Cassava witches’ broom disease (CWBD) has been present in the Philippines from the early 2010s and has since been considered a phytoplasma-caused disease. This assumption has guided CWBD diagnostics and management, yielding mixed results. However, recent results in continental Southeast Asia (SEA) indicate that the disease is rather associated with the fungus Ceratobasidium theobromae, the causal agent of Vascular Streak Dieback (VSD) of cacao, another important disease occurring in the Philippines. Field surveys showed that CWBD was present in all cassava-growing regions, reaching field level incidence values above 50%. C. theobromae was detected in symptomatic samples using a standard PCR assay, with a sensitivity of 91.79% and a specificity of 95.24%, supporting its causal association with CWBD, in contrast to phytoplasma detection, which failed to yield positive results. Genome analyses of C. theobromae, supported by an improved reference genome, indicate that Philippine isolates, whether infecting cassava or cacao, are more closely related to each other than to isolates from continental SEA. Furthermore, isolates from the recent outbreak in the Americas are more closely related to those from continental SEA than to those from the Philippines.

Context: Effective seed systems must distribute high-performing varieties efficiently, and slow or stop the spread of pathogens and pests. Epidemics increasingly threaten crops around the world, endangering the livelihoods of smallholder farmers. Responding to these challenges to food and economic security requires stakeholders to act quickly and decisively during the early stages of pathogen invasions, typically with limited resources. A current threat is the introduction of cassava mosaic virus in Southeast Asia. Objectives: Our goal in this study is to provide a decision-support framework for efficient management of healthy seed systems, applied to cassava mosaic disease. The specific objectives are to (1) evaluate disease risk in disease-free parts of Cambodia, Lao PDR, Thailand, and Vietnam; (2) incorporate estimated risk of disease establishment with seed exchange survey data and whitefly spread in the landscape to model epidemic spread; and (3) identify candidate regions to be prioritized in seed system management. Methods: We used machine learning to integrate disease occurrence, climate, topology, and land use, and network meta-population models of epidemic spread. We used scenario analyses to identify candidate priority regions for management. Results and conclusions: The analyses allow stakeholders to evaluate strategic options for allocating their resources in the field, guiding the implementation of seed system programs and responses. Consistently targeting initially high priority locations with clean seed produced more favorable outcomes in this model, as did prioritization of a higher number of districts for the deployment of smaller volumes of clean seed. Significance: The decision-support framework presented here can be applied widely to seed systems challenged by the dual goals of distributing seed efficiently and reducing disease risk. Data-driven approaches support evidence-based identification of optimized surveillance and mitigation areas in an iterative fashion, providing guidance early in an epidemic, and revising recommendations as data accrue over time.

Various cassava genotypes were developed with distinct starch characteristics, including amylose-free and smallgranule mutations. Despite these unique traits, the ethanol production potential of these starches has not been explored. Cassava starch plays a crucial role in ethanol production, particularly in tropical countries like Colombia. This study aimed to assess the physicochemical properties of different cassava starches (including the amylose-free and small granule mutations), and to evaluate their potential for ethanol production using the Simultaneous Liquefaction, Saccharification, and Fermentation process under very high gravity (SLSF-VHG) and no-cooking conditions. Comparative analysis revealed that two double mutant starches and small-granule starch (GM4694-1) exhibited lower resistant starch content than those from wild-type and amylose-free cassava, making them more susceptible to enzymatic breakdown. The amylose content for GM4694-1 and wild-type cassava was 21.9 and 16.1 %, respectively, while the remaining samples were amylose-free. In the SLSF-VHG process, GM4694-1 demonstrated a significant ethanol yield, surpassing 16 % v/v, equivalent to 80 % of the theoretical ethanol yield within 90 hours. This suggests that the GM4694-1 genotype has the potential to produce ethanol efficiently at a temperature of 30 degrees C. Furthermore, the solid residue obtained after the SLSF-VHG process could serve as a high-quality feed additive. This study enhances our understanding of the properties of special cassava starches and their correlation with ethanol production.

