Institut Sénégalais de Recherches Agricoles

Key message Genomic resources, alongside the tools and expertise required to leverage them, are essential for the effective improvement of globally significant millet crop species. Abstract Millets are essential for global food security and nutrition, particularly in sub-Saharan Africa and South Asia. They are crucial in promoting nutrition, climate resilience, economic development, and cultural heritage. Despite their critical role, millets have historically received less investment in developing genomic resources than major cereals like wheat, maize, and rice. However, recent advancements in genomics, particularly next-generation sequencing technologies, offer unprecedented opportunities for rapid improvement in millet crops. This review paper provides an overview of the status of genomic resources in millets and in harnessing the recent opportunities in artificial intelligence to address challenges in millet crop improvement to boost productivity, nutrition, and end quality. It emphasizes the significance of genomics in tackling global food security issues and underscores the necessity for innovative breeding strategies to translate genomics and AI into effective breeding strategies for millets.

Dalbergia melanoxylon Guill. & Perr. is a highly valued species in the Ferlo region, and its wood is used for various purposes by local populations, including firewood, service wood, and timber. This multifunctionality has weakened its populations, and it has been identified as threatened in previous research. The aim of this study was to investigate the genetic variability of three populations (LC, VC, and YC) along a north–south rainfall gradient, to support the species’ sustainable management and conservation. Eighteen microsatellite markers were used, including eight nuclear (nSSR) and 10 chloroplast (cpSSR) markers, to test their transferability to D. melanoxylon and study the genetic variability. The results showed that all nSSRs and cpSSRs were transferable, however, only five nSSRs and one cpSSR were polymorphic and used in the downstream analysis. Based on the nSSRs, comparatively high, but non-significantly different, genetic variation was found in all populations (LC: He = 0.650, VC: He = 0.674, YC: He = 0.706), however, indications of inbreeding were detected. For the single polymorphic cpSSR, three haplotypes were identified. Haplotype diversity (Hd) varied in LC (Hd = 0.536), VC (Hd = 0.577), and YC (Hd = 0.674). Low to moderate genetic differentiation was observed between populations (Fst nSSR = 0.019 and Fst cpSSR = 0.133) suggesting recent fragmentation of populations that has not yet impacted genetic variation but could become more pronounced in future generations. This finding underscores the need for further research on effective management and conservation strategies for D. melanoxylon populations in the Ferlo region.

The Canary Current Large Marine Ecosystem (CCLME) is one of the most productive Large Marine Ecosystems worldwide. Assessing the abundance, biomass and distribution of zooplankton in the southern part of this system, off the coast of West Africa, remains challenging due to limited sampling efforts and data availability. However, zooplankton is of primary importance for pelagic ecosystem functioning. We applied an inversion method with combined analysis of acoustic and biological data for copepod discrimination using a bi-frequency (38 and 120 kHz) approach. Large copepods with equivalent spherical radii > 0.5 mm were identified using differences in the mean volume backscattering strength (MVBS). Regarding abundance measured by net sampling, copepods strongly dominated the zooplankton community and the large fraction account for 18%. This estimate correlated significantly with MVBS values that were obtained using an inverse algorithm. We confirmed the utility of using 38 kHz for large copepod detection. An epipelagic biomass of large copepod was estimated at 120–850 mg m⁻² in March during upwelling season. It is worth noting that this estimation likely underestimates the true biomass due to inherent uncertainties associated with the measurement method. We recommend future investigations in the interest of using only nighttime data to improve the sampling pattern, particularly on the upper part of the water column (< 10 m) as well as on the shallow part of the continental shelf (< 20 m depth) not covered by fisheries vessel. Nevertheless, such high copepod biomass supports high fish production underlining the key role of copepod in the CCLME. Our results open the way to the analysis of the fluctuation and trend of copepod biomass, along with three decades of fisheries acoustics data available in the region. This helps to determine ecosystem changes, particularly under climate change, and to investigate the role of copepods in the southern CCLME carbon pump at the fine scale.

