Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya.

Funder: Bill and Melinda Gates Foundation; doi: http://dx.doi.org/10.13039/100000865BACKGROUND: Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. METHODS: Tomato leaf samples with virus-like symptoms were obtained from farmers' field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. RESULTS: Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. CONCLUSIONS: The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country

EVALUATION OF THE QUALITY STATUS OF AFRICAN NIGHTSHADE SEED PRODUCED BY FARMERS IN KENYA

Seed as an important input in crop production should be of high quality, pathogen free, have desired germination and emergence. This study was carried out to evaluate the quality status of African nightshade (Solanum scabrum and S. villosum Miller) seed produced by farmers in Kenya. A household survey was carried out in 240 farms using a structured questionnaire and a total of 164 samples of farm saved, market and certified seeds were obtained during this survey. Seed samples were tested in the laboratory at the University of Nairobi and Pearson’s correlation between seed quality and germination parameters was done. The analysis showed that majority of farmers use farm saved (50%) or seed purchased from the local markets (28%) which have low purity and germination rates. The farm, market and certified seed differed (p<0.05) significantly with regard to seed purity, moisture content, seedling vigor index and germination percentage. Farm saved and market seed had low seed purity 68.6% and 74% respectively, compared to certified seed 94.4%. In addition, only certified seed met the recommended moisture and germination percentage as per the International Seed Testing Association (ISTA) standards. There were significant (p≤ 0.05 and p≤0.01) positive correlation comparing seed quality and germination parameters, for example seed purity had significant positive correlation (r=0.76**) with germination percentage. This study affirms that the use of clean seed increases germination percentage of crops

Identification and Characterization of <i>Colletotrichum</i> Species Causing Sorghum Anthracnose in Kenya and Screening of Sorghum Germplasm for Resistance to Anthracnose

Anthracnose caused by Colletotrichum species is one of the most destructive fungal diseases of sorghum with annual yield losses of up to 100%. Although the resistance to anthracnose has been identified elsewhere, the usefulness of the resistance loci differs depending on the pathogen species and pathotypes. Accurate species identification of the disease-causing fungal pathogens is essential for developing and implementing suitable management strategies. The use of host resistance is the most effective strategy of anthracnose management and therefore identification of sources for resistance against unique pathogen pathotypes is fundamental. The aims of this study were to identify and characterize Colletotrichum species associated with sorghum anthracnose and screen sorghum germplasm for resistance to anthracnose. Symptomatic sorghum leaf samples were collected from smallholder farmers in lower eastern Kenya and used for the isolation, identification and characterization of Colletotrichum species using morpho-cultural and phylogenetic analyses with the sequences of the rDNA internal transcribed spacer (ITS) region. Pathogenicity tests of the seven fungal isolates showed that there were no significant differences in the pathogenicity on host plants. The fungal isolates were variable in cultural and morphological characters such as colony type and color, colony diameter, mycelia growth and hyaline. The phenotypic characters observed were useful in the identification of the genus Colletotrichum and not the species. Based on the sequence and phylogenetic analysis of ITS, Colletotrichum sublineola was revealed to be associated with anthracnose on sorghum. Germplasm screening for resistance to anthracnose showed differential reactions of sorghum genotypes to anthracnose under greenhouse and field conditions. The results revealed four resistant genotypes and ten susceptible genotypes against Colletotrichum sublineola. Significant (p ≤ 0.05) differences were observed in grain weight, grain yield, weight of 100 seeds and harvest index among the tested sorghum genotypes. The present study indicated that the Kenyan accessions could be an important source of resistance to anthracnose. The findings from this study provide a platform towards devising efficient disease control strategies and resistance breeding

Survey of Fungal Foliar and Panicle Diseases in Smallholder Sorghum Cropping Systems in Different Agro-Ecologies of Lower Eastern Kenya

Sorghum is a staple food crop and plays a critical role in subsistence farming in Kenya due to its adaptability to marginal agro-ecological zones. However, fungal diseases are among the major biotic constraints of sorghum production, causing over 70% yield loss in susceptible cultivars. Information on the distribution and severity of fungal diseases is important to establish efficient and improved strategies for integrated disease management of sorghum fungal diseases. The aim of this study was to determine the prevalence, incidence, severity and spatial distribution of fungal diseases on sorghum across agro-ecological zones of lower eastern Kenya. A total of 384 smallholder farmers&rsquo; fields were surveyed, and in each field, 30 plants were assessed for prevalence and incidence of fungal diseases using a W-shaped pattern to cover the whole field. Sorghum anthracnose was the most prevalent disease (71%), followed by leaf blight (70.18%), rust (68.41%), smut (63.02%), sorghum mildew (55.33%), Alternaria leaf spot (48.39%) and rough leaf spot (46.02%). Disease prevalence, incidence and severity varied among the investigated agro-ecological zones. There was a significant difference (p &le; 0.05) in fungal disease severity across the investigated agro-ecological zones. Spatially interpolated disease maps showed a high variation in the distribution of various sorghum fungal diseases across the investigated agro-ecological zones of lower eastern Kenya. Morpho-cultural identification revealed the association of Colletotrichum sublineola with anthracnose, Curvularia lunata and Bipolaris cynodontis with leaf blight, Puccinia purpurea with rust, Peronosclerospora sorghi with downy mildew, Alternaria alternata with Alternaria leaf spot, Ascochyta sorghi with rough leaf spot and Sporisorium sorghi with covered kernel smut symptoms. Information obtained in this study will be useful to update knowledge on sorghum fungal diseases and provide a basis for the development of strategies for management and control of the investigated diseases