Varietal turnover is a major mechanism for farmer adaptation to rapidly changing environmental and market conditions. Understanding factors related to varietal turnover is critical for safeguarding food security in the face of increasingly rapid changes to production contexts. Preference elicitation methods like experimental auctions reveal farmers' willingness to pay (WTP) for seeds with different characteristics. We engaged farmers growing cassava (Manihot esculenta Crantz) across a wide geographic scope in Cambodia (n = 321, 4 provinces) and Lao PDR (n = 391, 5 provinces) in modified second-price experimental auctions to determine WTP for three cassava seed classes: farmer-produced planting stems of an undescribed variety, farmer-produced planting stems of an elite variety with lower susceptibility to Cassava Mosaic Disease (CMD), and virus-free tested planting stems of the same elite variety. In Lao PDR, mean auction bids for a bundle of 20 planting stems were 0.54, 0.92, and 1.40 USD for farmer, elite, and elite tested stems, while in Cambodia the analogous mean bids were 0.58, 0.77, and 1.16 USD, respectively. A significantly higher WTP associated with elite variety and tested stems in both countries was influenced by both geographic location (province) and individual socioeconomic farmer characteristics. In Lao PDR this included lower WTP of women, higher WTP of ethnic minorities, and, for improved stems, lower WTP of farmers with increased cassava growing experience. In Cambodia fewer socioeconomic variables affected WTP. Our results indicate significant increases in WTP for clean planting materials and new varieties, supporting market-based clean seed approaches as a component of regional control strategies for the CMD epidemic currently threatening a global agri-food value chain.

In Southeast Asia (SEA) fastidious fungi of the Ceratobasidium genus are associated with proliferation of sprouts and vascular necrosis in cacao and cassava, crops that were introduced from the tropical Americas to this region. Here, we report the isolation and in vitro culture of a Ceratobasidium sp. isolated from cassava with symptoms of witches' broom disease (CWBD), a devastating disease of this crop in SEA. The genome characterization using a hybrid assembly strategy identifies the fungus as an isolate of the species C. theobromae, the causal agent of vascular streak dieback of cacao in SEA. Both fungi have a genome size > 31 Mb (G+C content 49%), share > 98% nucleotide identity of the Internal Transcribed Spacer (ITS) and > 94% in genes used for species-level identification. Using RNAscope (R) we traced the pathogen and confirmed its irregular distribution in the xylem and epidermis along the cassava stem, which explains the obtention of healthy planting material from symptom-free parts of a diseased plant. These results are essential for understanding the epidemiology of CWBD, as a basis for disease management including measures to prevent further spread and minimize the risk of introducing C. theobromae via long-distance movement of cassava materials to Africa and the Americas.

CONTEXT Early generation seed (EGS) production and delivery pathways are critical components of so-called formal seed systems, of principal importance in the release of improved varieties into national seed systems. Vegetatively propagated crops (VPCs), with clonal reproductive ability and considerable differences in production and dissemination patterns from sexually propagated crops, often challenge generalized assumptions about ‘business models’ for private sector-led EGS production. OBJECTIVE We evaluate production trends and institutional arrangements for early generation ‘seed’ (stem cutting) production in the Greater Mekong Subregion of Southeast Asia to compare models, stakeholders, production pathways, and economic efficiency. We systematically document three cases of formal EGS production underpinning this globally important agricultural commodity, and contextualize their development in regional cassava production trends. We then interrogate whether the observed models support common assumptions in contemporary debates about how VPC seed system development, in particular the logic of public and private participation. METHODS To contextualize EGS initiatives, we compiled district-level production data and processing factory locations from national sources across the Greater Mekong subregion, paired with data on varietal releases and international trade of cassava products. To evaluate institutional arrangements for cassava EGS production in this context, we conducted ten key informant interviews with stakeholders involved with three case studies in Cambodia, Thailand, and Vietnam. Using a seed value chains framework, we compared institutional participation, seed multiplication practices, and partial budgets of each case. RESULTS AND CONCLUSIONS The three cases represent diverse institutional arrangements that don't exhibit seed company-led, profit-motivated structures often recommended by experts. Despite the commercial nature of export-oriented Southeast Asian cassava products, public involvement remained central in cassava breeding and EGS delivery models, implemented via different actors and multiplication stages. Case histories and partial production budgets describe institutional arrangements with variable points of subsidy along the value chain, resulting in positive effects on varietal turnover and cassava production across the region. SIGNIFICANCE While private sector involvement was significant and variable, public involvement remains important, even for highly commercialized crops like cassava. Contrary to common assumptions, successful cassava EGS systems in Southeast Asia have initiated impressive impacts without pursuing conventionally profit-oriented seed business models. Value chain approaches reveal backing EGS yields tangible downstream benefits, but for VPCs additional innovations are required to ensure benefits support the sustainability of expensive upstream multiplication stages. Approaches considering institutional participation along seed and product value chains can identify mechanisms for doing so beyond conventional seed commercialization.

