| dc.description.abstract | Groundnut (Arachis hypogaea L.) is an economically important edible oilseed legume in Sub-Saharan Africa (SSA). Nearly 75% to 80% of the world’s groundnut is grown by resource poor smallholder farmers in developing countries, who routinely obtain yields of 500-800kg/ha, as opposed to the potential yield of >2.5t/ha. Groundnut rosette disease (GRD) is a major constraint in SSA, which can cause 100% yield losses in a devastating severe epidemic situation, to the extent of abandoning the fields. The disease is caused by two synergistic viruses; groundnut rosette assistor virus (GRAV, genus Luteovirus) and groundnut rosette virus (GRV, genus Umbravirus) associated with a satellite-ribonucleic acid (Sat-RNA). The complex etiology and lack of sensitive and specific diagnostic tools, are major limitations in understanding the epidemiology of GRD viruses, and developing appropriate management strategies for the disease. Simultaneous detection of the GRD causal agents is possible by multiplex RT-PCR but this depends on the availability of specific primers to known agents that occur in a specific area. This information is limited for GRD causal agents in western Kenya. This requires a robust detection method which can single out all the GRD agents and their variants. To date, lack of sufficient research on the occurrence, distribution and diversity of GRD causal agents has resulted in continued and increased yield losses amongst groundnut farmers. Recent observations made in groundnut farms in western Kenya have shown that GRD is very severe and highly variable in symptoms appearance. The causes of this is not well documented. This study will determine the occurrence of GRD and characterize GRD causal agents in western Kenya. Disease diagnostic surveys will be conducted in six counties; Bungoma, Busia, Homabay, Kakamega, Siaya and Vihiga. Disease incidence and severity will be scored on the disease score sheet. Symptomatic and asymptomatic groundnut leafy samples will be collected and preserved for laboratory analysis. Total RNA will be extracted by RNeasy Mini Kit (Qiagen), and sequenced using next generation sequencing technologies (NGS). Biological characterization of GRD will be done through mechanical inoculation on leguminous hosts and further vector and seed transmission studied. The data collected on incidence and severity will be subjected to analysis of variance (ANOVA), using Statistical Analysis Software (SAS) program (SAS Institute lnc.). Pairwise comparison of means will be done using Least Significance Difference (LSD) at P
0.05 confidence level. Sequence reads will be analyzed using an in-house, customized version of the Galaxy project bioinformatics pipeline. The reads will be mapped to a custom database of plant virus sequences using Bowtie2 2.2.3+, and further analysis done to establish diversity and other molecular characteristics. This research will provide comprehensive knowledge of GRD viruses, rosette symptoms, better crop protection technologies and acceptable agronomic farming practices, for considerable increased groundnut production. | en_US |