Monitoring the changes of ecosystem functioning is pivotal for understanding the global carbon cycle. Despite its size and contribution to the global carbon cycle, Africa is largely understudied in regard to ongoing changes of its ecosystem functioning and their responses to climate change. One of the reasons is the lack of long‐term in situ data. Here, we use eddy covariance to quantify the net ecosystem exchange (NEE) and its components—gross primary production (GPP) and ecosystem respiration ( R eco ) for years 2010–2022 for a Sahelian semiarid savanna to study trends in the fluxes. Significant negative trends were found for NEE (12.7 ± 2.8 g C m ² year ⁻¹ ), GPP (39.6 ± 7.9 g C m ² year ⁻¹ ), and R eco (32.2 ± 8.9 g C m ² year ⁻¹ ). We found that NEE decreased by 60% over the study period, and this decrease was mainly caused by stronger negative trends in rainy season GPP than in R eco . Additionally, we observed strong increasing trends in vapor pressure deficit, but no trends in rainfall or soil water content. Thus, a proposed explanation for the decrease in carbon sink strength is increasing atmospheric dryness. The warming climate in the Sahel, coupled with increasing evaporative demand, may thus lead to decreased GPP levels across this biome, and lowering its CO 2 sequestration.

Soil salinization has become a major global ecosystem sustainability issue. In Senegal, promising ecosystem restoration of salt-affected lands has been reached by the implementation of ecological engineering strategies based on beneficial associations between Casuarina species and salt-tolerant symbiotic microorganisms. However, the extent of impacts of symbiont inoculants on the native soil microbiota, and consequently soil functioning is fragmentary. The current study aimed at evaluating the changes in the native soil microbiota associated with the use of a symbiont inoculant in mixed Casuarinaceae plantations in salt-affected lands. The symbiont inoculation lead to a decrease of soil fungal diversity, but not bacteria. However, the whole soil microbiota structure was impacted by symbiont inoculation, as by salinity and Casuarina species. Casuarina species also impacted the diversity of dominant taxa constituting soil microbiota, but only salinity affected bacterial diversity. Important modifications of soil microbiota functionalities were revealed, notably a decrease of bacterial pathogens related to symbiont inoculation and increased abundance of fungal pathogens with salinity. Soil nutrient cycling was also impacted by symbiont inoculation, mostly micronutrient cycling and N fixation, but salinity and Casuarina species were the main factors affecting N cycling in soil.

Soil salinization has become a major global ecosystem sustainability issue. In Senegal, promising ecosystem restoration of salt-affected lands has been achieved by the implementation of ecological engineering strategies based on beneficial associations between Casuarina species and salt-tolerant symbiotic microorganisms. However, the extent of the impacts of symbiont inoculants on the native soil microbiota and, consequently, soil functioning is fragmentary. The current study aimed to evaluate the changes in the native soil microbiota associated with the use of a symbiont inoculant in mixed Casuarinaceae plantations in salt-affected lands. Symbiont inoculation led to a decrease in the diversity of soil fungi but not bacteria. However, the whole soil microbiota structure was impacted by symbiont inoculation, as was the case for salinity and Casuarina species. Casuarina species also impacted the diversity of the dominant taxa constituting the soil microbiota, but only salinity affected bacterial diversity. Important modifications of soil microbiota functionalities were revealed, notably, a decrease in the abundance of bacterial pathogens related to symbiont inoculation and an increase in the abundance of fungal pathogens with increasing salinity. Soil nutrient cycling, mostly micronutrient cycling and N fixation, was also impacted by symbiont inoculation, but salinity and Casuarina species were the main factors affecting N cycling in the soil.

The full text of this preprint has been withdrawn by the authors while they make corrections to the work. Therefore, the authors do not wish this work to be cited as a reference. Questions should be directed to the corresponding author.

