Pathogen Diversity in African Small Farming Systems for the Assessment of Food Security and the Improvement of African Agricultural Productivity

Abstract

African smallholder farmers play a pivotal role in meeting the future food demand in view of the global population growth. Small farms (usually smaller than two hectares,) dominate African agricultural systems. The 'maize mixed' farming system, including maize and a selection of different crops, is among the most common small farming systems in Sub-Saharan Africa (SSA). Whilst mixed cropping systems offer resilience to crop loss, they also support greater pathogen (and vector) diversity, leading to emergence and spread of new diseases. Identification of emerging diseases and associated risks is paramount for improving African food security, especially in the face of climate change and given that crop diseases are one of the major constraints to crop production in SSA. This project makes use of Illumina MiSeq technologies to assess the pathogen diversity in three 'maize mixed' farming systems in Kenya, representing different agro ecological zones, with special emphasis on host-vector interactions. Preliminary RNA sequencing results on different crops indicate the presence of rich viral diversity. Moreover, Maize Chlorotic mottle virus (MCMV) and Sugarcane mosaic virus (SMV) (the combination of which causes Maize lethal necrosis, MLN, a disease triggering severe losses in Kenya), have been detected. Virome comparison, geographical distribution, epidemic establishment and factors influencing the spread (in space and time) of pathogens between geographical regions will be analyzed. Methods for pathogen detection and characterization will be established in the region and information given to governmental policy makers aimed at strengthening control and response strategies