Alliance Bioversity CIAT Journal Articles

Permanent URI for this collectionhttps://hdl.handle.net/10568/106987

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Editorial: Sustainable and resilient food systems in times of crises
(Journal Item, 2025-02-11) Ben Hassen, Tarek; El Bilali, Hamid; Daher, Bassel; Burkart, Stefan
The global food system is facing multiple and multifaceted challenges and crises: increasing population, climate change, pandemics, conflicts, economic shocks, and natural disasters. These challenges have exposed its fragility and underscored the urgency of transitioning to sustainable and resilient food systems. Such systems ensure equitable access to nutritious food, minimize environmental impacts, and enhance resilience against shocks. In crises like the COVID-19 pandemic and the ongoing conflict in Ukraine, the vulnerabilities of the global food system have become starkly apparent, leading to disruptions in supply chains, food shortages, and inflation. Additionally, climate change and natural disasters further threaten food security worldwide. This Research Topic explores innovative approaches—including agroecological practices, circular economies, and localized food systems—to build resilience and sustainability. To provide a comprehensive understanding of these pressing issues, the 17 articles of this Research Topic are organized into four thematic areas: the impacts of crises on food systems, the effects of COVID-19 on food systems, sustainable food systems and practices, and the social, economic, and waste management dimensions of food systems.
The importance of genotyping within the climate-smart plant breeding value chain – integrative tools for genetic enhancement programs
(Journal Article, 2025-02-06) Garcia-Oliveira, Ana Luisa; Ortiz, Rodomiro; Sarsu, Fatma; Rasmussen, Søren K.; Agre, Paterne; Asfaw, Asrat; Kante, Moctar; Chander, Subhash
The challenges faced by today’s agronomists, plant breeders, and their managers encompass adapting sustainably to climate variability while working with limited budgets. Besides, managers are dealing with a multitude of issues with different organizations working on similar initiatives and projects, leading to a lack of a sustainable impact on smallholder farmers. To transform the current food systems as a more sustainable and resilient model efficient solutions are needed to deliver and convey results. Challenges such as logistics, labour, infrastructure, and equity, must be addressed alongside adapting to increasingly unstable climate conditions which affect the life cycle of transboundary pathogens and pests. In this context, transforming food systems go far beyond just farmers and plant breeders and it requires substantial contributions from industry, global finances, transportation, energy, education, and country developmental sectors including legislators. As a result, a holistic approach is essential for achieving sustainable and resilient food systems to sustain a global population anticipated to reach 9.7 billion by 2050 and 11.2 billion by 2100. As of 2021, nearly 193 million individuals were affected by food insecurity, 40 million more than in 2020. Meanwhile, the digital world is rapidly advancing with the digital economy estimated at about 20% of the global gross domestic product, suggesting that digital technologies are increasingly accessible even in areas affected by food insecurity. Leveraging these technologies can facilitate the development of climate-smart cultivars that adapt effectively to climate variation, meet consumer preferences, and address human and livestock nutritional needs. Most economically important traits in crops are controlled by multiple loci often with recessive alleles. Considering particularly Africa, this continent has several agro-climatic zones, hence crops need to be adapted to these. Therefore, targeting specific loci using modern tools offers a precise and efficient approach. This review article aims to address how these new technologies can provide a better support to smallholder farmers.
TreeEyed: A QGIS plugin for tree monitoring in silvopastoral systems using state of the art AI models
(Journal Article, 2025-01-29) Ruiz-Hurtado, Andres Felipe; Bolaños, Juliana Perez; Arrechea-Castillo, Darwin Alexis; Cardoso, Juan Andres
Tree monitoring is a challenging task due to the labour-intensive and time-consuming data collection methods required. We present TreeEyed, a QGIS plugin designed to facilitate the monitoring of trees using remote sensing RGB imagery and artificial intelligence models. The plugin offers several tools including tree inference process for tree segmentation and detection. This tool was implemented to facilitate the manipulation and processing of Geographical Information System (GIS) data from different sources, allowing multi-resolution, variable extent, and generating results in a standard GIS format (georeferenced raster and vector). Additional options like postprocessing, dataset generation, and data validation are also incorporated.
