Abstract
Sugarcane orange rust, caused by Puccinia kuehnii, was once considered a minor disease in the Australian sugar industry. However, in 2000 a new race of the pathogen devastated the high-performing sugarcane cultivar Q124, and caused the industry Aus$150–210 million in yield losses. At the time of the epidemic, very little was known about the genetic and pathogenic diversity of the fungus in Australia and neighbouring sugar industries. DNA sequence data from three rDNA regions were used to determine the genetic relationships between isolates within two P. kuehnii collections. The first collection comprised only recent Australian field isolates and limited sequence variation was detected within this population. In the second study, Australian isolates were compared with isolates from Papua New Guinea, Indonesia, China and historical herbarium collections. Greater sequence variation was detected in this collection and phylogenetic analyses grouped the isolates into three clades. All isolates from commercial cane fields clustered together including the recent Australianfield isolates and the Australian historical isolate from 1898.The other two clades included rust isolates from wild and garden canes in Indonesia and PNG. These rusts appeared morphologically similar to P. kuehnii and could potentially pose a quarantine threat to the Australian sugar industry. The results have revealed greater diversity in sugarcane rusts than previously thought.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bremer K (1994) Branch support and tree stability. Cladistics 10, 295–304. doi: 10.1111/j.1096-0031.1994.tb00179.x
Bruns TD, Fogel R, Taylor JW (1990) Amplification and sequencing of DNA from fungal herbarium specimens. Mycologia 82, 175–184. doi: 10.2307/3759846
Bruns TD, White TJ, Taylor JW (1991) Fungal molecular systematics. Annual Review of Ecology and Systematics 22, 525–564. doi: 10.1146/ annurev.es.22.110191.002521
Comstock JC, Sood SG, Glynn NC, Shine JM Jr, McKemy JM, Castlebury LA (2008) First report of Puccinia kuehnii, causal agent of orange rust of sugarcane, in the United States and western hemisphere. Plant Disease 92, 175. doi: 10.1094/PDIS-92-1-0175A
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791. doi: 10.2307/2408678
Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes — application to the identification of mycorrhizae and rusts. Molecular Ecology 2, 113–118. doi: 10.1111/j.1365-294X. 1993.tb00005.x
Huelsenbeck JP, Nielson R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310–2314. doi: 10.1126/science.1065889
Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics (Oxford, England) 17, 754–755. doi: 10.1093/bioinformatics/17.8.754
James TY, Moncalvo J, Li S, Vilgalys R (2001) Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune. Genetics 157, 149–161.
Keiper FJ, Hayden MJ, Park RF, Wellings CR (2003) Molecular genetic variability of Australian isolates of five cereal rust pathogens. Mycological Research 107, 545–556. doi: 10.1017/S0953756203 007809
Keiper FJ, Haque MS, Hayden MJ, Park RF (2006) Genetic diversity in Australian populations of Puccinia graminis f. sp. avenae. Phytopathology 96, 96–104. doi: 10.1094/PHYTO-96-0096
Kim WK, Zerucha T, Klassen GR (1992) A region of heterogeneity adjacent to the 5S ribosomal RNA gene of cereal rusts. Current Genetics 22, 101–105. doi: 10.1007/BF00351468
Magarey RC (2000) Orange rust. In ‘A guide to sugarcane diseases’. (Eds P Rott, RA Bailey, JC Comstock, BJ Croft, JC Girad, AS Saumtally) pp. 121–125. (CIRAD - ISSCT: Montpellier, France)
Magarey RC, Croft BJ, Willcox TG (2001a) An epidemic of orange rust on sugarcane in Australia. Proceedings of the International Society of Sugar Cane Technologists 24, 410–416.
Magarey R, Willcox T, Croft B, Cordingley A (2001b) Orange rust, a major pathogen affecting crops of Q124 in Queensland in 2000. Proceedings of the Australian Society of Sugar Cane Technologists 23, 274–280.