Lao PDR is undergoing a rapid agrarian transformation, underpinned by a growing commercial production of commodity crops such as cassava by smallholder farmers. The global nature of commodity crop markets increases the exposure of potentially vulnerable smallholder farmers to global price dynamics. We apply a cross-scalar and mixed-methods approach to investigate the role of institutional structures and the global-regional-domestic context in local price formation mechanisms at the farm gate. We focus our analysis on policy shocks created by the Chinese government's temporary purchase and storage policy (TSPS) for maize, and the experience and price risk mitigation strategies of smallholder cassava farmers in Lao PDR during this period. We find that the price level and volatility experienced by farmers are shaped by local-level market structures as much as global price dynamics and regional trade integration, demonstrating the importance of institutions across scales in price formation and transmission.

Cassava witches' broom disease (CWBD) is a devastating disease of cassava in Southeast Asia (SEA), of unknown etiology. Affected plants show reduced internodal length, proliferation of leaves and weakening of stems. This results in poor germination of infected stem cuttings (i.e., planting material) and significant reductions in fresh root yields and starch content, causing economic losses for farmers and processors. Using a metagenomic approach, we identified a fungus belonging to the Ceratobasidium genus, sharing more than 98.3–99.7% nucleotide identity at the Internal Transcribed Spacer (ITS), with Ceratobasidium theobromae a pathogen causing similar symptoms in cacao. Microscopy analysis confirmed the identity of the fungus and specific designed PCR tests readily showed (1) Ceratobasidium sp. of cassava is strongly associated with CWBD symptoms, (2) the fungus is present in diseased samples collected since the first recorded CWBD outbreaks in SEA and (3) the fungus is transmissible by grafting. No phytoplasma sequences were detected in diseased plants. Current disease management efforts include adjustment of quarantine protocols and guarantee the production and distribution of Ceratobasidium -free planting material. Implications of related Ceratobasidium fungi, infecting cassava, and cacao in SEA and in other potential risk areas are discussed.

Food security in Lao PDR, a small nation in southeast Asia categorized as low-income food-deficit, is strongly dependent on the success of the rainfed lowland rice crop in the southern provinces. Soils there are sandy in texture, low in water-holding capacity, and low in pH and available nutrients. Farmers are reluctant to apply recommended fertilizer doses, as rainfall and crop responses are unreliable. This paper examines fertilizer response, and considers opportunities to improve the risk profile. The effects of 12 fertilizer-water-genotype treatment combinations were examined across 60 locations, and combined analysis of variance and pattern analysis was used to examine crop response and its relationship to soil fertility, genotype, and climatic variability. The results showed there was little relationship between soil test and grain yield in unfertilized plots, suggesting nutrient release and capture were more important than soil nutrient concentration, so integrative measures of soil nutrient release should be more promising. Despite low yield in the absence of applied nutrients (0.89–2.66, mean 2.18 t ha-1), NPK alone increased yields by 1.0 t ha-1 on average (1.48–3.86, mean 3.12 t ha-1), while water and genotype together with NPK increased yields by up to a further 1.0 t ha-1 (1.95–4.76, mean 3.42 t ha-1). Fertilizer responses were greater and more reliable when soil nutrient buffering capacity was greater, which, together with seasonal expectations, could be used to better inform decisions on fertilizer application in relation to risk. A longer-term and moderate input strategy was proposed in order to gradually improve fine-fraction SOC, soil nutrient buffering, and soil microbial biomass, in order to improve soil nutrient and water retention and release characteristics. This strategy should be evaluated in future research.

