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Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.

Metcalfe CJ, Oliveira SG, Gaiarsa JW, Aitken KS, Carneiro MS, Zatti F, Van Sluys MA - J. Exp. Bot. (2015)

Bottom Line: We screened two genera closely related to Saccharum (Miscanthus and Erianthus), wild Saccharum, traditional cultivars, and 127 modern cultivars from Brazilian and Australian breeding programmes.Secondly, the history of insertion and timing of the three TEs examined supports our current understanding of the evolution of the Saccharum complex.Thirdly, all three TEs were found in only one of the two main lineages leading to the modern sugarcane cultivars and are therefore the first TEs identified that could potentially be used as markers for Saccharum spontaneum.

View Article: PubMed Central - PubMed

Affiliation: GaTE-Lab, Departamento de Botânica, IBUSP, Universidade de São Paulo, rua do Matao 277, 05508-090, SP, Brazil.

No MeSH data available.


Related in: MedlinePlus

UPGMA dendogram of S. officinarium samples and cultivars. Coloured circles and triangles indicate the type of sample: pink triangle, S. officinarum; green circle, RB series from RIDESA, Brazil; yellow circle, SP series from CTC (Centro de Technologia Canaveira), Brazil; grey circle, Q canes from SRA (Sugar Research Australia), Australia; blue circle, the F series, a population from RIDESA, Brazil; orange circle, all other cultivars. Across-plate replicates are indicated by the stars.
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Figure 3: UPGMA dendogram of S. officinarium samples and cultivars. Coloured circles and triangles indicate the type of sample: pink triangle, S. officinarum; green circle, RB series from RIDESA, Brazil; yellow circle, SP series from CTC (Centro de Technologia Canaveira), Brazil; grey circle, Q canes from SRA (Sugar Research Australia), Australia; blue circle, the F series, a population from RIDESA, Brazil; orange circle, all other cultivars. Across-plate replicates are indicated by the stars.

Mentions: We tested whether we could distinguish individual S. officinarum and cultivars. We included replicates across plates in the Nei–Li coefficient genetic distance matrix and resulting UPGMA dendrogram (indicated by stars in Fig. 3). The highest genetic distance between replicates was 0.0020 for 87S9021 (data not shown). The bootstrap values for the UPGMA were very low (<70%), so we were unable to use the UPGMA tree to distinguish the cultivars examined. These results suggested, however, that, combined with other scIvana elements or other TEs, the qPCR-RBIP method could be used to create a ‘TE profile’ of a cultivar.


Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.

Metcalfe CJ, Oliveira SG, Gaiarsa JW, Aitken KS, Carneiro MS, Zatti F, Van Sluys MA - J. Exp. Bot. (2015)

UPGMA dendogram of S. officinarium samples and cultivars. Coloured circles and triangles indicate the type of sample: pink triangle, S. officinarum; green circle, RB series from RIDESA, Brazil; yellow circle, SP series from CTC (Centro de Technologia Canaveira), Brazil; grey circle, Q canes from SRA (Sugar Research Australia), Australia; blue circle, the F series, a population from RIDESA, Brazil; orange circle, all other cultivars. Across-plate replicates are indicated by the stars.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4493790&req=5

Figure 3: UPGMA dendogram of S. officinarium samples and cultivars. Coloured circles and triangles indicate the type of sample: pink triangle, S. officinarum; green circle, RB series from RIDESA, Brazil; yellow circle, SP series from CTC (Centro de Technologia Canaveira), Brazil; grey circle, Q canes from SRA (Sugar Research Australia), Australia; blue circle, the F series, a population from RIDESA, Brazil; orange circle, all other cultivars. Across-plate replicates are indicated by the stars.
Mentions: We tested whether we could distinguish individual S. officinarum and cultivars. We included replicates across plates in the Nei–Li coefficient genetic distance matrix and resulting UPGMA dendrogram (indicated by stars in Fig. 3). The highest genetic distance between replicates was 0.0020 for 87S9021 (data not shown). The bootstrap values for the UPGMA were very low (<70%), so we were unable to use the UPGMA tree to distinguish the cultivars examined. These results suggested, however, that, combined with other scIvana elements or other TEs, the qPCR-RBIP method could be used to create a ‘TE profile’ of a cultivar.

Bottom Line: We screened two genera closely related to Saccharum (Miscanthus and Erianthus), wild Saccharum, traditional cultivars, and 127 modern cultivars from Brazilian and Australian breeding programmes.Secondly, the history of insertion and timing of the three TEs examined supports our current understanding of the evolution of the Saccharum complex.Thirdly, all three TEs were found in only one of the two main lineages leading to the modern sugarcane cultivars and are therefore the first TEs identified that could potentially be used as markers for Saccharum spontaneum.

View Article: PubMed Central - PubMed

Affiliation: GaTE-Lab, Departamento de Botânica, IBUSP, Universidade de São Paulo, rua do Matao 277, 05508-090, SP, Brazil.

No MeSH data available.


Related in: MedlinePlus