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Cultivated peanut or groundnut (Arachis hypogaea L.) is a grain legume grown in many developing countries by smallholder farmers for food, feed, and/or income. The speciation of the cultivated species, that involved polyploidization followed by domestication, greatly reduced its variability at the DNA level. Mobilizing peanut diversity is a prerequisite for any breeding program for overcoming the main constraints that plague production and for increasing yield in farmer fields. In this study, the Groundnut Improvement Network for Africa assembled a collection of 1,049 peanut breeding lines, varieties, and landraces from 9 countries in Africa. The collection was genotyped with the Axiom_Arachis2 48K SNP array and 8,229 polymorphic single nucleotide polymorphism (SNP) markers were used to analyze the genetic structure of this collection and quantify the level of genetic diversity in each breeding program. A supervised model was developed using dapc to unambiguously assign 542, 35, and 172 genotypes to the Spanish, Valencia, and Virginia market types, respectively. Distance-based clustering of the collection showed a clear grouping structure according to subspecies and market types, with 73% of the genotypes classified as fastigiata and 27% as hypogaea subspecies. Using STRUCTURE, the global structuration was confirmed and showed that, at a minimum membership of 0.8, 76% of the varieties that were not assigned by dapc were actually admixed. This was particularly the case of most of the genotype of the Valencia subgroup that exhibited admixed genetic heritage. The results also showed that the geographic origin (i.e. East, Southern, and West Africa) did not strongly explain the genetic structure. The gene diversity managed by each breeding program, measured by the expected heterozygosity, ranged from 0.25 to 0.39, with the Niger breeding program having the lowest diversity mainly because only lines that belong to the fastigiata subspecies are used in this program. Finally, we developed a core collection composed of 300 accessions based on breeding traits and genetic diversity. This collection, which is composed of 205 genotypes of fastigiata subspecies (158 Spanish and 47 Valencia) and 95 genotypes of hypogaea subspecies (all Virginia), improves the genetic diversity of each individual breeding program and is, therefore, a unique resource for allele mining and breeding., Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

This study aimed to evaluate the prevalence of E. coli, Pseudomonas spp., and Enterococcus spp. in Nile tilapia broodstock farms in Togo and their association with fish diseases. In total, 60 samples were collected from two tilapia broodstock farms, including 40 broodstock tilapia and 20 water samples. Each farm had concrete tanks supplied with water from two drills. Of the 40 fish samples, 20 were healthy, and the other 20 were diseased. Microbiological analysis of samples was conducted using standardized methods. The study revealed significant contamination in all collected water samples, detecting multiple bacterial populations. Bacterial infections were more prevalent in symptomatic fish, with 85% exhibiting co-infections (df = 1, χ 2  = 7.03, p = 0.008). Contamination levels varied among sample types, with higher counts observed in wastewater (E. coli: 0-300 CFU/mL, Pseudomonas spp.: 3-300 CFU/mL, Enterococcus spp.: 0-55 × 102 CFU/mL) compared to drilling water (Pseudomonas spp.: 0-300 CFU/mL, E. coli: 3-400 CFU/mL, Enterococcus spp.: 0-14 × 102 CFU/mL), and intestinal samples (E. coli: 0-120 × 102 CFU/mL, Enterococcus spp.: 0-170 × 102 CFU/mL, Pseudomonas spp.: 0-60 × 102 CFU/mL) (df = 21, χ 2  = 59.31, p < 0.000). Our findings emphasize the significant prevalence of pathogenic bacteria in Nile tilapia broodstock farms in Togo, highlighting the importance of water quality management and infection control strategies. Further studies are required to develop appropriate prevention strategies., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

This study aims to develop an Excel programming model to formulate feed for Nile tilapia ( Oreochromis niloticus ), mainly for small- and medium-sized fish feed manufacturers. The model allows users to formulate the least costly balanced diet of Nile tilapia species, giving them the ability to choose a specific ingredient in the formulation according to the realities of the local environment: space-temporary availability of ingredients, prices and nutritional quality. Computer programming of a database of 25 locally available feed components was carried out using the Excel Solver Add-in and Excel IF mathematical functions to incorporate/delete specific ingredients in real time in accordance with user objectives. The theoretical characteristics of the least-cost balanced diets performed