Survey of Fungal Foliar and Panicle Diseases in Smallholder Sorghum Cropping Systems in Different Agro-Ecologies of Lower Eastern Kenya

Sorghum is a staple food crop and plays a critical role in subsistence farming in Kenya due to its adaptability to marginal agro-ecological zones. However, fungal diseases are among the major biotic constraints of sorghum production, causing over 70% yield loss in susceptible cultivars. Information on the distribution and severity of fungal diseases is important to establish efficient and improved strategies for integrated disease management of sorghum fungal diseases. The aim of this study was to determine the prevalence, incidence, severity and spatial distribution of fungal diseases on sorghum across agro-ecological zones of lower eastern Kenya. A total of 384 smallholder farmers’ fields were surveyed, and in each field, 30 plants were assessed for prevalence and incidence of fungal diseases using a W-shaped pattern to cover the whole field. Sorghum anthracnose was the most prevalent disease (71%), followed by leaf blight (70.18%), rust (68.41%), smut (63.02%), sorghum mildew (55.33%), Alternaria leaf spot (48.39%) and rough leaf spot (46.02%). Disease prevalence, incidence and severity varied among the investigated agro-ecological zones. There was a significant difference (p ≤ 0.05) in fungal disease severity across the investigated agro-ecological zones. Spatially interpolated disease maps showed a high variation in the distribution of various sorghum fungal diseases across the investigated agro-ecological zones of lower eastern Kenya. Morpho-cultural identification revealed the association of Colletotrichum sublineola with anthracnose, Curvularia lunata and Bipolaris cynodontis with leaf blight, Puccinia purpurea with rust, Peronosclerospora sorghi with downy mildew, Alternaria alternata with Alternaria leaf spot, Ascochyta sorghi with rough leaf spot and Sporisorium sorghi with covered kernel smut symptoms. Information obtained in this study will be useful to update knowledge on sorghum fungal diseases and provide a basis for the development of strategies for management and control of the investigated diseases

Do the invasive Fall Armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), and the maize lepidopteran stemborers compete when sharing the same food?

International audiencen insect communities, the outcome of intra- and inter-specific competitions for food utilisation depend primarily upon density and duration even inter-specific competitions can occur when they are not sharing the same feeding niche such as between foliar feeders and stemborers. Experimental manipulations of larval densities and the durations of common diet feeding of fall armyworm (FAW), S. frugiperda, and the African lepidopteran stemborers, Busseola fusca, Sesamia calamistis and Chilo partellus, were conducted to determine how the density and the duration of resource utilization affected larval survival and the relative growth rate (RGR) in intra- and inter-specific interactions. The results showed both intra- and interspecific competitions were observed among all the four species and interspecific competition was significantly stronger between the stemborers than between the FAW and the stemborers. The results showed that multiple infestations of cereal plants with low larval densities of each species at optimum conditions will very likely prolong the coexistence between FAW and stemborers. In addition, the time partitioning of the resource use significantly influenced this coexistence

Influence of Temperature on the Interaction for Resource Utilization between Fall Armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), and a Community of Lepidopteran Maize Stemborers Larvae

Intra-and interspecific interactions within communities of species that utilize the same resources are characterized by competition or facilitation. The noctuid stemborers, Busseola fusca and Sesamia calamistis, and the crambid stemborer, Chilo partellus were the most important pests of maize in sub-Saharan Africa before the recent "invasion" of fall armyworm (FAW), Spodoptera frugiperda, which currently seriously limits maize yields in Africa. This new pest is interacting with the stemborer community at the larval stage in the use of maize resources. From previous works on the influence of temperature on the larval intra-and interspecific resources utilization within the community of Lepidoptera stemborers involving B. fusca, S. calamistis, and C. partellus, there is a need to update these studies by adding the new pest, S. frugiperda, in order to understand the effect of temperature on the larval interactions of all these four species under the context of climate change. The influence of temperature on intra-and interspecific larval interactions was studied using artificial stems kept at different constant temperatures (15 • C, 20 • C, 25 • C, and 30 • C) in an incubator and assessing survival and relative growth rates of each species in single and multi-species experiments. After the inclusion of FAW into the experiments, with regard to relative growth rates, both intra-and interspecific competition was observed among all four species. With regard to survival rates, cannibalism can also explain the intra-and interspecific interactions observed among all four species. Interspecific competition was stronger between the stemborers than between the FAW and the stemborers. Similar to lepidopteran stemborers, temperature affected both survival and relative growth rates of the FAW as well. Regardless of the temperature, C. partellus was superior in interspecific interactions shown by higher relative growth and survival rates. The results suggest that the FAW will co-exist with stemborer species along entire temperature gradient, though competition and/or cannibalism with them is weak. In addition, temperature increases caused by climate change is likely to confer an advantage to C. partellus over the fall armyworm and the other noctuids