Cassava (Manihot esculenta Crantz) is a rainfed, smallholder-produced crop in mainland Southeast Asia, and is currently facing a serious challenge posed by the introduction of cassava mosaic disease (CMD). This study assessed the susceptibility of popular Asian varieties to CMD, yield penalties associated with the disease, and the efficacy of selecting clean or asymptomatic plants as seed for the following season. Field experiments evaluated agronomic management practices (i.e., fertilizer application, use of symptomatic and asymptomatic seed stakes) in Cambodia with six to nine popular varieties over three seasons under natural disease pressure. Popular cassava varieties KU50 and Huaybong60 showed superior CMD tolerance, with consistently fewer symptomatic plants, lower disease progress measures, and higher yields. Plants demonstrating symptoms at early stages of development, i.e., 60 days after planting, yielded significantly less than those developing symptoms later (i.e., 270 DAP) or not at all. Plants grown from clean stems yielded on average 20% to 2.7-fold higher than those grown from symptomatic planting material. A yield decline of ~50% was recorded with symptomatic planting materials of susceptible varieties (e.g., SC8, ~25 t ha−1) over successive years. The findings emphasize that farmers could use positive selection by choosing asymptomatic plants to significantly reduce yield losses.

Cassava Mosaic Disease (CMD) caused by Sri Lankan cassava mosaic virus (SLCMV), has rapidly spread in Southeast Asia (SEA) since 2016. Recently it has been documented in Lao PDR. Previous reports have identified whitefly species of B. tabaci as potential vectors of CMD in SEA, but their occurrence and distribution in cassava fields is not well known. We conducted a countrywide survey in Lao PDR for adult whiteflies in cassava fields, and determined the abundance and genetic diversity of the B. tabaci species complex using mitochondrial cytochrome oxidase I (mtCOI) sequencing. In order to expedite the process, PCR amplifications were performed directly on whitefly adults without DNA extraction, and mtCOI sequences obtained using nanopore portable-sequencing technology. Low whitefly abundances and two cryptic species of the B. tabaci complex, Asia II 1 and Asia II 6, were identified. This is the first work on abundance and genetic identification of whiteflies associated with cassava in Lao PDR. This study indicates currently only a secondary role for Asia II in spreading CMD or as a pest. Routine monitoring and transmission studies on Asia II 6 should be carried out to establish its potential role as a vector of SLCMV in this region.

Cassava (Manihot esculenta Crantz) is a crucial staple crop, and provides carbohydrate energy to more than half a billion people in the tropics. Cassava mosaic disease (CMD) is the most important disease of cassava in Africa. Since Sri Lanka Cassava Mosaic Virus (SLCMV) was first reported in South East Asia in 2015, establishing sustainable solutions to CMD has become a top priority for the cassava program at the International Center for Tropical Agriculture (CIAT) and its partners. In the present study, we screened two populations for CMD resistance: VNM142, 142 clones collected from farms throughout Vietnam, and CIAT102, 102 clones resistant to CMD or mites, which were introduced from CIAT. High broad-sense heritability was observed in all the trials (>0.80). From the population VNM142, eight clones showed high CMD resistance with CMD severity scores less than 2.0. Two resistant clones had the same DNA fingerprinting with the accessions CR63 (PER262 or TAI9) and KM57 (VNM8) in the genebank, respectively. To our knowledge, this is the first report of CMD resistance in the genebank at CIAT. We also used the two populations to validate the CMD markers S12_7926132 and S14_4626854. Both markers explained 51% of the population variance in the segregating population CIAT102, but only 11% in the diverse population VNM142. Thus, we concluded that the two CMD markers could not be used to select for CMD resistance in diverse populations, but could predict the CMD resistance in segregating populations when the susceptible parents do not have resistant marker alleles and the resistance of the CMD2 donors is confirmed.

