Effect of environment and cultivar on the expression of banana streak disease symptoms in Kenya

Banana (Musa spp.) is grown for subsistence and income generation by 80% of small scale farmers all year round in Kenya hence it is an important food security crop. However viral diseases such as banana streak disease (BSD), caused by Banana streak virus, hamper the production of the crop. BSV has been reported to be present in all the commercial banana cultivars in Kenya. Tissue culture materials of 15 cultivars were evaluated for BSV expression so as to determine the tolerant cultivars under field and greenhouse conditions and stages of disease expression. A number of factors including plant age, cultivar, season and growth site were investigated in the greenhouse and field to assess their effect on BSD symptom expression. Statistical analysis system (SAS) for ANOVA was used for analysis of data for the experiments. Results indicated that BSD symptom expression is significantly influenced by all the factors under investigation. Significant correlation was also observed between symptom severity and plant height, girth, and number of leaves. Findings of this study will be invaluable to stakeholders and researchers in banana industry by laying a foundation for development and adoption of viable BSD management strategies.Keywords: Banana streak virus, Banana streak disease, symptoms expression, tissue culture, ELISAAfrican Journal of Biotechnology Vol. 12(16), pp. 1999-200

Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations.

Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of maize chlorotic mottle virus with Potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa

Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples were collected from maize and sorghum representing sixteen counties. Results: Complete and partial genomes were assembled for MCMV, SCMV, Maize streak virus (MSV) and Maize yellow dwarf virus-RMV (MYDV-RMV). These four viruses (MCMV, SCMV, MSV and MYDV-RMV) were found together in 30 of 68 samples. A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. Single nucleotide polymorphism, nucleotide and polyprotein sequence alignments identified three genetically distinct groups of SCMV in Kenya. Variation mapped to sequences at the border of NIb and the coat protein. Partial genome sequences were obtained for other four potyviruses and one polerovirus. Conclusion: Our results uncover the complexity of the maize lethal necrosis epidemic in Kenya. MCMV, SCMV, MSV and MYDV-RMV are widely distributed and infect both maize and sorghum. SCMV population in Kenya is diverse and consists of numerous strains that are genetically different to isolates from other parts of the world. Several potyviruses, and possibly poleroviruses, are also involved

A first global phylogeny of<i>Maize chlorotic mottle virus</i>

ABSTRACT Maize chlorotic mottle virus has been rapidly spreading around the globe over the past decade. The interactions of Maize chlorotic mottle virus with potyviridae viruses causes an aggressive synergistic viral condition - maize lethal necrosis, which can cause total yield loss. Maize production in sub-Saharan Africa, where it is the most important cereal, is threatened by the arrival of maize lethal necrosis. We obtained Maize chlorotic mottle virus genome sequences from across East Africa and for the first time from Ecuador and Hawaii, and constructed a phylogeny which highlights the similarity of Chinese to African isolates, and Ecuadorian to Hawaiian isolates. We used a measure of clustering, the adjusted Rand index, to extract region-specific SNPs and coding variation that can be used for diagnostics. The population genetics analysis we performed shows that the majority of sequence diversity is partitioned between populations, with diversity extremely low within China and East Africa

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Additional file 6: of Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

SCMV contigs used for phylogenetic analysis. (FASTA 193 kb

Additional file 1: of Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Figure S1. A schematic representation of sampling strategy, RNA sequencing, analysis, and virus identification. (PDF 301 kb

Additional file 5: of Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

MCMV contigs used for phylogenetic analysis. (FASTA 132 kb

Additional file 9: of Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

MYDV-RMV contigs used for phylogenetic analysis. (FASTA 27 kb

Additional file 3: of Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Figure S2. Size and frequency of de novo-assembled representative contigs with high similarity to known viruses. In total 68 samples were sequenced and analyzed. Contig size is represented in 0.5 Kb increments in the X axis. The Y axis represents the number of contigs per size class. For each virus, the number of samples categorized as infected is indicated. a MCMV. b SCMV. c MSV. d MYDV-RMV. (PDF 278 kb