Unlocking the microbiome communities of Banana (Musa spp.) under disease stressed (Fusarium wilt) and non-stressed conditions

We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots, and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots, and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e., without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa

AR-NAFAKA Project Aflatoxin Management: 2016-2017 Progress

United States Agency for International Developmen

A new multi locus variable number of tandem repeat analysis scheme for epidemiological surveillance of Xanthomonas vasicola pv. musacearum, the plant pathogen causing bacterial wilt on banana and enset

Xanthomonas vasicola pv. musacearum (Xvm) which causes Xanthomonas wilt (XW) on banana (Musa accuminata x balbisiana) and enset (Ensete ventricosum), is closely related to the species Xanthomonas vasicola that contains the pathovars vasculorum (Xvv) and holcicola (Xvh), respectively pathogenic to sugarcane and sorghum. Xvm is considered a monomorphic bacterium whose intra-pathovar diversity remains poorly understood. With the sudden emergence of Xvm within east and central Africa coupled with the unknown origin of one of the two sublineages suggested for Xvm, attention has shifted to adapting technologies that focus on identifying the origin and distribution of the genetic diversity within this pathogen. Although microbiological and conventional molecular diagnostics have been useful in pathogen identification. Recent advances have ushered in an era of genomic epidemiology that aids in characterizing monomorphic pathogens. To unravel the origin and pathways of the recent emergence of XW in Eastern and Central Africa, there was a need for a genotyping tool adapted for molecular epidemiology. Multi-Locus Variable Number of Tandem Repeat Analysis (MLVA) is able to resolve the evolutionary patterns and invasion routes of a pathogen. In this study, we identified microsatellite loci from nine published Xvm genome sequences. Of the 36 detected microsatellite loci, 21 were selected for primer design and 19 determined to be highly typeable, specific, reproducible and polymorphic with two- to four- alleles per locus on a sub-collection. The 19 markers were multiplexed and applied to genotype 335 Xvm strains isolated from seven countries over several years. The microsatellite markers grouped the Xvm collection into three clusters; with two similar to the SNP-based sublineages 1 and 2 and a new cluster 3, revealing an unknown diversity in Ethiopia. Five of the 19 markers had alleles present in both Xvm and Xanthomonas vasicola pathovars holcicola and vasculorum, supporting the phylogenetic closeliness of these three pathovars. Thank to the public availability of the haplotypes on the MLVABank database, this highly reliable and polymorphic genotyping tool can be further used in a transnational surveillance network to monitor the spread and evolution of XW throughout Africa.. It will inform and guide management of Xvm both in banana-based and enset-based cropping systems. Due to the suitability of MLVA-19 markers for population genetic analyses, this genotyping tool will also be used in future microevolution studies

Effect of Inoculation Pressure on Maize Dwarf Mosaic Virus Strain-A Disease Incidence, Severity and Titer in Sorghum.

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Ultrastructure of the infection of sorghum bicolor and zea mays by pythium species

Research PaperThe practice of cultivating mixed crops is common in Tropical Africa and elsewhere especially in areas of high population density. The practice of mixed cropping can promote disease spread especially in multi-host pathosystems. Pythium is a soil borne oomycete with a wide host range affecting both cereal and legumes. In this paper we examine pathogenesis by Pythium species in maize and sorghum, crops commonly included as intercrops in south western Uganda. In this study, both electron and light microscopy were used to study infection process using bean derived Pythium species-Pythium ultimum (MS 61) and Pythium irregulare (DFD 47) on beans, maize and sorghum. Electron microscopy revealed that on maize P.irregulare hyphae remained extracellular while P. ultimum hyphae in epidermis underwent necrosis after 9 days. In sorghum on the contrary, P. ultimum and P. irregulare extensively colonised both the epidermis and endodermis. In this study, P. ultimum also had two types of hyphae which mediated infection thus making it more virulent than P. irregulare. The results of this study confirm that Pythium spp. are pathogenic on sorghum and therefore the role of sorghum in Pythium inoculum build-up in bean fields cannot be precluded.The practice of cultivating mixed crops is common in Tropical Africa and elsewhere especially in areas of high population density. The practice of mixed cropping can promote disease spread especially in multi-host pathosystems. Pythium is a soil borne oomycete with a wide host range affecting both cereal and legumes. In this paper we examine pathogenesis by Pythium species in maize and sorghum, crops commonly included as intercrops in south western Uganda. In this study, both electron and light microscopy were used to study infection process using bean derived Pythium species-Pythium ultimum (MS 61) and Pythium irregulare (DFD 47) on beans, maize and sorghum. Electron microscopy revealed that on maize P.irregulare hyphae remained extracellular while P. ultimum hyphae in epidermis underwent necrosis after 9 days. In sorghum on the contrary, P. ultimum and P. irregulare extensively colonised both the epidermis and endodermis. In this study, P. ultimum also had two types of hyphae which mediated infection thus making it more virulent than P. irregulare. The results of this study confirm that Pythium spp. are pathogenic on sorghum and therefore the role of sorghum in Pythium inoculum build-up in bean fields cannot be precluded