Citation: Gahn, M.C.B.; Diouf, G.; Cissé, N.; Ciss, M.; Bordier, M.; Ndiaye, M.; Bakhoum, M.T.; Djiba, M.L.; Brown, C.; Faburay, B.; et al. Abstract: Crimean-Congo hemorrhagic fever (CCHF) and Rift Valley fever (RVF) are among the list of emerging zoonotic diseases that require special attention and priority. RVF is one of the six priority diseases selected by the Senegalese government. Repeated epidemic episodes and sporadic cases of CCHF and RVF in Senegal motivated this study, involving a national cross-sectional serological survey to assess the distribution of the two diseases in this country throughout the small ruminant population. A total of 2127 sera from small ruminants (goat and sheep) were collected in all regions of Senegal. The overall seroprevalence of CCHF and RVF was 14.1% (IC 95%: 12.5-15.5) and 4.4% (95% CI: 3.5-5.3), respectively. The regions of Saint-Louis (38.4%; 95% CI: 30.4-46.2), Kolda (28.3%; 95% CI: 20.9-35.7), Tambacounda (22.2%; 95% CI: 15.8-28.6) and Kédougou (20.9%; 95% CI: 14.4-27.4) were the most affected areas. The risk factors identified during this study show that the age, species and sex of the animals are key factors in determining exposure to these two viruses. This study confirms the active circulation of CCHF in Senegal and provides important and consistent data that can be used to improve the surveillance strategy of a two-in-one health approach to zoonoses.

Iron (Fe) toxicity presents a significant challenge to rice production in lowland ecosystems globally. The identification of genetic factors responsible for Fe toxicity tolerance is crucial for the development of tolerant rice varieties. This study aimed to unravel the genetic bases of Fe toxicity tolerance using quantitative trait locus (QTL) mapping. We conducted phenotypic evaluations for Fe toxicity tolerance on 54 chromosome segment substitution lines (CSSLs) obtained from a cross between the moderately susceptible IR64 ( O. sativa ) and the tolerant donor TOG5681 ( O. glaberrima ) under Fe toxicity stress. QTL analysis was performed using agro-morphological traits and microsatellite genotypic data. High heritability estimates were observed for key traits such as leaf bronzing score (LBS) and grain yield. Several loci associated with agronomic traits, including plant height (qPH2.1), panicle number (qPN4.1), grain weight (qGW4.1), harvest index (qHI4.1), maturity (qMat6.1) and shoot weight (qSW6.1 and qSW11.1), were identified. Additionally, a major QTL (qLBS11.1) linked to leaf bronzing (LBS) was identified, housing the OsbHLHq11 gene involved in iron homeostasis regulation. A comparative analysis revealed colocation with previously reported QTLs, validating their significance. OsbHLHq11 was found to be conserved across diverse rice germplasm, including lowland NERICA (NEw RICe for Africa) varieties, which were developed through crossing O. sativa and O. glaberrima . The discovery of qLBS11.1 and the candidate gene OsbHLHq11 offers insights into the genetic mechanisms governing Fe toxicity tolerance, highlighting potential targets for breeding tolerant rice varieties using marker-assisted selection or genetic engineering strategies.

Starting from the vantage point that animal geographies remain primarily concerned with present animals, what might we learn from an attentiveness to the absence(s) of animals in the context of human-nonhuman relations as approached by the subdiscipline? This prompt is addressed in this commentary by placing (the absences of) West African sardinellas-small pelagic fish-in Senegal on the animal geographies map. Focusing on a derivative of sardinellas, keccax (artisanally smoked and dried fish), and its traces in fish-processing infrastructures in one fishing town on the Senegalese seaboard, the following remarks address twofold absences of the fish: sardinellas' absence in the animal geographies literature; and sardinellas' absence in certain locales in Senegal at the current moment. Against these absences, I argue that animal geographies would significantly benefit, both empirically and theoretically, from more deliberate inquiries into how humans experience animals as absent, across their life and death cycle. Such an attentiveness to animal absences, their diverse and always situated manifestations, and the ways they are being experienced by humans entangled in transforming more-than-human political economies, affords inquiring into ways of remaining 'afloat' in such post-colonial geographies of protracted extractivism as the one presented in this intervention. ARTICLE HISTORY

