An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles
Sangita Shrestha A B E , Stephen W. Adkins A E F , Glenn C. Graham C and Donald S. Loch DA School of Land and Food Sciences, University of Queensland, Brisbane, Qld 4072, Australia.
B Royal Nepal Academy of Science and Technology (RONAST), Lalitpur, Nepal.
C Centre for Identification and Diagnostics (CID), University of Queensland, Brisbane, Qld 4072, Australia.
D Queensland Department of Primary Industries, Redland Research Station, Redland Bay, Brisbane, Qld 4156, Australia.
E Tropical and Sub-Tropical Weed Research Unit, University of Queensland, Brisbane, Qld 4072, Australia.
F Corresponding author. Email: s.adkins@uq.edu.au
Australian Journal of Agricultural Research 56(2) 157-167 https://doi.org/10.1071/AR04180
Submitted: 4 August 2004 Accepted: 13 December 2004 Published: 28 February 2005
Abstract
Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [viz. S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur and Schinz, S. fertilis (Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified of polymorphic DNA (RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD profiling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51490 for S. pyramidalis and S. natalensis; UBC43310, 2000, 2100 for S. fertilis and S. africanus; and OPA20850 and UBC43470 for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the ‘S. indicus complex’. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species (major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.
Additional keywords: diagnostics, fingerprinting, genetic diversity, PCR, rat’s tail grasses, species identification.
Acknowledgments
We thank B. K. Simon, Queensland Herbarium, for morphological identification of adult plants as well as for providing some of the Sporobolus seed samples used in this study. We extend our sincere thanks to S. Bray, J. Hilden, and all QDPI extension personnel who provided seed samples for the study. Our sincere thanks also go to Prof. W. Whaley, The University of New England, B. Worboys, Maitland City Council, and T. Schmitzer, NSW Agriculture, for providing further Sporobolus seed samples.
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