A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences

Xanthomonas vasicola pv. musacearum (Xvm) is a bacterial pathogen responsible for the economically important Xanthomonas wilt disease on banana and enset crops in Sub-Saharan Africa. Given that the symptoms are similar to those of other diseases, molecular diagnosis is essential to unambiguously identify this pathogen and distinguish it from closely related strains not pathogenic on these hosts. Currently, Xvm identification is based on polymerase chain reaction (PCR) with GspDm primers, targeting the gene encoding general secretory protein D. Experimental results and examination of genomic sequences revealed poor specificity of the GspDm PCR. Here, we present and validate five new Xvm-specific primers amplifying only Xvm strains

Potential impact of current agricultural practices on mycotoxin occurrence and mycotoxin knowledge along the cassava value chain in Uganda

Cassava is the second most important staple food crop for Uganda and is prone to contamination with mycotoxins. This study aimed at understanding the current agricultural practices, their potential influence on mycotoxin occurrence, as well as assessing mycotoxin knowledge among key cassava value chain actors, including farmers, wholesalers, and processors. Data were collected through individual interviews (210), key informant interviews (34), and 4 focus group discussions. The findings revealed that 51% of farmers peeled cassava directly on bare ground, resulting in direct contact with soil that potentially harbors mycotoxin-producing fungi, such as Aspergillus section Flavi. During postharvest handling, 51.6% of farmers dried cassava chips directly on bare ground. Nearly, all (95.2%) of wholesalers packed cassava chips in local gunny bags and placed them on ground instead of pallets. In the processing of cassava chips into flour, only one of the 14 processing machines was certified by the Uganda National Bureau of Standards. Additionally, there was only one processing machine available for every 180 (1:180) consumers bringing their cassava for processing. 50.8% of cassava consumers interviewed admitted to consuming cassava flour regardless of quality, while 73% blended cassava flour with flour from mycotoxin-susceptible crops mainly maize, millet, and sorghum. Most (96.2%) of the people along the cassava value chain did not understand what the term mycotoxins meant. However, 56% of interviewed respondents were familiar with the term aflatoxins. Of the cassava value chain actors aware of mycotoxins, 82.9% knew of methods for reducing aflatoxin contamination, but only 40.9% were putting such methods into practice. More farmers (47.9%) managed aflatoxins compared to wholesalers (33.3%) and processors (21.4%). Knowledge on aflatoxins was significantly associated with value chain actor (P = 0.026), head of household (P = 0.004), region (P = 0.033), age (P = 0.001), and experience (P = 0.001). This study highlights the critical areas of mycotoxin contamination within the cassava value chain in Uganda and underscores the need to improve the knowledge among value chain actors especially farmers.Commonwealth Scientific and Industrial Research OrganisationJournal of Food Protectio

Genome-wide association study and QTL mapping reveal genomic loci associated with Fusarium ear rot resistance in tropical maize germplasm

Published online: 14 October 2016; Open Access JournalFusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1% to 4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four bi-parental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight co-located loci on Chromosomes 2, 3, 4, 5, 9 and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize

Aspects of current research to combat Fusarium wilt of banana with a special focus on TR4. Brief proceedings of an RTB virtual mini-symposium. FP3 Resilient Crops - Cluster BA3.3 Fungal and Bacterial Wilts.

Sharing both recent research results and plans for future studies are vital components of RTB’s strategy to contribute to tackling the threat posed by Foc TR4, and it was for this reason that researchers from BA3.3 convened a mini symposium entitled ‘Aspects of current research to combat Fusarium Wilt of banana with a special focus onTR4’. This brought together more than 60 researchers from across the world for a two-day virtual exchange of cutting-edge research presentations and discussion. Importantly, the results presented are to be published through a special issue of the Journal of Fungi. The work presented in this booklet, which summarizes the proceedings of the mini symposium, constitutes cutting-edge research to address the challenges posed by Foc TR4 that threatens Cavendish as well as other key susceptible cultivars. The research reveals new insights into the spread of Foc TR4 in southern Africa, the Greater Mekong Delta, and Latin America; evaluating biocontrol agents; the survival of Fusarium spores in water; the effects of nematodes and weevils in pathogen spread and infection; and in breeding for resistance. There are great opportunities to harness potential synergies from the many complementarities revealed in the symposium, and a need to scale the research from in vitro to field studies, with the ultimate goal of implementing scalable findings at farm and plantation level. Fusarium wilt will continue to be a challenge for banana producers in the near future. However, as control technologies described here are scaled out, there is real hope that production of what is one of humanity’s most treasured fruits will be restored and that livelihoods of all those that depend on it will be enhanced