Next-generation drought intensity–duration–frequency curves for early warning systems in Ethiopia’s pastoral region
(Journal Article, 2025-02-02) Tegegne, Getachew; Alemayehu, Sintayehu; Dejene, Sintayehu Workeneh; Gebre, Liyuneh; Zeleke, Tadesse Terefe; Tesfaye, Lidya; Abdulhamid, Numery
The pastoral areas of Ethiopia are facing a recurrent drought crisis that significantly affects the availability of water resources for communities dependent on livestock. Despite the urgent need for effective drought early warning systems, Ethiopia’s pastoral areas have limited capacities to monitor variations in the intensity–duration–frequency of droughts. This study intends to drive drought intensity–duration–frequency (IDF) curves that account for climate-model uncertainty and spatial variability, with the goal of enhancing water resources management in Borana, Ethiopia. To achieve this, the study employed quantile delta mapping to bias-correct outputs from five climate models. A novel multi-model ensemble approach, known as spatiotemporal reliability ensemble averaging, was utilized to combine climate-model outputs, exploiting the strengths of each model while discounting their weaknesses. The Standardized Precipitation Evaporation Index (SPEI) was used to quantify meteorological (3-month SPEI), agricultural (6-month SPEI), and hydrological (12-month SPEI) droughts. Overall, the analysis of historical (1990–2014) and projected (2025–2049, 2050–2074, and 2075–2099) periods revealed that climate change significantly exacerbates drought conditions across all three systems, with changes in drought being more pronounced than changes in mean precipitation. A prevailing rise in droughts’ IDF features is linked to an anticipated decline in precipitation and an increase in temperature. From the derived drought IDF curves, projections for 2025–2049 and 2050–2074 indicate a significant rise in hydrological drought occurrences, while the historical and 2075–2099 periods demonstrate greater vulnerability in meteorological and agricultural systems. While the frequency of hydrological droughts is projected to decrease between 2075 and 2099 as their duration increases, the periods from 2025 to 2049 and from 2050 to 2074 are expected to experience more intense hydrological droughts. Generally, the findings underscore the critical need for timely interventions to mitigate the vulnerabilities associated with drought, particularly in areas like Borana that depend heavily on water resources availability.
Private sector led multi-stakeholder platforms positively influence certified seed supply in Malawi
(Journal Article, 2024-08-24) Gondwe, Wanangwa; Phiri, Alexander; Birachi, Eliud; Magreta, Ruth; Larochelle, Catherine; Machira, Kennedy; Mutua, Mercy; Rubyogo, Jean Claude; Nkhata, Wilson
Common bean yields in Malawi remain low, primarily due to the use of low-yielding, recycled local seeds by most smallholder farmers. The low uptake of certified bean seed is attributed to limited incentives from the private sector. This study hypothesizes that the sustainable adoption of market-preferred varieties can be achieved by synchronizing and linking seed production to the grain market through committed value chain actors in a private sector-led multi-stakeholder platform. This paper examines the role of private sector-led multi-stakeholder platforms in the supply of certified common bean seed in Malawi. The research draws on both qualitative and quantitative primary data collected through a semi-structured questionnaire and interviews with key informants. Data were analyzed using an Ordinary Least Squares (OLS) regression model. The results indicate that several variables representing membership in multi-stakeholder platforms (MSPs) significantly affect the supply of certified common bean seed. Participation in MSPs, contractual arrangements, market structure, extension services, and seed demonstrations positively influenced seed supply. The findings underscore the need for a well-coordinated multi-stakeholder platform to enhance the supply of certified common bean seed, supported by effective policies and incentives from policymakers.