were within the margin of the nutrients requirement of the target fish size with protein levels of 35 per cent (fry diet: $1.07/kg), 32 per cent (fingerlings diet: $0.48/kg), 29 per cent (growth diet: $0.43/kg) and 27.12 per cent (final diet: $0.39/kg). The digestible energy of these diets was between 3016.5 ± 93.8 kcal. In addition, the model shows that an increase in soya meal prices by 75 per cent led the local feed industry to rely on imported fish meals, as the number included reached 52.28 per cent. However, the cost of the diet margin did not vary significantly. Nevertheless, it would be important to test the balanced diet developed with the model before production and scaling., Competing Interests: Competing InterestsThe authors declare no competing interests., (© The Author(s), under exclusive licence to Springer Nature Switzerland AG 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Trypanosoma (T.) vivax is one of the animal trypanosomes species causing calf mortality and economic losses in Togo. Despite its importance as the most widely distributed trypanosome species, T. vivax has received little attention because it is difficult to cultivate most field isolates in rodents. No molecular diagnostic tools for the identification of drug-resistant in T. vivax are currently available. Herein, four field isolates of T. vivax from Togo were cryopreserved and assessed for susceptibility to diminazene aceturate (DA) and isometamidium chloride (ISM) in goats. For field isolate preparation, 1 ml of blood from an infected goat was diluted in 111 µl of phosphate-buffered-saline and stored in liquid nitrogen. The in vivo experiment drug test was performed using twenty Sahelian goats with six-month of age and weighing 14.5 ± 1.6 kg. These experimental goats were purchased from a tsetse free-area Dori, a Sahelian region of Burkina Faso. The cryopreserved T. vivax isolates with unknowns, DA, and ISM sensitivity was inoculated to five goats and one goat was used as control. Each animal was inoculated by intravenously route 1 × 10 5 trypanosomes from the donor goat. Relapses were earlier in the first phase of treatment (14.85 ± 1.08 days) compared with the second phase (20 ± 3.39 days). The overall mean PCV of the control group decreased from 32% to 17% at day-60 (P-value < 0.001). Three isolates were phenotypically resistant to 0.5 mg per kg body weight (BW) ISM and one for 3.5 mg per kg BW of DA. There were no relapses with the 7 mg per kg BW dose DA. This study shows the resistance of T. vivax to two main trypanocidal drugs in different villages of Mango. The results suggest the extension of surveillance strategies to remote villages in Togo and will guide the veterinarian or herder in choosing a mass treatment strategy. Further studies will be needed to better understand the molecular basis of the observed resistance., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The effects of tsetse-transmitted trypanosomosis control in high tsetse flies (Glossina spp.) challenge and trypanocidal drug resistance settings remain poorly understood in Togo owing to poor data coverage on the current disease impact. From March 2014 to November 2017, a database of zoo-sanitary surveys integrating the evolution of disease incidence and intervention coverage made it possible to quantify the apparent effects attributable to the control effort, focused on all sedentary cattle breeds in the 1,000 km² area of Mô in Togo. The strategy involved an initial phase with cross-sectional entomological and parasitological. Then, three times a year, 20% of the bovine animals of the study area received α-cypermethrin pour-on, and infected cattle with poor health (798 cattle in 2014 and 358 in 2017) were individually given diminazene aceturate at 7 mg/kg of body weight. The tsetse density in the area decreased significantly, from 1.78 ± 0.37 in March 2014 before the α-cypermethrin application to 0.48 ± 0.07 in February 2017. The α-cypermethrin pour-on application and diminazene aceturate treatment of cattle led to the largest reduction in disease incidence, from 28.1% in 2014 to 7.8% in 2017, an improvement in hematocrit from 24.27 ± 4.9% to 27.5 ± 4.6%, and a reduction in calf mortality from 15.9 ± 11% to 5.9%. Improved access to these interventions for different types of livestock and maintaining their effectiveness, despite high tsetse (Diptera: Glossinidae) challenges, should be the primary focus of control strategies in many areas of Togo., (© The Author(s) 2021. