Crop and Pasture Science Crop and Pasture Science Society
Plant sciences, sustainable farming systems and food quality

AFLP analysis of genetic diversity within Saccharum officinarum and comparison with sugarcane cultivars

K. S. Aitken A D E , J.-C. Li A D , P. Jackson B D , G. Piperidis C D and C. L. McIntyre A D

A CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Qld 4067, Australia.

B CSIRO Plant Industry, Davies Laboratory, Private Mail Bag, Aitkenvale, Qld 4814, Australia.

C BSES Limited Central, PMB 57, Mackay, Qld 4741, Australia.

D Co-operative Research Centre for Sugar Industry Innovation through Biotechnology, Level 5, John Hines Building, University of Queensland, St Lucia, Qld 4072, Australia.

E Corresponding author. Email:

Australian Journal of Agricultural Research 57(11) 1167-1184
Submitted: 9 November 2005  Accepted: 10 July 2006   Published: 27 October 2006


Molecular diversity among 421 clones of cultivated sugarcane and wild relatives was analysed using AFLP markers. Of these clones, 270 were Saccharum officinarum and 151 were either cultivars produced by the Australian breeding program or important parents used in the breeding program. The S. officinarum clones were obtained from a collection that contained clones from all the major regions where S. officinarum is grown. Five AFLP primer combinations generated 657 markers of which 614 were polymorphic. All clones contained a large number of markers; a result of the polyploid nature and heterozygosity of the genome. S. officinarum clones from New Guinea displayed greater diversity than S. officinarum clones from other regions. This is in agreement with the hypothesis that New Guinea is the centre of origin of this species. The S. officinarum clones from Hawaii and Fiji formed a separate group and may correspond to clones that have been introgressed with other members of the ‘Saccharum complex’. Greater diversity was found in the cultivars than in the S. officinarum clones due to the introgression of S. spontaneum chromatin. These cultivars clustered as expected based on pedigree. The major contribution of clones QN66-2008 and Nco310 to Australian sugarcane cultivars divided the cultivars into 2 main groups. Although only a few S. officinarum clones are known to have been used in the breeding of current cultivars, about 90% of markers present in the S. officinarum clone collection (2n = 80) were also present in the cultivar collection. This suggests that most of the observed genetic diversity in S. officinarum has been captured in Australian sugarcane germplasm.

Additional keywords: molecular markers, hybrids, introgression.


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