Harnessing the power of citizen science for agroecological transitions: The case of the One Million Voices of Agroecology Initiative and Digital Platform
(Journal Article, 2025-01-31) Fuchs, Lisa Elena; van Dien, Lily Cannell; Mondardini, Maria Rosa Rosy; Penunia, Ma Estrella Esther; Baguilat, Irish; Larrea Macías, Sergio Iván; Souza, Marcelo Soares; Formighieri, Eduardo Fernandes; Gonçalves, Murilo Gelain; Westphalen, Rodrigo B.; Pimentel, Vitória; Ricci, Fabio; Levina, Daria; Geck, Matthias
The One Million Voices (OMV) citizen science initiative aimed to harness the power of citizen science to support agroecological transitions globally. Its goal was to co-develop a citizen science platform that enables farmers, producer organizations, and consumers around the world to participate in agroecology movements, support agroecology adoption, and contribute to the co-creation and sharing of knowledge on the performance of agroecology. The OMV initiative used a facilitated co-design process that involved a global review, regional partnerships, and structured dialogues in four regions of the world, and a collective prioritization process to develop the scope and features of the emerging platform. Following the recommendation of the global review to build on existing networks, the project team partnered with Agroecology Map to develop the OMV of Agroecology platform. The key research question addressed by the platform is: What agroecological practices are being implemented around the world, with what effects, and by whom? Its main functions include the participatory mapping of innovative on-farm and off-farm agroecological practices, their characterization, and their evaluation. Users can also connect with each other, consult maps listing locations and practices, and access personalized summary data analyses. The data provide scientific evidence on the geographic spread and application of agroecology, preferences of agroecology actors, and context-specific performance assessments. Herein, we demonstrate how a global co-created citizen science process can be structured and leveraged in a transdisciplinary way. The OMV platform’s contribution to strengthening and shaping agroecological transitions worldwide will depend on decisive, broad, and diverse participation.
Improving governance arrangements for vegetable value chains in sub-Saharan Africa: the case of Bahir Dar, Ethiopia and Cotonou, Benin
(Journal Article, 2025-01-28) Isoto, Rosemary Emegu; Turinawe, Alice; Nakamatte, Irene; Sumelius, John; Chen, Qiuzhen; Prosperi, Paolo; Sell, Mila; Bodjrenou, Fifali Sam Ulrich; Koukou, Elie; Bello, Faïck; Amoussa Hounkpatin, Waliou; Alemayehu, Melkamu; Desta, Gashaw Tilahun; Assaye, Hirut; Adgo, Enyew; Bankole, Bissola Malikath
Abstract Improved governance arrangements are central in strengthening value chains with sustainable, resilient farming and healthy nutrition. This study explored governance arrangements important to the vegetable value chains in Food System Labs in Bahir Dar (Ethiopia) and Cotonou (Benin). The study collected data through face-to-face interviews from different actors including input suppliers, producers, processors, wholesalers, retailers and from different supporting institutions such as credit organizations in the vegetable value chains in the two regions. The paper uses descriptive analysis for quantitative data, content analysis for qualitative data, and the strengths, weaknesses, opportunities, and threats (SWOT) analysis method in the context of the indicator-based assessment framework to examine governance arrangements. Results indicate that multiple but also alternating modes of governance arrangements exist along the vegetables value chain. Spot market relations dominate at the successive stages of the value chain where different actors randomly interact at every transaction. Relational governance in terms of information sharing is notable among producers who attach high relevance to farmer associations as well as traders who largely trust and source information from amongst themselves. The value chains are typical of limited collaboration between actors coupled with weak processing skills. In addition, unconducive storage facilities undermine the potential of upgrading despite changing preferences and growing demand for vegetables. The study recommends development and strengthening of actor organizations such as cooperatives and associations, provision of an enabling environment where vegetable value chains can thrive, and national level efforts to develop post-harvest handling skills and infrastructure, as well as exploitation of last mile digitization initiatives to increase competitiveness of vegetable trade.
