DNA fingerprints of rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats

J. Provan, G. Corbett, R. Waugh, J. W. McNicol, M. Morgante, W. Powell

    Research output: Contribution to journalArticle

    40 Citations (Scopus)

    Abstract

    The aim of this research was to develop a convenient polymerase chain reaction-based assay that would allow intraspecific chloroplast variability to be detected. Our approach is based on the detection of length polymorphism within chloroplast mononucleotide microsatellite loci. Information from the fully sequenced rice chloroplast genome was used to identify 12 regions with a minimum of ten uninterrupted mononucleotide repeats. Primers flanking these repeats were used in conjunction with polymerase chain reaction to examine levels of polymorphism in six wild and 14 cultivated rice accessions. A total of six of the primer pairs revealed length polymorphism with between two and five size variants being detected. Diversity indices varied between 0.07 and 0.72. The length variation detected at multiple, physically linked sites was used to identify 15 unique haplotypes with an overall diversity index of 0.90. This level of polymorphism is sufficiently high to allow chloroplast variability to be studied at the intraspecific level. An additional 47 Oryza sativa accessions were also assayed with 31 unique chloroplast haplotypes being detected. The distribution of these haplotypes is described in relation to isozyme groupings and subspecies differentiation. The relevance and implications of these results for plant population genetics and the management of germplasm collections is discussed.

    Original languageEnglish
    Pages (from-to)1275-1281
    Number of pages7
    JournalProceedings of the Royal Society B: Biological Sciences
    Volume263
    Issue number1375
    DOIs
    Publication statusPublished - 22 Oct 1996

    Fingerprint

    DNA Fingerprinting
    Chloroplasts
    Polymorphism
    DNA fingerprinting
    chloroplast
    Microsatellite Repeats
    Oryza sativa
    rice
    chloroplasts
    genetic polymorphism
    microsatellite repeats
    Haplotypes
    DNA
    polymorphism
    haplotypes
    Polymerase chain reaction
    diversity index
    polymerase chain reaction
    Chloroplast Genome
    Polymerase Chain Reaction

    Cite this

    Provan, J. ; Corbett, G. ; Waugh, R. ; McNicol, J. W. ; Morgante, M. ; Powell, W. / DNA fingerprints of rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats. In: Proceedings of the Royal Society B: Biological Sciences. 1996 ; Vol. 263, No. 1375. pp. 1275-1281.
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    DNA fingerprints of rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats. / Provan, J.; Corbett, G.; Waugh, R.; McNicol, J. W.; Morgante, M.; Powell, W.

    In: Proceedings of the Royal Society B: Biological Sciences, Vol. 263, No. 1375, 22.10.1996, p. 1275-1281.

    Research output: Contribution to journalArticle

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    AU - Corbett, G.

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