The African fan palm, Borassus aethiopum, is widely distributed in West and Central Africa. To contribute to the understanding of its evolutionary history and geographical distribution, we have performed the analysis of its genetic diversity and population structure through a wide samples collection in different countries. Simple sequences repeat (SSR) markers were used to assess the population structure and genetic diversity of such samples. Genetic diversity was estimated for a total of 201 samples of B. aethiopum using 13 SSR markers. The result of our analysed populations indicated a mean value of expected heterozygosity (He) of 0.395, suggesting a moderate genetic diversity, with 62% and 37% of molecular variance within individuals and among populations, respectively. Clustering analysis by using Bayesian method and principal component analysis clustered populations into two main groups corresponding to the two sampling regions (West and Central Africa), and each group consists of two genetic clusters. In addition to this, we tested the ability of the same SSR markers to discriminate between both fan palm species occurring in sub-Saharan Africa, namely B. aethiopum and B. akeassii. Hence, our markers can be used as molecular tools for differentiating both species and furthermore for genetic diversity of B. akeassii populations.

Background Antibiotic resistance (ABR) has emerged as a major threat to health. Properly informed decisions to mitigate this threat require surveillance systems that integrate information on resistant bacteria and antibiotic use in humans, animals, and the environment, in line with the One Health concept. Despite a strong call for the implementation of such integrated surveillance systems, we still lack a comprehensive overview of existing organizational models for integrated surveillance of ABR. To address this gap, we conducted a scoping review to characterize existing integrated surveillance systems for ABR. Methods The literature review was conducted using the PRISMA guidelines. The selected integrated surveillance systems were assessed according to 39 variables related to their organization and functioning, the socio-economic and political characteristics of their implementation context, and the levels of integration reached, together with their related outcomes. We conducted two distinct, complementary analyses on the data extracted: a descriptive analysis to summarize the characteristics of the integrated surveillance systems, and a multiple-correspondence analysis (MCA) followed by a hierarchical cluster analysis (HCA) to identify potential typology for surveillance systems. Results The literature search identified a total of 1330 records. After the screening phase, 59 references were kept from which 14 integrated surveillance systems were identified. They all operate in high-income countries and vary in terms of integration, both at informational and structural levels. The different systems combine information from a wide range of populations and commodities -in the human, animal and environmental domains, collection points, drug-bacterium pairs, and rely on various diagnostic and surveillance strategies. A variable level of collaboration was found for the governance and/or operation of the surveillance activities. The outcomes of integration are poorly described and evidenced. The 14 surveillance systems can be grouped into four distinct clusters, characterized by integration level in the two dimensions. The level of resources and regulatory framework in place appeared to play a major role in the establishment and organization of integrated surveillance. Conclusions This study suggests that operationalization of integrated surveillance for ABR is still not well established at a global scale, especially in low and middle-income countries and that the surveillance scope is not broad enough to obtain a comprehensive understanding of the complex dynamics of ABR to appropriately inform mitigation measures. Further studies are needed to better characterize the various integration models for surveillance with regard to their implementation context and evaluate the outcome of these models.

