The complex genetic structure of sugarcane limits identification of additional SNP-defined simplex alleles in microsatellite loci

McIntyre, Cathrine Lynne, Goode, Mayling, Monks, Thea and Bonnett, Graham D. (2009) The complex genetic structure of sugarcane limits identification of additional SNP-defined simplex alleles in microsatellite loci. Tropical Plant Biology, 2 3: 133-142. doi:10.1007/s12042-009-9035-4


Author McIntyre, Cathrine Lynne
Goode, Mayling
Monks, Thea
Bonnett, Graham D.
Title The complex genetic structure of sugarcane limits identification of additional SNP-defined simplex alleles in microsatellite loci
Journal name Tropical Plant Biology   Check publisher's open access policy
ISSN 1935-9756
1935-9764
Publication date 2009
Year available 2009
Sub-type Article (original research)
DOI 10.1007/s12042-009-9035-4
Open Access Status
Volume 2
Issue 3
Start page 133
End page 142
Total pages 10
Place of publication New York, NY United States
Publisher Springer New York LLC
Collection year 2010
Language eng
Abstract Cultivated sugarcane possesses a large number of chromosomes (typically >80) which can be organised into eight homology groups, each containing approximately 12 homo(eo)logous chromosomes. Currently, microsatellite (SSR) markers are the most easily used markers for marker-assisted selection and other genetic applications. However, only SSR alleles that segregate as simplex and duplex markers can be incorporated into sugarcane maps using populations of ~300 progeny. Consequently only a subset of possible alleles have been mapped for a given SSR locus and are available for subsequent QTL analyses. Three sugarcane SSR loci, mSSCIR8, mSSCIR17 and mSSCIR18, were amplified, cloned and sequenced from the parents of an Australian sugarcane mapping population, IJ76-514 and Q165D{hooktop}. The sequences were examined to identify nucleotide sequence polymorphisms in the flanking regions that could provide additional simplex SSR allele markers. Alignment of the sequences revealed SNP, indel and repeat length variation and the pattern of sequence variation suggested multiple alleles for each SSR, including all of the alleles previously scored by fragment length. While the flanking regions of the SSR loci contained numerous SNPs and indels, none defined new simplex alleles within multiplex fragments and no new SSR simplex alleles were mapped. Furthermore, many of the sequence-defined alleles appear to be spurious and may have arisen from PCR-mediated recombination. These results confirm the difficulties associated with characterising allelic diversity in a polyploid species and the complexity of mapping in sugarcane.
Keyword Allele
Simplex
Sugarcane
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Biological Sciences Publications
 
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