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

BACKGROUND: 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.

Effect of sterilants and plant growth regulators in regenerating commonly used cassava cultivars at the Kenyan coast.

Cassava is an important root crop whose seed system is undeveloped. Micropropagation of explants in vitro has the potential of addressing the challenge of the unavailability of healthy cassava planting materials. Therefore, the study determined the effect of sterilization and plant growth regulators on cassava explants to produce certified disease-free plants of commonly used cultivars at the coast of Kenya. The apical nodes drawn from the three cultivars of cassava, Tajirika and Kibandameno and Taita, were used as explants. The sterilant sodium hypochlorite (NaOCl) at 5, 10 and 15% and 70% ethanol for 1 and 5 min and sprayed for 20 s were tested for the effect on the explant. Similarly, the effect of BAP (6-Benzyl amino purine) and NAA (1-Naphthalene acetic acid) Plant Growth Regulators (PGRs) each at 0.5, 1 and 5 mg/L under optimal conditions of sterilization was determined. Surface sterilization using 10% NaOCl followed by spraying 70% ethanol for 20 s had 85% initiation on Tajirika whereas 5% NaOCl followed by spraying 70% ethanol for 20 s had 87% and 91% initiation in Kibandameno and Taita cultivars, respectively. In Tajirika, significantly (p < 0.05) high shooting of 68% was from 5 mg/L BAP in MS media whereas approximately 50% rooting was from either 0.5 mg/L BAP or 5 mg/L NAA in MS media. Kibandameno and Taita cultivars had approximately 50% shooting from MS media without PGRs. Kibandameno had >37% rooting from 0.5 to 5 mg/L BAP or NAA in MS media whereas Taita had approximately 50% rooting from 0 to 5 mg/L NAA in MS media. This protocol showed at least 50% success rate of initiation, shooting and rooting as a rapid multiplication regeneration of Tajirika and Kibandameno and Taita cultivar plantlets with little modification of humidity and temperatures in the growth chambers. This protocol requires validation for use in large-scale production of cassava plantlets to alleviate the inadequacy of cassava planting materials among farmers.

Identification and Characterization of Colletotrichum 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.

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 a work done by Ntiri et al. [13] 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 this study 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 in the same protocol of Ntiri et al. [13] 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.

Carry-Over Niches for Lepidopteran Maize Stemborers and Associated Parasitoids during Non-Cropping Season.

Sources of infestation are the key elements to be considered in the development of habitat management techniques for the control of maize stemborers. Several wild plants, grasses mostly, have been identified that serve as hosts for stemborers and their parasitoids during the off-season when maize is not present in the field. However, their abundance is much lower in wild plants compared to cultivated fields. Thus, the role of wild plants as a reservoir for cereal stemborers and their parasitoids is still controversial, particularly in agro-ecosystems with reduced wild habitat. We studied the occurrence of different maize stemborers and associated parasitoids in maize stem residues and wild grasses during non-cropping seasons as potential carry-over populations to subsequent early season maize plants. Surveys were conducted in the central region of Kenya during long and short dry seasons in maize residues and wild grasses as well as during the two rainy seasons in maize plants at earlier and late whorl stages during the years of 2017 and 2018. Wild habitat had a higher species diversity than maize residues habitat, but maize residues had a higher abundance of maize stemborer species, such as Busseola fusca, Sesamia calamistis, and Chilo partellus, and of associated parasitoid species (i.e., Cotesia flavipes and Cotesia sesamiae) than wild plants. Our surveys, complemented by field parasitoid releases of C. flavipes and C. sesamiae, indicated that maize residues constitute a better refugia reservoir not only of the maize stemborers but also of C. flavipes and C. sesamiae during non-cropping seasons as compared to wild plants and, thus, might constitute in this region the main source of both stemborers and C. flavipes/C. sesamiae carry-over in maize plants during the subsequent cropping season. Thus, systematic destruction of maize residues would not help the biological control of lepidopteran stemborers. This is particularly true in areas with reduced wild habitat.