Samuel Mutiga

Extent and Drivers of Mycotoxin Contamination: Inferences from a Survey of Kenyan Maize Mills

The prevalence of aflatoxin and fumonisin was investigated in maize intended for immediate human consumption in eastern Kenya at a time in 2010 when an aflatoxin outbreak was recognized. Samples were collected from people who brought their maize for processing at local commercial mills. Sites were selected using a geographical information system overlay of agroecological zones and Kenyas administrative districts. Interviews and collection of maize flour samples was conducted from 1,500 people who processed maize at 143 mills in 10 administrative districts. Mycotoxins were analyzed using enzyme-linked immunosorbent assays for aflatoxin and fumonisin, leading to detection at levels above the respective maximum tolerable limits in 39 and 37% of the samples, respectively. Samples with aflatoxin contamination above the legal limit ranged between 22 and 60% across the districts. A higher occurrence of aflatoxin was associated with smaller maize farms, lower grain yield, and monocropping systems, while a larger magnitude of the toxin was observed in the subhumid agroecological zone, in samples with more broken kernels, and, curiously, less maize ear damage at harvest. Analysis of paired grain samples (visually sorted and unsorted) showed that sorting reduced fumonisin by 65%, from above to below the legal limit of 1,000 ppb. Sorting did not, however, reduce aflatoxin levels. Although the aflatoxin problem is widely acknowledged, the high prevalence of fumonisin has not previously been reported. There is need for surveillance of the two mycotoxins and establishment of intervention strategies to reach vulnerable small-scale farmers.

Assessment of the Virulence Spectrum and Its Association with Genetic Diversity in Magnaporthe oryzae Populations from Sub-Saharan Africa

A collection of 122 isolates of Magnaporthe oryzae, from nine sub-Saharan African countries, was assessed for virulence diversity and genetic relatedness. The virulence spectrum was assessed by pathotype analysis with a panel of 43 rice genotypes consisting of differential lines carrying 24 blast resistance genes (R-genes), contemporary African rice cultivars, and susceptible checks. The virulence spectrum among isolates ranged from 5 to 80%. Five isolates were avirulent to the entire rice panel, while two isolates were virulent to ∼75% of the panel. Overall, cultivar 75-1-127, the Pi9 R-gene donor, was resistant to all isolates (100%), followed by four African rice cultivars (AR105, NERICA 15, 96%; NERICA 4, 91%; and F6-36, 90%). Genetic relatedness of isolates was assessed by single nucleotide polymorphisms derived from genotyping-by-sequencing and by vegetative compatibility tests. Phylogenetic analysis of SNPs of a subset of isolates (n = 78) revealed seven distinct clades that differed in virulence. Principal component analysis showed isolates from East Africa were genetically distinct from those from West Africa. Vegetative compatibility tests of a subset of isolates (n = 65) showed no common groups among countries. This study shows that blast disease could be controlled by pyramiding of Pi9 together with other promising R-genes into rice cultivars that are adapted to East and West African regions.

Effects of integrating companion cropping and nitrogen application on the performance and infestation of collards by Brevicoryne brassicae

Sustainable management of cabbage aphids, Brevicoryne brassicae (L.) (Hemiptera: Aphididae), is a major goal for collard, Brassica oleracea (L.) var. acephala (Brassicaceae), growers globally. Host finding ability of insect pests is significantly affected by diversified cropping systems, and this approach is being utilized currently as a pest management tool. Soil nutrition and its interaction with the cropping systems could have a significant effect on the general performance of collards and the infestation by cabbage aphids. In a search for a sustainable cabbage aphid control, a two‐season field experiment was carried out with two intercrops, collards and chilli, Capsicum frutescens (L.) (Solanaceae), and collards and spring onions, Allium cepa (L.) (Alliaceae), and a collard monoculture. For each of the cropping systems, nitrogen (N) was applied to the soil as a top‐dress at 20, 25, 30, and 35 g per collard plant. The response factors monitored were collard yield (fresh weight) and aphid infestation on collards. Spring onion‐collard intercrop had the lowest aphid density and the highest yield. Collard monoculture had the highest aphid infestation and the lowest yield. High levels of N led to increased infestation of collards by aphids, but also led to a significant increase in the yield of collards. Significant interactions between the N rates and the cropping systems were observed on some sampling dates, with the highest yield being realized under a combination of spring onion‐collard intercrop at a N rate of 30 g per plant. High aphid density led to a decrease in the yield of collards. It was concluded that with a spring onion‐collard intercrop, the soil N level could be raised from the blanket rate of 20–30 g per plant and this would lead to an increase in yield.

Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa

Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.

A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa

The fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.