A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences

Berkman, Paul J., Bundock, Peter C., Casu, Rosanne E., Henry, Robert J., Rae, Anne L. and Aitken, Karen S. (2014) A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences. Tropical Plant Biology, 7 2: 71-83. doi:10.1007/s12042-014-9139-3


Author Berkman, Paul J.
Bundock, Peter C.
Casu, Rosanne E.
Henry, Robert J.
Rae, Anne L.
Aitken, Karen S.
Title A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences
Formatted title
A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences
Journal name Tropical Plant Biology   Check publisher's open access policy
ISSN 1935-9764
1935-9756
Publication date 2014
Sub-type Article (original research)
DOI 10.1007/s12042-014-9139-3
Open Access Status
Volume 7
Issue 2
Start page 71
End page 83
Total pages 13
Place of publication New York, NY, United States
Publisher Springer New York
Collection year 2015
Language eng
Formatted abstract
Sugarcane (Saccharum spp.) is a crop of substantial international significance for both food and fuel, however its highly polyploid nature challenges investigation of its genetic composition. Efforts to generate the full sugarcane genome sequence are underway, however in the meantime crop improvement efforts are somewhat limited by the lack of genome sequence resources available for physiological characterization. Low-coverage survey sequence data was generated and assembled for six sugarcane genotypes representing a range of significant S. spontaneum, S. officinarum, and S. hybrid cultivar accessions from around the world. These data were explored to investigate the composition of repetitive sequences and variations in chloroplast genome sequence, as well as assembled into a conglomerate monoploid genome sequence for polymorphism comparison between the genotypes. Almost half (47 %) of the inter-genomic polymorphisms analysed in these data represented poly-allelic variations which cannot be applied in traditional present/absent marker analysis, suggesting that new approaches are required to better understand and access genetic diversity within the Saccharum genus. These results support previous assertions that S. spontaneum is both less repetitive (62 % repetitive k-mers in Mandalay vs. 65 % in IJ76-514) and more highly polymorphic (17 % poly-alleles in Mandalay vs. 10 % poly-alleles in IJ76-514) than S. officinarum, with S. hybrids being intermediate between the two. However, contrary to previous analysis the monoploid genome size of S. spontaneum does not appear to differ significantly from that of S. officinarum as had been expected. This genomic survey assembly will be a very useful resource for sugarcane genomics in the absence of a monoploid or polyploid genome sequence, and will be made available upon request.
Keyword Next generation sequencing
Saccharum
Sugarcane
Survey sequencing
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2015 Collection
 
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