Context: The COVID-19 pandemic has been affecting health and economies across the world, although the nature of direct and indirect effects on Asian agrifood systems and food security has not yet been well understood. Objectives: This paper assesses the initial responses of major farming and food systems to COVID-19 in 25 Asian countries, and considers the implications for resilience, food and nutrition security and recovery policies by the governments. Methods: A conceptual systems model was specified including key pathways linking the direct and indirect effects of COVID-19 to the resilience and performance of the four principal Asian farming and food systems, viz, lowland rice based; irrigated wheat based; hill mixed; and dryland mixed systems. Based on this framework, a systematic survey of 2504 key informants (4% policy makers, 6% researchers or University staff, 6% extension workers, 65% farmers, and 19% others) in 20 Asian countries was conducted and the results assessed and analysed. Results and conclusion: The principal Asian farming and food systems were moderately resilient to COVID-19, reinforced by government policies in many countries that prioritized food availability and affordability. Rural livelihoods and food security were affected primarily because of disruptions to local labour markets (especially for off-farm work), farm produce markets (notably for perishable foods) and input supply chains (i.e., seeds and fertilisers). The overall effects on system performance were most severe in the irrigated wheat based system and least severe in the hill mixed system, associated in the latter case with greater resilience and diversification and less dependence on external inputs and long market chains. Farming and food systems' resilience and sustain ability are critical considerations for recovery policies and programmes, especially in relation to economic performance that initially recovered more slowly than productivity, natural resources status and social capital. Overall, the resilience of Asian farming and food systems was strong because of inherent systems characteristics reinforced by public policies that prioritized staple food production and distribution as well as complementary welfare programmes. With the substantial risks to plant-and animal-sourced food supplies from future zoonoses and the institutional vulnerabilities revealed by COVID-19, efforts to improve resilience should be central to recovery programmes. Significance: This study was the first Asia-wide systems assessment of the effects of COVID-19 on agriculture and food systems, differentiating the effects of the pandemic across the four principal regional farming and food systems in the region.

AbstractDespite the widespread adoption of mechanised land preparation, improved varieties, and low levels of inorganic fertilisers, rainfed lowland rice production in Laos remains an economically marginal activity, with limited incentives for farmers to intensify production beyond household needs. This is a challenge for the government, which promotes rice intensification by setting high official yield targets. We analyse farmers’ decisions regarding the intensification of rainfed lowland rice systems in two lowland provinces—Savannakhet and Champasak. We demonstrate that farmers have selectively adopted a range of new technologies and continue to respond to changing incentives. However, this has largely involved the adoption of Low-Input, more labour-efficient, and more stable production systems rather than commercially oriented, High-Input, high-yield systems. We use activity budgeting and sensitivity analysis to explore the economic performance of several input scenarios, ranging from farmers’ practice to input levels required to achieve government policy targets. The budget models show that, given their resource endowments and the high degree of production and market risk they encounter, households in the rainfed lowlands have been rational in adopting a Low-Input system rather than intensifying rice production to achieve government yield and production targets. We argue that the strategy of diversifying livelihoods while maintaining a largely subsistence-oriented rice production system is likely to persist, given current economic trends.