Background This study was carried out in Linguere department, Louga region of Senegal. Its objective was to explore the socio-economic factors that influence small ruminant producers’ decisions on vaccination against peste des petits ruminants. Methods We carried out a willingness to vaccinate and willingness to pay for vaccination using a choice experiment approach with 200 small ruminant producers. Results Results showed that the key factors that influence willingness to vaccinate, include perceived benefits of vaccination (98, 95%CI: 96–100%), the type of vaccinator (91, 95%CI: 87–95%), the access to information (86, 95%CI: 81–91%), the vaccine availability (80, 95%CI: 74–86%), and the possession of a vaccination certificate by the producer (76, 95%CI: 70–82%). Preferences of producers leaned toward home vaccination (preference weight = 0.74, p = 1%), individual herd vaccination (preference weight = 0.45, p = 1%), elective participation to vaccination (preference weight = 0.33, p = 0.01), and low-cost services (preference weight = −0.004, p = 0.1). Producers expressed a willingness to pay for vaccination per animal of XOF 184 (USD 0.3), XOF 113 (USD 0.18), and XOF 82 (USD 0.13) for home, individual herd, and elective vaccination, respectively. Conclusion The findings underscore the importance of targeted awareness campaigns and bringing vaccination services closer to the producers.

The One Health approach calls for collaboration across various sectors and different scales to improve understanding of complex health issues. Regarding epidemiological surveillance, this implies the development of integrated systems that link several surveillance components operating in different domains (human, domestic animals, environment) and involving several actor networks. However, surveillance continues to operate in a very compartmentalized way, with little interaction between sectoral institutions and with the community for the governance and operation of surveillance activities. This is partly explained by the insufficient consideration of the local context and the late involvement of national stakeholders when developing programmes that aimed at strengthening the integration of surveillance. In low- and middle-income countries in particular, there is a strong influence of external partners on the development of intersectoral programmes, including surveillance systems. In this context, we developed and implemented a participatory planning process to support stakeholders of the surveillance system of anthrax in Burkina Faso, in the definition of the One Health surveillance system they wish for and of the pathway to reach it. The workshop produced an action plan that reflects the views and perspectives of representatives of the different categories of stakeholders and beneficiaries of surveillance. In addition, the participation of stakeholders in this participatory co-construction process has also improved their knowledge and mutual understanding, fostering a climate of trust conducive to further collaboration for surveillance activities. However, the quality of the participation raises some questions over the results, and contextual factors may have influenced the process. This underlines the need to include a monitoring and evaluation plan in the process to assess its implementation and ability to produce One Health surveillance modalities that are appropriate, accepted and applied over the long term.

Transhumants move their herds based on strategies simultaneously considering several environmental and socio-economic factors. There is no agreement on the influence of each factor in these strategies. In addition, there is a discussion about the social aspect of transhumance and how to manage pastoral space. In this context, agent-based modeling can analyze herd movements according to the strategy based on factors favored by the transhumant. This article presents a reductionist agent-based model that simulates herd movements based on a single factor. Model simulations based on algorithms to formalize the behavioral dynamics of transhumants through their strategies. The model results establish that vegetation, water outlets and the socio-economic network of transhumants have a significant temporal impact on transhumance. Water outlets and the socio-economic network have a significant spatial impact. The significant impact of the socio-economic factor demonstrates the social dimension of Sahelian transhumance. Veterinarians and markets have an insignificant spatio-temporal impact. To manage pastoral space, water outlets should be at least $15\ km$ 15 k m from each other. The construction of veterinary centers, markets and the securitization of transhumance should be carried out close to villages and rangelands.

Fisheries science has been trying to identify the best way to analyze and predict fish biomass and its spatial distribution since several decades using, among others, kirigng model, co-kiriging model, Species Distribution Modeling and Joined Species Distribution Modeling, based on conventional statistical methods as Generalized Linear Models and Generalized Additive Models, with contested results. We consider a bio-ecological issue applying a non parametric spatial prediction based on a spatio-functional regression models, in a fixed design sampling context, as a supervised classification method when the variable of interest belongs to a predefined class set. The proposed predictor takes into account the spatial fish distribution and environmental variable such as salinity and temperature. The development of the method depends on two kernels to control both interactions between observations and locations. The results show that this nonparametric spatial functional supervised classification method is an efficient tool applied to predict spatial distribution of demersal coastal fish off Senegal.