Abstract
Cowpea, (Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as “poor man’s meat”, cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso. Besides the three cowpea-infecting virus species which have previously been reported from Burkina Faso (Cowpea aphid borne mosaic virus [Family Potyviridae], the Blackeye cowpea mosaic virus—a strain of Bean common mosaic virus—[Family Potyviridae] and Cowpea mottle virus [Family Tombusviridae]) five additional viruses were identified: Southern cowpea mosaic virus (Sobemovirus genus), two previously uncharacterised polerovirus-like species (Family Luteoviridae), a previously uncharacterised tombusvirus-like species (Family Tombusviridae) and a previously uncharacterised mycotymovirus-like species (Family Tymoviridae). Overall, potyviruses were the most prevalent cowpea viruses (detected in 65.5% of samples) and the Southern Sudan zone of Burkina Faso was found to harbour the greatest degrees of viral diversity and viral prevalence. Partial genome sequences of the two novel polerovirus-like and tombusvirus-like species were determined and RT-PCR primers were designed for use in Burkina Faso to routinely detect all of these cowpea-associated viruses.
Highlights
Cowpea, (Vigna unguiculata L. (Walp)), which is one of the most important subsistence legumes cultivated in West Africa [1] is an annual tropical grain legume that has seeds and leaves with a 25–30% protein content [2,3,4]
A total of 669,589 reads were obtained from the 384 cowpea samples that were processed using the virion-associated nucleic acids (VANA) approach (S1 Table)
BlastN and BlastX comparisons between the VANA-reads and GenBank sequences indicated that 20.89% of the processed reads were potentially related to plant RNA viruses and that among the 307 field plants in which reads were obtained, 203 were positive for the presence of virus-related reads (66.1%; S1 Table)
Summary
Cowpea, (Vigna unguiculata L. (Walp)), which is one of the most important subsistence legumes cultivated in West Africa [1] is an annual tropical grain legume that has seeds and leaves with a 25–30% protein content [2,3,4]. (Walp)), which is one of the most important subsistence legumes cultivated in West Africa [1] is an annual tropical grain legume that has seeds and leaves with a 25–30% protein content [2,3,4]. While members of 140 virus species can naturally or artificially infect cowpea (reviewed in [8]), only twelve of these species have so far been found in Africa (Table 1), from which, only three have been reported from Burkina Faso. Given that a far broader diversity of cowpea-infecting viruses has been discovered elsewhere in Africa, it is likely that additional cowpea-infecting viruses remain to be discovered in Burkina Faso. The limited available knowledge on cowpea infecting viruses in this country hinders the control of diseases, with respect to the production of disease-free seeds and the creation of virus-resistant cowpea varieties.
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