Influence of Temperature on the Interaction for Resource Utilization between Fall Armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), and a Community of Lepidopteran Maize Stemborers Larvae

Intra- and interspecific interactions within communities of species that utilize the same resources are characterized by competition or facilitation. The noctuid stemborers, Busseola fusca and Sesamia calamistis, and the crambid stemborer, Chilo partellus were the most important pests of maize in sub-Saharan Africa before the recent &ldquo;invasion&rdquo; of fall armyworm (FAW), Spodoptera frugiperda, which currently seriously limits maize yields in Africa. This new pest is interacting with the stemborer community at the larval stage in the use of maize resources. From previous works on the influence of temperature on the larval intra- and interspecific resources utilization within the community of Lepidoptera stemborers involving B. fusca, S. calamistis, and C. partellus, there is a need to update these studies by adding the new pest, S. frugiperda, in order to understand the effect of temperature on the larval interactions of all these four species under the context of climate change. The influence of temperature on intra- and interspecific larval interactions was studied using artificial stems kept at different constant temperatures (15 &deg;C, 20 &deg;C, 25 &deg;C, and 30 &deg;C) in an incubator and assessing survival and relative growth rates of each species in single and multi-species experiments. After the inclusion of FAW into the experiments, with regard to relative growth rates, both intra- and interspecific competition was observed among all four species. With regard to survival rates, cannibalism can also explain the intra- and interspecific interactions observed among all four species. Interspecific competition was stronger between the stemborers than between the FAW and the stemborers. Similar to lepidopteran stemborers, temperature affected both survival and relative growth rates of the FAW as well. Regardless of the temperature, C. partellus was superior in interspecific interactions shown by higher relative growth and survival rates. The results suggest that the FAW will co-exist with stemborer species along entire temperature gradient, though competition and/or cannibalism with them is weak. In addition, temperature increases caused by climate change is likely to confer an advantage to C. partellus over the fall armyworm and the other noctuids

Impact of the exotic fall armyworm on larval parasitoids associated with the lepidopteran maize stemborers in Kenya

Exotic invasive insect herbivores have the potential to interfere with existing herbivore-natural enemy interactions in new environments. Fall armyworm (FAW), Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae), is a new invasive pest in maize fields in Africa. Understanding the acceptability and suitability of FAW to existing maize stemborer-parasitoid interactions is the first step in elucidating the impact that this exotic insect pest can have on the existing natural enemies used in biological control of maize stemborers in Kenya. The most commonly used larval parasitoids for biological control programs against maize stemborer communities in East Africa are Cotesia flavipes Cameron (Hymenoptera: Braconidae) and two populations of the native Cotesia sesamiae (Cs-Inland and Cs-Coast) Cameron (Hymenoptera: Braconidae). All these parasitoid species attacked FAW larvae but none yielded offspring, although they induced high non-reproductive host mortality when compared to natural mortality. Furthermore, the parasitoids that inserted their ovipositor into FAW larvae exhibited no significant preference between FAW larvae and their respective stemborer hosts under dual-choice bioassays. In olfactometer bioassays, the parasitoids were more attracted to plants infested by FAW than uninfested plants and even showed a marked preference for the odours of plants infested by FAW over those of plants infested by their natural host counterparts. This study illustrates that exotic pests, such as FAW, can impact existing stemborer-parasitoid interactions associated with maize, even if they cannot be used as hosts by parasitoids associated with these stemborers. Although additional studies are needed, FAW might therefore have a negative impact on stemborer biological control existing before its invasion

Caterpillar-induced plant volatiles attract conspecific and heterospecific adults for oviposition within a community of lepidopteran stemborers on maize plant

Olfactory cues may influence host plant preferences for oviposition of female moths within a community of stemborers that utilise the same resource. This study aimed to evaluate plant preferences for oviposition of gravid females of noctuid stemborers, Busseola fusca and Sesamia calamistis, and the crambid Chilo partellus for uninfested maize plants and plants infested by conspecific or heterospecific larvae. The involvement of volatile organic compounds (VOCs) emitted by uninfested and maize plants infested by conspecific or heterospecific larvae on moth orientation was studied in Y-tube olfactometer assays and in the field. All gravid female moths significantly preferred VOCs emitted by plants infested by conspecific or heterospecific larvae over those from uninfested plants, and female moths did not systematically prefer VOCs emitted by plants infested by conspecifics. Field trials confirmed these results. Chemical analysis by coupled gas chromatography/mass spectrometry showed that VOCs emitted by larvae-infested plants, regardless of the stemborer species, were compositionally richer than those released by uninfested plants but their emission intensity varied with species involved in the infestation. Busseola fusca larvae induced a compositionally richer VOCs profile than S. calamistis and C. partellus larvae. Eight candidate attractants were associated with larvae-infested plants. These results open new avenues to develop attractants specific to trap female stemborer moths in the field