Felix rotich | Egerton University (original) (raw)

Papers by Felix rotich

Plants

We conducted a survey to assess the occurrence and severity of rice blast and brown spot diseases... more We conducted a survey to assess the occurrence and severity of rice blast and brown spot diseases on popular cultivars grown in the Busia, Kirinyaga, and Kisumu counties of Kenya in 2019. Working with agricultural extension workers within rice production areas, we interviewed farmers (n = 89) regarding their preferred cultivars and their awareness of blast disease, as this was the major focus of our research. We scored the symptoms of blast and brown spot and assessed the lodging, plant height, and maturity of the crops (days after planting). Furthermore, we collected leaf and neck tissues for the assessment of the prevailing fungal populations. We used specific DNA primers to screen for the prevalence of the causal pathogens of blast, Magnaporthe oryzae, and brown spot, Cochliobolus miyabeanus, on asymptomatic and symptomatic leaf samples. We also conducted fungal isolations and PCR-sequencing to identify the fungal species in these tissues. Busia and Kisumu had a higher diversity ...

The blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae</e... more The blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae) is able to cause disease on more than 50 grass species, including important cereal crops such as rice, wheat and finger millet (Couch and Kohn 2002; Zhang et al. 2016). Understanding the evolutionary relationships between host-limited forms of the blast fungus is critical to being able to devise effective control strategies for the devastating diseases that they cause. For example, identifying host-specificity determinants may be valuable in identifying cognate disease resistance loci that could be deployed between different host species (Sweigard et al. 1995). This strategy has the capacity to lead to more durable disease control (Kawashima et al. 2016). Here, we present whole genome sequence information for a set of 60 Magnaporthe oryzae isolates collected between 1964 and 2017 from 14 countries and 5 different host plant species. Host g...

Plant Disease, 2021

Rice is a key food security crop in Africa. The importance of rice has led to increasing country-... more Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multip...

Rice is steadily becoming a staple food to the majority of people in Africa, yet its production i... more Rice is steadily becoming a staple food to the majority of people in Africa, yet its production is outstripped by demand, resulting in net imports from abroad. Rice blast disease is a major factor that has led to decline in rice production in Africa. This international collaborative research for development project is aiming at overcoming rice yield losses caused by blast disease and hence increasing rice production in sub-Saharan Africa. Breeding for durable blast resistance requires knowledge about the genetic diversity of the pathogen population and its virulence spectrum; durable resistance represents the most sustainable rice blast control strategy. The project has characterized blast pathogen collections from East and West Africa using genomics, and a panel of rice genotypes including those carrying the 24 known resistance genes (R-genes). Based on the results, the project has initiated a breeding program which combines the most promising R-genes into adapted African cultivars...

Phytopathology, 2015

Rice blast, caused by Magnaporthe oryzae, is a disease that can cause severe losses in rice yield... more Rice blast, caused by Magnaporthe oryzae, is a disease that can cause severe losses in rice yields. Recent studies showed that demand for rice is increasing faster than the increase in production in Africa, and there is a need to mitigate production challenges such as rice blast. Breeding for resistance to rice blast in Africa requires knowledge of M. oryzae diversity and the history of resistance in the pathosystem. A core collection isolates of M. oryzae (n=100) from nine African countries (Benin, Burkina Faso, Ghana, Kenya, Mali, Nigeria, Tanzania, Togo, and Uganda) were assessed for vegetative compatibility groups (VCG) and for disease reactions based on an International Rice Research Institute set of differential lines and African interspecific cultivars. Preliminary analysis showed that VCGs were unique for each country, but the virulence phenotypes of isolates were not associated with the country of origin. Avirulence was observed in a range 25%-75% of the subset (n=49) of th...

ABSTRACTThe fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice ... more ABSTRACTThe 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...

Phytopathology, Sep 18, 2017

Understanding the genetic diversity of rice germplasm is important for the sustainable use of gen... more 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 chr...

Phytopathology, Jul 5, 2017

A collection of 122 isolates of Magnaporthe oryzae, from nine sub-Saharan African countries, was ... more 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 ...

Crop Protection, 2020

Sweet potato is an important food security crop but its production is limited by various biotic c... more Sweet potato is an important food security crop but its production is limited by various biotic constraints including plant-parasitic nematodes (PPN). In Kenya, current PPN management practices in sweet potato have several limitations hence the need for alternative low-cost management strategies. This study evaluated the impact of intercropping maize and sweet potato (MS) and application of Tithonia diversifolia (MG), cow (CM) and goat manure (GM) on population dynamics of PPN and the effect on metabolic footprints, ecological and functional indices. Field experiments were established in a randomized complete block design involving the four treatments and unamended controls. Soil samples were collected during long (LR) and short (SR) rains seasons. Forty-seven nematode genera were identified in both seasons. Principle response curves analysis revealed that goat manure had the most pronounced effect on PPN. There were differences in metabolic footprints, ecological and functional indices during LR and SR. In CM plots, predator footprint was high during the long rains season. Functional metabolic footprints categorized all plots as degraded in both seasons except MS which was structured in SR. However, CM bordered a structured ecosystem in both seasons while GM bordered a structured ecosystem in LR. Goat manure may have enhanced the natural ability of soil to regulate PPN affecting sweet potato and it may provide an alternative sustainable method of PPN control for smallholders.

Plants

Plant Disease, 2021

Phytopathology, 2015

Phytopathology, Sep 18, 2017

Phytopathology, Jul 5, 2017

Crop Protection, 2020