An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

Shrestha, Sangita, Adkins, Stephen W., Graham, Glenn C. and Loch, Donald S. (2005) An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles. Australian Journal of Agricultural Research, 56 2: 157-167. doi:10.1071/AR04180


Author Shrestha, Sangita
Adkins, Stephen W.
Graham, Glenn C.
Loch, Donald S.
Title An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles
Journal name Australian Journal of Agricultural Research   Check publisher's open access policy
ISSN 0004-9409
Publication date 2005-02-28
Year available 2005
Sub-type Article (original research)
DOI 10.1071/AR04180
Volume 56
Issue 2
Start page 157
End page 167
Total pages 11
Place of publication Collingwood, Melbourne
Publisher C S I R O Publishing
Collection year 2005
Language eng
Subject 300204 Plant Protection (Pests, Diseases and Weeds)
620199 Field crops not elsewhere classified
0607 Plant Biology
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 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 pro. ling 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 UBC51(490) for S. pyramidalis and S. natalensis; UBC43(310,2000,2100) for S. fertilis and S. africanus; and OPA20(850) and UBC43(470) 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.
Keyword Diagnostics
Fingerprinting
Genetic Diversity
PCR
Rat's Tail Grasses
Species Identification
Q-Index Code C1

 
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