Abstract:

Cowpea (Vigna unguiculata L. Walp) grain constitutes an important source of protein for several households in Africa. In Uganda, cowpea is the third most important legume crop after common beans and groundnuts with production mainly concentrated in the eastern and northern regions of the country. However, productivity of cowpea is still very low, estimated at less 500 kg ha'1. Widespread occurrence of viral diseases contributes greatly to the low productivity of the crop. Viral infections also reduce protein content of the grain thus affecting its nutritional value. The use of resistant varieties is the most feasible, effective and environmentally friendly approach for management of viral infections. However, success of this approach requires a better understanding of the pathogens, availability of reliable diagnostic assays and good sources of resistance to guide design of appropriate breeding programs. The objectives of this study were; (i) to identify and characterize viruses infecting cowpea in Uganda; (ii) to develop a molecular diagnostic assay for Cowpea aphid-borne mosaic virus (CABMV) in Uganda; and (iii) to determine the level of virus resistance among cowpea genotypes under Held conditions. Next-generation sequencing (NGS) using illumina platform identified four viruses; Cowpea aphid-borne mosaic virus (CABMV; genus Polyvirus), Peanut mottle virus (PcMoV; genus Potyvirus), Sugarcane mosaic virus (SCMV: genus Potyvirus) and Maize chlorotic mottle virus (MCMV; genus Machlomovirus) from symptomatic leaf samples collected from farmer’s Helds. With the exception of CABMV, the other viruses had never been reported on cowpea or known to infect cowpea in Uganda. This is also the first report of the occurrence of SCMV and MCMV on a leguminous crop like cowpea. NGS also led to the assembly of the first complete genome from a Ugandan isolate of CABMV. The Ugandan isolates of CABMV clustered separately from isolates from other African countries indicating phylogenetic affinity to geographic origin. Ugandan isolates of CABMV also showed high nucleotide percentage identity (89.3 to 94.3%) indicating that they belong to the same strain. A new reverse transcriptase polymerase chain reaction (RT-PCR) diagnostic assay based on CABFF1(5'-GGT AAC AAY AGT GGR CAA CC- 3')/CABRRl (5'-CTG AGC AC I CM A ACC GGG-3') was developed and tested for detection of CABMV. The assay accurately detected CABMV in infected leaf samples yielding a fragment of-1642 bp. The assay is recommended for use in rapid screening of segregating progeny in cowpea breeding programs, quarantine and epidemiological studies of CABMV.