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food that is widely cultivated in sub-Saharan Africa. In August 2018, a survey was conducted in the main producing regions of Burkina Faso, and leaf samples were analyzed using virion-associated nucleic acid (VANA)-based metagenomic approach and Illumina sequencing. A new virus, tentatively named "Pennisetum glaucum marafivirus" (PGMV), was detected, and its complete nucleotide sequence of 6364 nucleotides was determined. The sequence contains a large open reading frame (ORF) encoding a polyprotein of 224.2 kDa with five domains (methyltransferase, papain-like protease, helicase, RNA-dependent RNA polymerase, and coat proteins), typical of marafiviruses. Additionally, a characteristic conserved marafibox domain was detected in the genome. The nucleotide sequence of the complete PGMV genome shares 68.5% identity with that of sorghum bicolor marafivirus, and its coat protein shares 58.5% identity with that of oat blue dwarf virus. Phylogenetic analysis confirmed that the pearl millet virus is unambiguously grouped with members of the genus Marafivirus in the family Tymoviridae. This is the first report on the occurrence of a marafivirus in pearl millet., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Main Conclusion: Plant traits of interest for sorghum breeders to develop dual-purpose varieties are stem diameter, flag leaf size, crop cycle, and number of grains per panicle. To develop dual-purpose varieties, breeders need to improve traits linked both to grain and biomass production. To identify these traits, we studied the phenotypic plasticity of eighteen traits and the performance of ten contrasting sorghum genotypes, used in West Africa. Trials were carried out in a randomized complete blocks design with four replicates from 2013 to 2016 in Bambey, Sinthiou Malem and Nioro du Rip in Senegal. The results revealed three plant types. The first type, "biomass production", contained genotypes IS15401 and SK5912, and was linked to cycle duration, leaf area, and plant height. The second type, "grain production", grouped the caudatum race sorghum 621B, F2-20 and Soumba, and was associated with the number of grains per panicle and the width of the flag leaf. The third group, "dual-purpose", corresponding to the genotypes Fadda, Nieleni and Pablo, combined some favourable traits for grain and biomass: stem diameter, internode length, number of green leaves and number of grains per panicle. The study showed that high and stable grain yields were associated with stability in flag leaf size, phenology and number of grains per panicle, and a high and stable biomass yield was associated with stability in stem diameter. Those stable plant traits might be of interest for sorghum breeders selecting to develop dual-purpose varieties.

Background: Information on population structure and genetic diversity of germplasm in a breeding programme is useful because it enhances judicious utilisation of genetic resources to achieve breeding objectives. Seventy early maturing provitamin A (PVA) quality protein maize (QPM) inbreds developed by the IITA- maize improvement programme were genotyped using 8171 DArTseq markers. Furthermore, 96 hybrids derived from 24 selected inbreds plus four checks were evaluated under low-N and optimal environments in Nigeria during 2016 and 2017. Genotypic and phenotypic data of inbreds and hybrids respectively, were analysed to (i) assess the level of genetic dissimilarities and population structure of the inbreds, and (ii) investigate the grain yield performance of derived hybrids under low-N, optimal and across environments., Results: Genetic diversity among the seventy inbreds was high varying from 0.042 to 0.500 with an average of 0.357. Sixty-six inbred lines with probabilities ≥0.70 were assigned to a single group. The population structure analysis, the UPGMA phylogeny, and the principal Coordinate Analysis (PCoA) of the DArTseq markers revealed a clear separation of five groups and each followed pedigree records. Clustered inbreds displayed common characteristics including high PVA levels, and drought and low-N tolerance. The top performing hybrid, TZEIORQ 40 × TZEIORQ 26 out-yielded the best hybrid control, TZEIOR 127 × TZEIOR 57 by 8, 3, and 9% under low-N, optimal, and across environments, respectively. High repeatability estimates were detected for grain yield under each and across environments. Similarly, high breeding efficiency of 71, 70 and 72% were computed under low-N, optimal, and across environments, respectively., Conclusions: The UPGMA clustering, the structure analysis, and the PCoA consistently revealed five groups which largely followed pedigree information indicating the existence of genetically distinct groups in the inbred lines. High repeatability and breeding efficiency values estimated for grain yield of hybrids under low-N, optimal and across environments demonstrated that high productive hybrids could be developed using inbreds from the opposing clusters identified by the DArTseq markers. The 15 top performing hybrids identified, particularly TZEIORQ 40 × TZEIORQ 26 and TZEIORQ 29 × TZEIORQ 43 should be further evaluated for release and commercialization in SSA.