Nature-Positive Agriculture—A way forward towards resilient agrifood systems
(Journal Article, 2025-01-31) Kaushal, Manoj; Atieno, Mary; Odjo, Sylvanus; Baijukya, Frederick; Gebrehawaryat, Yosef; Fadda, Carlo
Current food production systems rely heavily on resource-poor small-scale farmers in the global south. Concomitantly, the agrifood systems are exacerbated by various a/biotic challenges, including low-input agriculture and climate crisis. The recent global food crisis further escalates the production and consumption challenges in the global market. With these challenges, coordinated efforts to address the world’s agrifood systems challenges have never been more urgent than now. This includes the implementation of deeply interconnected activities of food, land, and water systems and relationships among producers and consumers that operate across political boundaries. Nature-positive agriculture represents interventions both at the farm and landscape level that include a systems approach for the management of diverse issues across the land-water-food nexus. In the present article, we focus on the history of traditional farming and how it evolved into today’s nature-positive agriculture, including its limitations and opportunities. The review also explains the most impactful indicators for successful nature-positive agriculture, including sustainable management of soil, crops, seeds, pests, and mixed farming systems, including forages and livestock. Finally, the review explains the dynamics of nature-positive agriculture in the context of small-scale farming systems and how multilateral organizations like the CGIAR are converting this into transformative actions and impact. To address the climate crisis, CGIAR established the paradigm of nature-positive solutions as part of its research and development efforts aimed at transforming food, land, and water systems into more resilient and sustainable pathways.
Comparative profitability of agroecological practices in Ethiopian wheat farming
(Journal Article, 2025-01-30) Ng-Ang-A, Stanley Karanja; Ogutu, Sylvester Ochieng; Tibebe, Degefie; Akinyi, Devinia; Mockshell, Jonathan
Introduction Agroecology is increasingly promoted as a pathway to sustainable food production, aiming to maximize natural resource use while minimizing external inputs with harmful environmental effects. Agroecological practices can enhance farm productivity while ensuring environmental sustainability. However, these practices often require higher initial investments compared to business-as-usual (BAU) practices, and their profitability and relative risks are not well studied. This research evaluates the profitability and risk of adopting agroecological practices among wheat farmers in Ethiopia. Methods We conducted a deterministic cost-benefit analysis (CBA) incorporating sensitivity and scenario analysis to evaluate the profitability and relative risks associated with three agroecological practices: certified wheat seed, optimal site-specific inorganic fertilizer application rates, and drainage of waterlogged soils. The analysis considered yield uncertainty, market price fluctuations, and implementation variability to provide robust insights for decision-making. Results The deterministic CBA revealed that among the three practices, the use of certified seeds was the most profitable, with a net present value (NPV) of US$ 2,531 ha –1 . This was followed by optimal site-specific inorganic fertilizer application, with an NPV of US$ 2,371 ha –1 . Drainage of waterlogged soils yielded the lowest profitability, with an NPV of US$ 2,099 ha –1 . Discussion The results indicate that certified seeds and optimal fertilizer rates offer higher financial returns, making them attractive investments for wheat farmers. However, profitability alone does not guarantee adoption. Other factors, including social and behavioral aspects, influence farmer decisions. Future research should integrate these dimensions to develop comprehensive strategies for promoting agroecological practices. Conclusion Adopting agroecological practices has clear economic benefits for Ethiopian wheat farmers, with certified seeds emerging as the most profitable option. These findings provide evidence for stakeholders to design targeted interventions that maximize returns while addressing barriers to adoption.
