise information constraints are essential for unravelling the adoption puzzle.
In the name of food security, governments and NGOs purchase large volumes of maize seed in non-relief situations to provide at reduced or no cost to producers. At the same time, efforts to build formal maize seed systems have been frustrated by slow turnover rates – the dominance of older seed products in the market over newer, higher performing ones. Under certain conditions, governments and NGO seed aid purchases can support formal seed systems development in three ways: i) support increased producer awareness of new products, ii) support local private seed industry development, and iii) advance equity goals by targeting aid to the most vulnerable of producers who lack the capacity to purchase seeds. This study explores the objectives and activities of seed aid programmes in Uganda and their interactions with the maize seed sector. We draw insights from interviews with representatives of seed companies, NGOs and government agencies, as well as focus group discussions with producers. The findings indicated that seed aid programme objectives are largely disconnected from broader seed systems development goals. There is little evidence of public-private collaboration in design of these programmes. Better designed programs have the potential to align with varietal turnover objectives, commercial sector development and targeting of underserved markets could promote equity and ‘crowd in’ demand.
Spodoptera frugiperda (J.E. Smith), fall armyworm (FAW), a polyphagous Noctuid pest, was first reported in Uganda in 2016. Farmers were trained to identify and manage the pest, but there was a lack of information on farmer knowledge, perceptions and practices deployed to control it. Therefore, we conducted a survey to assess maize farmers’ knowledge, perceptions and management of the pest during the invasion. We interviewed 1,289 maize farmers from 10 maize-growing agro-ecological zones (AEZ) of Uganda using well-structured questionnaires. The data were analyzed using R version 4.2.3. The respondents faced many constraints, including pests, drought, poor soils and labor constraints. Among the pests, FAW was ranked by most (85%) of the respondents as the number one pest problem in maize, and some farmers reported having noticed it way back in 2014. By 2018, more than 90% of the farmers had seen or heard about FAW, and about 80% saw FAW in their fields. The most common FAW symptoms reported by maize farmers were windowing, near tunnel damage, and holes on the cobs. The developmental stages of FAW identified by farmers included eggs (10%), young larvae (78.7%), mature larvae (73.5%) and adult moths (6.7%). Insecticides were the major control tactic, although some farmers used plant extracts, hand-picking, sand, and ash. Farmers sourced information on FAW from various sources, including fellow farmers, radio/TV, extension agents, input dealers, print media, research and NGO extension. There is a need to package clear and uniform information for the farmers and to develop and promote a sustainable solution for FAW management, including harnessing biological control and cultural practices.