Diversity assessment of 94 groundnut accessions from Togo and Senegal, using agro-morphological and SNP markers, revealed high variability for many quantitative traits such as late leaf spot (LLS) incidence, number of pods per plant and yield per plant. For qualitative traits, the Simpson Index showed high diversity for primary seed colour (0.75), stem pigmentation (0.60), and Growth habit (0.59). Principal component analysis underscored quantitative traits such as hundred seed weight, days to maturity, and LLS incidence, as the main traits contributing to the divergence. Correlation and path coefficient analysis showed that the number of pods per plant was the main yield-related trait positively affecting yield (r = 0.95, PC = 0.84; p = 0.01). Overall, 990 SNP markers revealed moderate genetic variability in the genotypes and the percentage of heterozygous genotypes varied from 0 to 50% for all loci. Analysis of molecular variance revealed that only 1.1% of the total molecular variance accounted for geographical contribution to the diversity. Co-analysis of phenotypic and SNP data delineated three clusters harbouring useful alleles and interesting phenotypic features such as LLS resistance, large number of pods per plant and early maturity indicating that differences observed at the phenotypic level are underlined by genotypic differences. The phenotypic and genotypic diversity observed could be exploited for the identification of parents with preferred traits for use in the breeding program. However, the low population structure highlights the necessity to improve groundnut diversity in Togo through introduction from various sources., Competing Interests: Conflicts of interestThe authors declare that they have no competing interests., (© Prof. H.S. Srivastava Foundation for Science and Society 2020.)

Pearl millet plays a major role in food security in arid and semi-arid areas of Africa and India. However, it lags behind the other cereal crops in terms of genetic improvement. The recent sequencing of its genome opens the way to the use of modern genomic tools for breeding. Our study aimed at identifying genetic components involved in early drought stress tolerance as a first step toward the development of improved pearl millet varieties or hybrids. A panel of 188 inbred lines from West Africa was phenotyped under early drought stress and well-irrigated conditions. We found a strong impact of drought stress on yield components. This impact was variable between inbred lines. We then performed an association analysis with a total of 392,493 SNPs identified using Genotyping-by-Sequencing (GBS). Correcting for genetic relatedness, genome wide association study identified QTLs for biomass production in early drought stress conditions and for stay-green trait. In particular, genes involved in the sirohaem and wax biosynthesis pathways were found to co-locate with two of these QTLs. Our results might contribute to breed pearl millet lines with improved yield under drought stress., Competing Interests: The authors have declared that no competing interests exist.

Background: Buruli Ulcer (BU) is a neglected tropical skin infection caused by Mycobacterium ulcerans. Residence near aquatic areas has been identified as an important source of transmission of M. ulcerans with increased risk of contracting Buruli ulcer. However, the reservoir and the mode of transmission are not yet well known. The aim of this study was to identify the presence of M. ulcerans in the environment and its relationship with Buruli ulcer occurrence in Zio and Yoto districts of the maritime region in south Togo., Methods: A total of 219 environmental samples including soil (n = 119), water (n = 65), biofilms/plants (n = 29) and animals' feces (n = 6) were collected in 17 villages of Zio and Yoto districts of the maritime region in Togo. DNA of M. ulcerans including IS2404 and IS2606 insertions sequences and mycolactone ketoreductase-B gene (KR-B) was detected using real time PCR amplification (qPCR) technique. In parallel, clinical samples of patients were tested to establish a comparison of the genetic profile of M. ulcerans between the two types of samples. A calibration curve was generated for IS2404 from a synthetic gene of M. ulcerans Transposase pMUM001, the plasmid of virulence., Results: In the absence of inhibition of the qPCR, 6/219 (2.7%) samples were tested positive for M. ulcerans DNA containing three sequences (IS2404/IS2606/KR-B). Positive samples of M. ulcerans were consisting of biofilms/plants (3/29; 10.3%), water (1/65; 1.7%) and soil (2/119; 1.5%). Comparative analysis between DNA detected in environmental and clinical samples from BU patients showed the same genetic profile of M. ulcerans in the same environment. All these samples were collected in the environment of Haho and Zio rivers in the maritime region., Conclusion: This study confirms the presence of M. ulcerans in the environment of the Zio and Yoto districts of the maritime region of Togo. This may explain partially, the high rates of Buruli ulcer patients in this region. Also, water, plants and soil along the rivers could be possible reservoirs of the bacterium. Therefore, Haho and Zio rivers could be potential sources of infection with M. ulcerans in humans in these districts., Competing Interests: The authors have declared that no competing interests exist.