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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

qPCR-RBIP. (A) Flow chart of the method used. (B) Schematic of the two qPCRs. Black arrows show the location of the primers, and triangles are the LTRs of the scIvana elements, depicted in grey. Flanking regions are shown as a dark grey line. Fluorescent probes used for qPCR are shown as curved arrows. When the scIvana element is present at the locus, forward primer 2 and the reverse primer are able to amplify the occupied site, while forward primer 1 and the reverse primer will not amplify because the resulting product would be too long to amplify under the PCR conditions chosen. When the scIvana element is absent at the locus, forward primer 1 and the reverse primer are able to amplify the non-occupied site because the ~5kb scIvana is not present. (This figure is available in colour at JXB online.)
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Figure 2: qPCR-RBIP. (A) Flow chart of the method used. (B) Schematic of the two qPCRs. Black arrows show the location of the primers, and triangles are the LTRs of the scIvana elements, depicted in grey. Flanking regions are shown as a dark grey line. Fluorescent probes used for qPCR are shown as curved arrows. When the scIvana element is present at the locus, forward primer 2 and the reverse primer are able to amplify the occupied site, while forward primer 1 and the reverse primer will not amplify because the resulting product would be too long to amplify under the PCR conditions chosen. When the scIvana element is absent at the locus, forward primer 1 and the reverse primer are able to amplify the non-occupied site because the ~5kb scIvana is not present. (This figure is available in colour at JXB online.)

Mentions: Two sets of primers and probes were designed for each locus using the Integrated DNA Technologies website (http://www.idtdna.com/site), one set for the loci with the TE present, and one for the loci with no TE (Fig. 2). Primer and probe sequences are shown in Supplementary Table S2 (available at JXB online).


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)

qPCR-RBIP. (A) Flow chart of the method used. (B) Schematic of the two qPCRs. Black arrows show the location of the primers, and triangles are the LTRs of the scIvana elements, depicted in grey. Flanking regions are shown as a dark grey line. Fluorescent probes used for qPCR are shown as curved arrows. When the scIvana element is present at the locus, forward primer 2 and the reverse primer are able to amplify the occupied site, while forward primer 1 and the reverse primer will not amplify because the resulting product would be too long to amplify under the PCR conditions chosen. When the scIvana element is absent at the locus, forward primer 1 and the reverse primer are able to amplify the non-occupied site because the ~5kb scIvana is not present. (This figure is available in colour at JXB online.)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: qPCR-RBIP. (A) Flow chart of the method used. (B) Schematic of the two qPCRs. Black arrows show the location of the primers, and triangles are the LTRs of the scIvana elements, depicted in grey. Flanking regions are shown as a dark grey line. Fluorescent probes used for qPCR are shown as curved arrows. When the scIvana element is present at the locus, forward primer 2 and the reverse primer are able to amplify the occupied site, while forward primer 1 and the reverse primer will not amplify because the resulting product would be too long to amplify under the PCR conditions chosen. When the scIvana element is absent at the locus, forward primer 1 and the reverse primer are able to amplify the non-occupied site because the ~5kb scIvana is not present. (This figure is available in colour at JXB online.)
Mentions: Two sets of primers and probes were designed for each locus using the Integrated DNA Technologies website (http://www.idtdna.com/site), one set for the loci with the TE present, and one for the loci with no TE (Fig. 2). Primer and probe sequences are shown in Supplementary Table S2 (available at JXB online).

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