Gold mining and social accountability: An empirical approach in Colombia
(Journal Article, 2025-01-24) Saldarriaga-Isaza, Adrián; Florez-Herrera, Fernando; Ibáñez-Diaz, Marcela
This paper aims to understand the impact of potential gold mining on social accountability. By using the Mediation Analysis method, we have developed an impact evaluation for a region of Colombia, through an empirical strategy that allows for the comparison of municipalities with and without potential gold mining. Our model's estimation considered two set of indicators: social accountability and social capital, which underwent Principal Component Analysis. We found that potential gold mining has a positive effect on social accountability, meaning that in municipalities with gold mining potential there is a greater use of participation tools, surveillance and control mechanisms by the local community. This effect is mediated by social capital, i.e., social capital causes the population of gold mining municipalities to implement social accountability. Some policy recommendations and conclusions are presented below.
A simple age-structured, temperature-dependent population growth model of brown rice hopper (Nilaparvata lugens (Stal))
(Preprint, 2025-01-19) Wei, Xiaojing; Balanza, Jane Girly; Ngoc, Vu Thi Bich; Giles, James Edward; Swaans, Cornelis
Brown rice hopper (BRH), a key insect pest to rice, is known can change its longevity and fecundity due to rising temperature. Here we modeled the response of BRH population growth to temperature using an age-structured population growth model, based on reported responses of BRH development time, survival, and fecundity to temperature. We applied this model to predict historical level of BRH population growth in the Mekong River Delta (MRD) and compared the predictions with historically observed percentages of rice fields infested by BRH. The model was able to capture the seasonal variation in BRH infestation and the optimal temperature for BRH activities (app. 26.5 degrees C). These results highlighted the importance of temperature in regulating BRH population growth. The model, with further improvements as discussed, could be used for projecting BRH activity under rising temperatures or predicting BRH outbreaks due to seasonal temperature anomalies.
Unleashing strategies to mitigate methane emissions in rice fields and livestock system
(Journal Article, 2024-12-02) Joseph-Fernando, Ezhilmathi Angela; Selvaraj, Michael; Arango, Jacobo
Participatory plant breeding to develop biofortified upland rice for marginal environments
(Journal Article, 2024-10-29) Castro-Pacheco, Sergio Antonio; Rabekijana, Ravo; Andriamiarana, Mahevanirina; Raveloson, Harinjaka; Rakotomalala, Joël; Ramanantsoanirina, Alain; Garin, Vincent; Grenier, Cecile; vom Brocke, Kirsten
Abstract In the Highlands of Madagascar, where rice is the main staple food, explosive demographic growth has driven the need for the development of upland rice. In that context, a Participatory Plant Breeding (PPB) program conducted by the FOFIFA-Cirad partnership, aims to develop upland rice varieties adapted to farmers’ needs, with superior agronomic performances, and with high grain zinc concentration. In the area, where ferralitic soils with N and P deficiencies prevail, limited fertilizer usage persists due to elevated costs, and upland rice varieties must adapt to these low fertility environments. Thus, this paper aims to identify the adequate selection conditions and methods that allow combining the above-mentioned criteria for selection. So, 56 rice breeding lines, including high-zinc genotypes, were evaluated in field trials with contrasting fertility conditions. A relative selection efficiency analysis demonstrated that selection for yield should be done in moderate fertility environments, while selection for grain zinc concentration could be done across a diverse range of conditions. Through participatory evaluations, we identified that, for this case, grain appreciation was the most important character for deciding whether to select a line, followed by productivity and earliness. We also noted that farmers were more willing to accept a variety if it had higher grain zinc concentration. Finally, we proposed a selection index that combines agronomic, farmers’ and nutritional criteria, with the purpose of selecting lines that fulfill the expectations on these areas. Overall, this paper proposes an adapted methodology for the combination of PPB and biofortification in marginal environments.
