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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.


3D scatterplot for the cultivar series examined from the Australian and Brazilian breeding programmes. Green, RB series from RIDESA, Brazil; yellow, SP series from CTC (Centro de Technologia Canaveira); Brazil; grey, Q canes from SRA (Sugar Research Australia), Australia; blue, F series, a population from RIDESA, Brazil. The RB series formed a distinct cluster apart from the other cultivars.
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Figure 4: 3D scatterplot for the cultivar series examined from the Australian and Brazilian breeding programmes. Green, RB series from RIDESA, Brazil; yellow, SP series from CTC (Centro de Technologia Canaveira); Brazil; grey, Q canes from SRA (Sugar Research Australia), Australia; blue, F series, a population from RIDESA, Brazil. The RB series formed a distinct cluster apart from the other cultivars.

Mentions: We examined cultivars from several breeding programmes. A one- or two-letter code denotes which breeding programme the cultivar comes from. Cultivars with the two-letter code RB are from Rede Interuniversitária para o Desenvolvimento do Setor Sucroalcooleiro (RIDESA), a consortium of Brazilian Universities; those with the code F are from a single cross from RIDESA; those with the code SP are from Centro de Technologia Canaveira (CTC), the research arm of Copersucar, a Brazilian commercial company; and those with the code Q are from Sugar Research Australia (SRA). A 3D scatterplot of these cultivars showed that the RB cultivars tended to cluster apart from cultivars from other breeding programmes (Fig. 4). The Q canes and SP series were divided approximately equally between the two groups, while the F series fell into the first group away from the RB cultivars (Fig. 4). We examined whether, based on the information we had, the two groups could be distinguished by a particular trait or group of traits. In both groups, a similar percentage of cultivars fell into the main category for each trait, for example, 75% of group 1 and 73% of group 2 had average fibre content (Supplementary Table S4, available at JXB online). We then examined the parentage of each group. For each non-unique parent, we calculated what percentage of each group had the same parent. For group 1, every cultivar had unique parents, or shared a parent with only one other cultivar. For group 2, 44% had SP71-1088 as a parent (Supplementary Table S1). This suggested that the groupings seen in Figs 3 and 4 were the result of closely related crosses. Moreover, the genetic diversity in sugarcane breeding programmes for these loci was low.


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)

3D scatterplot for the cultivar series examined from the Australian and Brazilian breeding programmes. Green, RB series from RIDESA, Brazil; yellow, SP series from CTC (Centro de Technologia Canaveira); Brazil; grey, Q canes from SRA (Sugar Research Australia), Australia; blue, F series, a population from RIDESA, Brazil. The RB series formed a distinct cluster apart from the other cultivars.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: 3D scatterplot for the cultivar series examined from the Australian and Brazilian breeding programmes. Green, RB series from RIDESA, Brazil; yellow, SP series from CTC (Centro de Technologia Canaveira); Brazil; grey, Q canes from SRA (Sugar Research Australia), Australia; blue, F series, a population from RIDESA, Brazil. The RB series formed a distinct cluster apart from the other cultivars.
Mentions: We examined cultivars from several breeding programmes. A one- or two-letter code denotes which breeding programme the cultivar comes from. Cultivars with the two-letter code RB are from Rede Interuniversitária para o Desenvolvimento do Setor Sucroalcooleiro (RIDESA), a consortium of Brazilian Universities; those with the code F are from a single cross from RIDESA; those with the code SP are from Centro de Technologia Canaveira (CTC), the research arm of Copersucar, a Brazilian commercial company; and those with the code Q are from Sugar Research Australia (SRA). A 3D scatterplot of these cultivars showed that the RB cultivars tended to cluster apart from cultivars from other breeding programmes (Fig. 4). The Q canes and SP series were divided approximately equally between the two groups, while the F series fell into the first group away from the RB cultivars (Fig. 4). We examined whether, based on the information we had, the two groups could be distinguished by a particular trait or group of traits. In both groups, a similar percentage of cultivars fell into the main category for each trait, for example, 75% of group 1 and 73% of group 2 had average fibre content (Supplementary Table S4, available at JXB online). We then examined the parentage of each group. For each non-unique parent, we calculated what percentage of each group had the same parent. For group 1, every cultivar had unique parents, or shared a parent with only one other cultivar. For group 2, 44% had SP71-1088 as a parent (Supplementary Table S1). This suggested that the groupings seen in Figs 3 and 4 were the result of closely related crosses. Moreover, the genetic diversity in sugarcane breeding programmes for these loci was low.

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.