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.
iv
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105 cowpea genotypes were evaluated in 2012 for two consecutive seasons (2012A and
201213) in Sererc, Budaka and Tororo in a 10 x 11 alpha lattice design to assess the level of
resistance to virus infestation under natural conditions, The landraces had low virus infection
levels compared to the introduced cowpea genotypes. Cowpea genotypes WC48, NE43,
NE15, WC35A, WC39, WC33, WC35C and WC18 showed broad resistance to virus
infestation and could be used as donor parents in developing virus resistant varieties. With
regard to yield and AUDPC, Sererc, Budaka and Tororo formed a single mega-environment.
However, with regard to incidence, two mega-environments were formed, the first megaenvironment
comprised of Serere and Tororo while the second one comprised of Budaka.
WC5I, NE48, MU20, WC32, NE51, NE37, WC2, WC42. NE15, WC53, SECOW2W and
NE50 were high yielding and stable.