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Banana bunchy top virus (BBTV) is a six-component ssDNA virus (genus Babuvirus, family Nanoviridae) transmitted by aphids, infecting monocots (mainly species in the family Musaceae) and likely originating from South-East Asia where it is frequently associated with self-replicating alphasatellites. Illumina sequencing analysis of banana aphids and leaf samples from Africa revealed an alphasatellite that should be classified in a new genus, phylogenetically related to alphasatellites of nanoviruses infecting dicots. Alphasatellite DNA was encapsidated by BBTV coat protein and accumulated at high levels in plants and aphids, thereby reducing helper virus loads, altering relative abundance (formula) of viral genome components and interfering with virus transmission by aphids. BBTV and alphasatellite clones infected dicot Nicotiana benthamiana, followed by recovery and symptomless persistence of alphasatellite, and BBTV replication protein (Rep), but not alphasatellite Rep, induced leaf chlorosis. Transcriptome sequencing revealed 21, 22 and 24 nucleotide small interfering (si)RNAs covering both strands of the entire viral genome, monodirectional Pol II transcription units of viral mRNAs and pervasive transcription of each component and alphasatellite in both directions, likely generating double-stranded precursors of viral siRNAs. Consistent with the latter hypothesis, viral DNA formulas with and without alphasatellite resembled viral siRNA formulas but not mRNA formulas. Alphasatellite decreased transcription efficiency of DNA-N encoding a putative aphid transmission factor and increased relative siRNA production rates from Rep- and movement protein-encoding components. Alphasatellite itself spawned the most abundant siRNAs and had the lowest mRNA transcription rate. Collectively, following African invasion, BBTV got associated with an alphasatellite likely originating from a dicot plant and interfering with BBTV replication and transmission. Molecular analysis of viru

PR, IFPRI3; ISI; G Cross-cutting gender theme; CRP3.2; 1 Fostering Climate-Resilient and Sustainable Food Supply, MTID, CGIAR Research Program on Maize (MAIZE); CGIAR Gender Platform, Globalization and changing climates are aggravating the occurrence and impacts of transboundary pests, and driving the emergence of new threats. Most of the low- and middle-income countries in Africa, Asia and Latin America are not fully prepared in terms of surveillance, diagnostics, and deployment of plant health solutions due to several factors: adequate investment is lacking; knowledge is inadequate; and connections from the local to global, and global to local are insufficient. Effectively countering the current and emerging threats to plant health requires a holistic approach that includes: 1) globally coordinated diagnostic and surveillance systems; 2) epidemiological modelling, risk assessment, forecasting and preparedness for proactive management and containment; and 3) implementation of context-sensitive, eco-friendly, gender-responsive and socially inclusive integrated disease and pest management approaches to reduce the impacts of devastating transboundary pests and diseases. Despite several success stories where major pests and diseases have been brought to control through integrated approaches, further multi-institutional and multi-disciplinary efforts are necessary. Plant health management requires stronger interface between the biophysical and social sciences, and empowerment of local communities. These reflections derive from the proceedings of a webinar on “Transboundary Disease and Pest Management,” organized by CGIAR (Consultative Group on International Agricultural Research) on March 3, 2021, in recognition of the United Nations designated International Year of Plant Health.

Non-PR, IFPRI1; 1 Fostering Climate-Resilient and Sustainable Food Supply; 4 Transforming Agricultural and Rural Economies, DSGD; EPTD, Despite the potential importance of seed quality to agricultural productivity growth, many governments in sub-Saharan Africa lack the capacity to expand quality assurance systems even where there is expressed interest. This study aims to evidence the value of quality assurance systems with an analysis of efforts to produce and distribute certified seed in Nigeria. We assess the associations between quantities of certified seeds produced and spatial variations in production locations proxied by headquarter locations of seed companies producing certified seeds, on the one hand, with spatial variations in the use of certified seed, yields, and output at the farm level, on the other hand. Our analysis covers three crops that are important to food security in Nigeria: maize, rice, and cowpea. Our analysis integrates information on seed quantities produced and locations of seed companies with nationally representative panel data from a survey of farm households and spatially explicit rainfall and temperature data. We find a positive relationship between certified seed production in proximity to farm households and farm-level use of certified seeds, yields, and output, although this effect is diminishing at the margin. These diminishing marginal effects may be partly due to two factors. First, the yield gains from certified seeds tend to vary considerably within each state, suggesting that either quality issues persist in the seed supply chain or farmers are not using complementary inputs or appropriate management techniques when using quality seed. Second, it may be that as certified seed becomes more available to farmers, its use spreads from higher-return farms to lower-return farms, thereby diminishing the gains on the extensive margin. Although more rigorous assessments of causal effects and cost-effectiveness are needed to validate these findings, these results are consistent with the hypothesis that there are diminishing returns to seed quality assurance. Policymake

Non-PR, IFPRI5; CRP2; CRP3.4; Genetic resources and seed systems policy; 1 Fostering Climate-Resilient and Sustainable Food Supply; 3 Building Inclusive and Efficient Markets, Trade Systems, and Food Industry; 5 Strengthening Institutions and Governance, DSGD; PIM, CGIAR Research Program on Policies, Institutions, and Markets (PIM); CGIAR Research Program on Roots, Tuber, and Bananas (RTB), In many African countries south of the Sahara, farmers depend on the cultivation of vegetatively propagated crops (VPCs) for both consumption and commercial purposes. Yet yields for these crops remain at low levels due, in part, to the persistent use of low-quality planting material. Efforts to improve the quality of planting material exchanged in markets or through other channels are often hampered by the unique biological and economic characteristics of vegetative propagation—characteristics that distinguish VPCs from the major cereal crops that drive and shape the policy and investment choices made in many of these countries. This suggests that continued investment in new technologies and systems to produce, package, and distribute VPC planting materials will require customized policies and policy support if these systems are to supply farmers with quality planting material at any significant and sustained scale. This paper explores these issues in the context of the cassava seed system in Nigeria by drawing on (1) prior research, public policy documents, and government statistics; (2) key informant interviews and focus group discussions with seed system actors; and (3) a unique dataset from the 2015 Cassava Monitoring Survey of Nigeria (CMS). The paper examines the production and supply of cassava planting material, the influence of various quality assurance systems on production and supply, and the implications for smallholder farmers in Nigeria. We describe the market, non-market, and regulatory systems that shape the cassava seed market in Nigeria, focusing on effectiveness, influence, and reach. We then explore the ground realities—how farmers actually acquire and use cassava planting material—given the (weak) state of markets and regulation. This is followed by a discussion of alternative policy and regulatory approaches to managing and expanding the cassava seed system, emphasizing a more decentralized approach that prioritizes investment in innovative cap

To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus “yam virus Y” (YVY). Twenty-three of the samples in which YVY was detected showed mosaic and chlorotic leaf symptoms, but Yam mosaic virus was also detected in these samples. Complete genome sequences of two YVY viral isolates were assembled and found to contain five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further work is needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production.