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    PCR-DGGE analysis: unravelling complex mixtures of badnavirus sequences present in yam germplasm

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    U17ArtTurakiAnalysisInthomNodev.pdf (3.673Mb)
    Date
    2017-07-11
    Author
    Turaki, A.A.
    Bömer, M.
    Silva, G.
    Kumar, P.L.
    Seal, S.E.
    Type
    Journal Article
    Target Audience
    Scientists
    Metadata
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    Abstract/Description
    Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.
    http://dx.doi.org/10.3390/v9070181
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/1937
    Digital Object Identifier (DOI)
    http://dx.doi.org/10.3390/v9070181
    IITA Subjects
    Genetic Improvement; Plant Genetic Resources; Yam
    Agrovoc Terms
    Yams; Integration; Breeding Lines; Badnavirus; Sequence Diversity; Dioscorea Spp.; Endogenous Pararetrovirus; Episomal Badnavirus; Detection; Germplasm
    Regions
    Africa; West Africa
    Countries
    Nigeria
    Journals
    Viruses
    Collections
    • Journal and Journal Articles4835
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