Magarey RC, Irawan, Kuniata LS, Allsopp PG (2002) Sik na binatang bilong suka — diseases and pests encountered during a survey of Saccharum germplasm ‘in the wild’ in Papua New Guinea. Proceedings of the Australian Society of Sugar Cane Technologists 24, 31. (CD-ROM)
Magarey RC, Kuniata LS, Croft BJ, Chandler KJ, Irawan, Kristini A, Spall VE, Samson PR, Allsopp PG (2003) International activities to minimise industry losses from exotic pests and diseases. Proceedings of the Australian Society of Sugar Cane Technologists 25, 18. (CD-ROM)
O’Donnell K (1993) Fusarium and its near relatives. In ‘The fungal holomorph: mitotic, meiotic and pleomorphic speciation in fungal systematics’. (Eds DR Reynolds, JW Taylor) pp. 225–233. (CAB International: Wallingford, UK)
Ovalle W, Comstock JC, Glynn NC, Castlebury LA (2008) First report of Puccinia kuehnii, causal agent of orange rust of sugarcane, in Guatemala. Plant Disease 92, 973. doi: 10.1094/PDIS-92-6-0973C
Pillay L, McFarlane SA, Rutherford RS (2005) A preliminary report on genetic diversity in populations of sugarcane rust in KwaZulu-Natal. Proceedings of the South African Sugar Technologists Association 79, 132–136.
Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics (Oxford, England) 14, 817–818. doi: 10.1093/bioinformatics/14.9.817
Rambaut A (2002) Se-Al: Sequence alignment editor. Version 2.0a11. (Oxford: University of Oxford, UK)
Roose-Amsaleg C, de Vallavieille-Pope C, Brygoo Y, Levis C (2002) Characterization of a length polymporphism in the two intergenic spacers of ribosomal RNA in Puccinia striiformis f. sp. tritici, the causal agent of wheat yellow rust. Mycological Research 106, 918–924. doi: 10.1017/S0953756202006251
Ryan CC, Egan BT (1989) Rust. In ‘Diseases of sugarcane — major diseases’. (Eds C Ricaud, BT Egan, AG Gilaspie Jr, CG Hughes) pp. 189–210. (Elsevier: Amsterdam, The Netherlands)
Simmons MP, Ochotorena H (2000) Gaps as characters in sequence based phylogenetic analyses. Systematic Biology 49, 369–381. doi: 10.1080/ 10635159950173889
Swofford DL (2002) PAUP* v.4.0 beta. Phylogenetic Analysis Using Parsimony (* and other Methods). Version 4b10. (Sinauer Associates, Sunderland, Massachusetts, USA)
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673–4680. doi: 10.1093/nar/ 22.22.4673
Virtudazo EV, Nakamura H, Kakishima M (2001a) Phylogenetic analysis of sugarcane rusts based on sequences of ITS, 5.8s rDNA and D1/D2 regions of LSU rDNA. Journal of General Plant Pathology 67, 28–36. doi: 10.1007/PL00012983
Virtudazo EV, Nojima H, Kakishima M (2001b) Taxonomy of Puccinia species causing rust diseases on sugarcane. Mycoscience 42, 167–175. doi: 10.1007/BF02464133
Virtudazo EV, Nakamura H, Kakishima M (2001c) Ribosomal DNA-ITS sequence polymorphism in the sugarcane rust, Puccinia kuehnii. Mycoscience 42, 447–453. doi: 10.1007/BF02464341
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In ‘PCR protocols: A guide to methods and applications’. (Eds MA Innis, DH Gelfand, JJ Sninsky, TJ White) pp. 315–322. (Academic Press: San Diego, USA)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Braithwaite, K.S., Croft, B.J., Magarey, R.C. et al. Phylogenetic placement of the sugarcane orange rust pathogen Puccinia kuehnii in a historical and regional context. Australasian Plant Pathology 38, 380–388 (2009). https://doi.org/10.1071/AP09012
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1071/AP09012