The cassava sector in South East Asia is a multi-billion dollar industry, with smallholder producers connected to final consumers via complex and diverse value chains. Public sector research conducted with farmers over several decades has generated technologies with the potential to improve farmer livelihoods. However, translating these research outputs into widespread adoption by farmers, with scaling beyond intervention sites, has had mixed success. This has prompted the question whether private sector actors in the cassava industry can have a greater role in knowledge transfer. We develop a framework in which value chain characteristics, as well as the inherent characteristics of technologies and farming communities, affect the potential for scaling of research outputs and widespread adoption by farmers. We apply this framework to an analysis of six contrasting case studies in four South East Asian countries, ranging from underdeveloped value chains around small-scale processing of animal feed to highly-commercialised international value chains for starch. We find that, in particular contexts, such as when farmer adoption of a technology generates increased supply to a single processor, the processor has an incentive to invest in the extension of research outputs to farmers in its supply zone. In other contexts, however, such as when there is intense competition among processors for smallholder output or where the benefits of the technology are not immediate, there is little incentive for private sector involvement. In all cases, we find that support from a knowledge broker, such as a public sector or non-government actor with the capacity to work with farmers, is also required. Hence, the private sector is not a panacea for generating research impacts at scale.

Broom grass (Thysanolaena maxima) is an important non-timber forest product throughout the northern provinces of Lao PDR, playing akey role in the livelihoods of rural populations during the dry season from December to February. Nevertheless, the market chain of broom grass in Laos has been poorly documented and described. This study involved 85 semi-structured interviews with collectors or traders of broom grass in three districts of Luang Prabang province, and aims to better understand the market chain of broom grass. Collectors (smallholder farmers and their families) rely on two sources of broom grass: wild material collected from communal lands, and to alesser extent, harvested from their upland fields, with very little broom grass specifically planted as acrop. The collection, processing, and marketing of broom grass involved all members of the household, ranging in age from 4 to 80 years; however, the female members (women and girls) have adominant role, participating in all activities from collection to sale of broom grass. The study has identified key points of the market chain of broom grass where efforts may improve returns to smallholder farmers. Investments to support the development of this industry will have social, economic, and environmental benefits.

Abstract Cassava farming in North Sumatera is prominently for cash crops as feedstock to the tapioca starch factory. Multiple stakeholder engagement is needed to develop the value chain linkage to improve the smallholder cassava production system in North Sumatera. The project activity started in 2018 to improve the cassava farming system by introduced new cassava varieties, training on soil and fertilizer management, and linkage between multiple stakeholders to support the smallholder cassava farming. A Focus Group Discussion (FGD) and household surveys were conducted in 2019 to evaluate the changes in farmers’ behavior and perspective toward the improvement of the farming system. The results showed that most of the farmers had improved their farming system, and consequently, the cassava tuber yield than in turn, increased the tapioca starch company productivity. However, several issues need to be solved in order to effectively upscaling the smallholder cassava farming in the region.

Cassava mosaic disease, one of the ten most economically important crop viral diseases in the world, was first reported in Southeast Asia from a single plantation in Cambodia in 2015. To determine the presence and incidence of Sri Lankan cassava mosaic virus (SLCMV) one year after first detection, a total of 6,480 samples from 419 fields were systematically collected from cassava production areas across Cambodia (3,840 samples; 240 fields) and Vietnam (2,640samples; 179 fields) in the 2016 cropping season. Using PCR-based diagnostics, we identified 49 SLCMV-infected plants from nine fields, representing 2% of the total number of fields sampled. Infected fields were geographically restricted to two provinces of Eastern Cambodia, while no infection was detected from any of the other sampled sites in either country. Symptom expression patterns in infected plants suggested that SLCMV may have been transmitted both through infected planting materials, and by Bemisia tabaci, the known whitefly vector of SLCMV. In addition, 14% of virus infected plants did not express typical symptoms of cassava mosaic disease on their leaves, highlighting that molecular-based validation is needed to confirm the presence of SLCMV in the field. None of the owners of the SLCMV-infected fields indicated acquired planting materials from the plantation in Ratanakiri where SLCMV was first reported. The surveillance baseline data generated for both countries is discussed in light of future options to control and manage cassava mosaic disease.