Salt tolerance in mungbean is associated with controlling Na and Cl transport across roots, regulating Na and Cl accumulation in chloroplasts and maintaining high K in root and leaf mesophyll cells
(Journal Article, 2024-09) Iqbal, Md Shahin; Clode, Peta L.; Malik, Al Imran; Erskine, William; Kotula, Lukasz
Salinity tolerance requires coordinated responses encompassing salt exclusion in roots and tissue/cellular compartmentation of salt in leaves. We investigated the possible control points for salt ions transport in roots and tissue tolerance to Na
Artificial intelligence in science and society: The vision of USERN
(Journal Article, 2025-01-01) Dorigo, Tommaso; Brown, Gary D.; Casonato, Carlo; Cerdà, Artemi; Ciarrochi, Joseph; da Lio, Mauro; D’Souza, Nicole; Gauger, Nicolas R.; Hayes, Steven C.; Hofmann, Stefan G.; Johansson, Robert; Liwicki, Marcus; Lotte, Fabien; Nieto, Juan J.; Olivato, Giulia; Parnes, Peter; Perry, George; Plebe, Alice; Rao, Idupulapati; Rezaei, Nima; Sandin, Fredrik; Ustyuzhanin, Andrey; Vallortigara, Giorgio; Vischia, Pietro; Yazdanpanah, Niloufar
The recent rise in relevance and diffusion of Artificial Intelligence (AI)-based systems and the increasing number and power of applications of AI methods invites a profound reflection on the impact. The Universal Scientific Education and Research Network (USERN), an organization that promotes initiatives to support interdisciplinary science and education across borders and actively works to improve science policy, collects here the vision of its Advisory Board members, together with a selection of AI experts, to summarize how we see developments in this exciting technology impacting science and society in the foreseeable future. In this review, we first attempt to establish clear definitions of intelligence and consciousness, then provide an overview of AI’s state of the art and its applications. A discussion of the implications, opportunities, and liabilities of the diffusion of AI for research in a few representative fields of science follows this. Finally, we address the potential risks of AI to modern society, suggest strategies for mitigating those risks, and present our conclusions and recommendations
Farming for the future: Understanding factors enabling the adoption of diversified farming systems
(Journal Article, 2024-12-10) Sanchez-Bogado, Andrea Cecilia; Estrada-Carmona, Natalia; Beillouin, Damien; Chéron-Bessou, Cecile; Rapidel, Bruno; Jones, Sarah
Diversified farming practices offer a promising pathway to sustainable food production by providing economic, environmental, and social benefits to farmers and society. However, the factors influencing their adoption are poorly understood, hindering the development of effective promotion strategies. This study presents a comprehensive global meta-analysis of 154 peer-reviewed studies analysing factors influencing adoption. We examined the effects of 71 factors across nine key categories—biophysical context, farm management characteristics, farmers’ attitudes, political and institutional context (access to knowledge, land tenure, financial risk management), and five forms of capital (financial, human, natural, physical, and social)—on the adoption of ten diversified practices in 42 countries across five UN regions. Our results reveal that access to knowledge, social capital, and farmers’ attitudes are key enablers of adoption, surpassing financial, physical, human, and natural capital. Specifically, access to extension services, strong social networks, and perceived environmental benefits significantly correlate with adoption. Land ownership, household income, literacy levels, and shallow soils have smaller positive effects. The influence of these factors varies across practices and geographic contexts, highlighting the complex and multifaceted nature of adoption. These findings emphasize the need for holistic agricultural initiatives and policies to promote the adoption of sustainable practices. Strategies that build technical knowledge and social capital and that are tailored to local contexts, sociocultural norms, and market structures, considering farmers' perceptions and attitudes through codesign processes, are more likely to succeed. Adaptive and context-specific strategies are crucial for fostering the widespread adoption of diversified farming practices and a more sustainable agricultural future.
Agroecología para mejorar los sistemas alimentarios más allá del rendimiento
(News Item, 2024-10-30) Estrada Carmona, Natalia
Op-ed about Agroecology and its role in the 16th Conference of Parties of the Convention on Biological Diversity. Published in El Espectador, a national-wide newspaper in Colombia
Participatory AI for inclusive crop improvement
(Journal Article, 2024-07-24) Lasdun, Violet; Guerena, David Tonatiuh; Ortiz-Crespo, Berta; Mutuvi, Stephen Mutisya; Selvaraj, Michael Gomez; Assefa, Teshale
Crop breeding in the Global South faces a 'phenotyping bottleneck' due to reliance on manual visual phenotyping, which is both error-prone and challenging to scale across multiple environments, inhibiting selection of germplasm adapted to farmer production environments. This limitation impedes rapid varietal turnover, crucial for maintaining high yields and food security under climate change. Low adoption of improved varieties results from a top-down system in which farmers have been more passive recipients than active participants in varietal development.
