Characterisation of single nucleotide polymorphisms in sugarcane ESTs

Cordeiro, Giovanni M., Eliott, Frances, McIntyre, C. Lynne, Casu, Rosanne E. and Henry, Robert J. (2006) Characterisation of single nucleotide polymorphisms in sugarcane ESTs. Theoretical and Applied Genetics, 113 2: 331-343. doi:10.1007/s00122-006-0300-8

Author Cordeiro, Giovanni M.
Eliott, Frances
McIntyre, C. Lynne
Casu, Rosanne E.
Henry, Robert J.
Title Characterisation of single nucleotide polymorphisms in sugarcane ESTs
Journal name Theoretical and Applied Genetics   Check publisher's open access policy
ISSN 0040-5752
Publication date 2006-07-01
Sub-type Article (original research)
DOI 10.1007/s00122-006-0300-8
Volume 113
Issue 2
Start page 331
End page 343
Total pages 13
Place of publication Heidelberg, Germany
Publisher Springer
Language eng
Abstract Commercial sugarcane cultivars (Saccharum spp. hybrids) are both polyploid and aneuploid with chromosome numbers in excess of 100; these chromosomes can be assigned to 8 homology groups. To determine the utility of single nucleotide polymorphisms (SNPs) as a means of improving our understanding of the complex sugarcane genome, we developed markers to a suite of SNPs identified in a list of sugarcane ESTs. Analysis of 69 EST contigs showed a median of 9 SNPs per EST and an average of 1 SNP per 50 bp of coding sequence. The quantitative presence of each base at 58 SNP loci within 19 contiguous sequence sets was accurately and reliably determined for 9 sugarcane genotypes, including both commercial cultivars and ancestral species, through the use of quantitative light emission technology in pyrophosphate sequencing. Across the 9 genotypes tested, 47 SNP loci were polymorphic and 11 monomorphic. Base frequency at individual SNP loci was found to vary approximately twofold between Australian sugarcane cultivars and more widely between cultivars and wild species. Base quantity was shown to segregate as expected in the IJ76-514 × Q165 sugarcane mapping population, indicating that SNPs that occur on one or two sugarcane chromosomes have the potential to be mapped. The use of SNP base frequencies from five of the developed markers was able to clearly distinguish all genotypes in the population. The use of SNP base frequencies from a further six markers within an EST contig was able to help establish the likely copy number of the locus in two genotypes tested. This is the first instance of a technology that has been able to provide an insight into the copy number of a specific gene locus in hybrid sugarcane. The identification of specific and numerous haplotypes/alleles present in a genotype by pyrophosphate sequencing or alternative techniques ultimately will provide the basis for identifying associations between specific alleles and phenotype and between allele dosage and phenotype in sugarcane.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
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Created: Wed, 09 Feb 2011, 22:02:40 EST