In situ and ex situ conservation gap analyses of crop wild relatives from Northeast Africa
(Journal Article, 2025-01-20) Aldow, Ahmed; Brehm, Joana Magos; Gaisberger, Hannes; Maxted, Nigel
Crop Wild Relatives (CWR) are wild plant taxa closely related to domesticated crops that play a vital role in enhancing crop resilience. This study assessed the conservation status of 97 priority CWR in Northeast Africa through a comprehensive approach, incorporating ecogeographic data and complementarity analysis. The analysis of 4551 occurrence records from 57 CWR highlighted significant gaps in in situ conservation. Notably, the highest number of occurrence records within Protected Areas (PAs) were found in Ethiopia, particularly in Borena National Park, Kafa UNESCO-MAB Biosphere Reserve, and Bonga National Forest Priority Area. However, only 40 taxa (~ 42%) were identified within existing PAs, with Solanum campylacanthum Hochst. cx A. Rich, and Coffea arabica L. being the most prevalent. Ecogeographic Land Characterization (ELC) maps identified 45 distinct ecological zones representing the region’s diverse habitats. Ex situ analysis revealed 1295 occurrence records from 52 taxa (54%) conserved in genebanks, although only 8% of these taxa were represented by more than 50 accessions. S. camplyacanthum and Avena vaviloviana (Malz.) Mordv. had the highest number of accessions. Ecogeographical analysis indicated that ELC zones 8, 17, and 18 had the highest frequencies of occurrence in both PAs and genebanks. Complementarity analysis identified 34 potential genetic reserve areas, covering 42 taxa (43%), compared to 33 taxa conserved across 18 PAs identified by coverage analysis. These findings highlight the urgent need for a comprehensive CWR conservation strategy to protect valuable genetic diversity for future crop breeding programs, ultimately enhancing crop resilience in the face of ongoing and future agricultural challenges.
Unravelling genomic drivers of speciation in musa through genome assemblies of wild banana ancestors
(Journal Article, 2025-01-23) Martin, Guillaume; Istace, Benjamin; Baurens, Franc-Christophe; Belser, Caroline; Hervouet, Catherine; Labadie, Karine; Cruaud, Corinne; Noel, Benjamin; Guiougou, Chantal; Salmon, Frederic; Mahadeo, Joël; Ahmad, Fajarudin; Volkaert, Hugo A.; Droc, Gaëtan; Rouard, Mathieu; Sardos, Julie; Wincker, Patrick; Yahiaoui, Nabila; Aury, Jean-Marc; D’Hont, Angélique
Hybridization between wild Musa species and subspecies from Southeast Asia is at the origin of cultivated bananas. The genomes of these cultivars are complex mosaics involving nine genetic groups, including two previously unknown contributors. This study provides continuous genome assemblies for six wild genetic groups, one of which represents one of the unknown ancestor, identified as M. acuminata ssp. halabanensis . The second unknown ancestor partially present in a seventh assembly appears related to M. a . ssp. zebrina . These assemblies provide key resources for banana genetics and for improving cultivar assemblies, including that of the emblematic triploid Cavendish. Comparative and phylogenetic analyses reveal an ongoing speciation process within Musa , characterised by large chromosome rearrangements and centromere differentiation through the integration of different types of repeated sequences, including rDNA tandem repeats. This speciation process may have been favoured by reproductive isolation related to the particular context of climate and land connectivity fluctuations in the Southeast Asian region.

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