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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

Evolutionary history of Saccharum species modified from Grivet et al. (2006). Solid and dashed lines with arrows indicate hybridization events and minor contributions to modern sugarcane cultivars, respectively. Grey ovals show whole genome duplication events. 2n refers to chromosome numbers from Grivet et al. (2006). Red arrows show the timing of insertion of the scIvana element. The numbers in brackets after the scIvana element indicates the estimated age of the insertion of the element (mya, million years ago). Outline of the box and box colour indicate type of sugarcane and number of scIvana elements identified, respectively; dashed outline, wild species; solid outline, domesticated species; white, no scIvana element found; pale grey scIvana 1.4 only found; grey, scIvana 1.4 and 1.2 found; dark grey all 3 scIvana elements found.The number in brackets after the species name indicates the number of samples examined. (This figure is available in colour at JXB online.)
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Figure 1: Evolutionary history of Saccharum species modified from Grivet et al. (2006). Solid and dashed lines with arrows indicate hybridization events and minor contributions to modern sugarcane cultivars, respectively. Grey ovals show whole genome duplication events. 2n refers to chromosome numbers from Grivet et al. (2006). Red arrows show the timing of insertion of the scIvana element. The numbers in brackets after the scIvana element indicates the estimated age of the insertion of the element (mya, million years ago). Outline of the box and box colour indicate type of sugarcane and number of scIvana elements identified, respectively; dashed outline, wild species; solid outline, domesticated species; white, no scIvana element found; pale grey scIvana 1.4 only found; grey, scIvana 1.4 and 1.2 found; dark grey all 3 scIvana elements found.The number in brackets after the species name indicates the number of samples examined. (This figure is available in colour at JXB online.)

Mentions: Modern sugarcane cultivars are highly polyploid or aneuploid hybrids derived from interspecific hybridization between Saccharum officinarum and Saccharum spontaneum, a wild sugarcane (Moore et al., 2014) (Fig. 1). S. officinarium and S. spontaneum have contrasting attributes in terms of sucrose and fibre content: S. officinarium has high sucrose and low fibre content, while S. spontaneum has low sucrose and high fibre content (Moore et al., 2014). Hybrids between S. officinarum and S. spontaneum show 2n+n transmission, where 2n is the entire genome of S. officinarum. This phenomena remains true in the first backcross between the 2n+n F1 and the female S. officinarum, but generally breaks down in subsequent backcrosses (Bremer, 1961; Piperidis et al., 2010). Early breeders used this phenomenon to introduce vigour and resistance genes from S. spontaneum, while quickly recovering the high sugar content of S. officinarum (Roach, 1972). The modern sugarcane cultivar has chromosome numbers ranging from 100 to 120, 70–80% of which are from S. officinarum, 10–23% from S. spontaneum, and a small portion being recombinants (D’Hont, 2005; Piperidis et al., 2010). The number of alleles most likely varies from 8 to 14 (Aitken et al., 2014b). For almost all cultivars the genome size is unknown; the modern R570 cultivar has a genome size of ~10 Gb (D’Hont and Glaszmann, 2001). Current molecular evidence suggests that S. officinarum itself is derived from the wild sugarcane, Saccharum robustum (Lu et al., 1994; D’Hont et al., 1998). The older traditional cultivars Saccharum barberi (North India) and Saccharum sinense (China) are thought to be natural hybrids (D’Hont et al., 2002).


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)

Evolutionary history of Saccharum species modified from Grivet et al. (2006). Solid and dashed lines with arrows indicate hybridization events and minor contributions to modern sugarcane cultivars, respectively. Grey ovals show whole genome duplication events. 2n refers to chromosome numbers from Grivet et al. (2006). Red arrows show the timing of insertion of the scIvana element. The numbers in brackets after the scIvana element indicates the estimated age of the insertion of the element (mya, million years ago). Outline of the box and box colour indicate type of sugarcane and number of scIvana elements identified, respectively; dashed outline, wild species; solid outline, domesticated species; white, no scIvana element found; pale grey scIvana 1.4 only found; grey, scIvana 1.4 and 1.2 found; dark grey all 3 scIvana elements found.The number in brackets after the species name indicates the number of samples examined. (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 1: Evolutionary history of Saccharum species modified from Grivet et al. (2006). Solid and dashed lines with arrows indicate hybridization events and minor contributions to modern sugarcane cultivars, respectively. Grey ovals show whole genome duplication events. 2n refers to chromosome numbers from Grivet et al. (2006). Red arrows show the timing of insertion of the scIvana element. The numbers in brackets after the scIvana element indicates the estimated age of the insertion of the element (mya, million years ago). Outline of the box and box colour indicate type of sugarcane and number of scIvana elements identified, respectively; dashed outline, wild species; solid outline, domesticated species; white, no scIvana element found; pale grey scIvana 1.4 only found; grey, scIvana 1.4 and 1.2 found; dark grey all 3 scIvana elements found.The number in brackets after the species name indicates the number of samples examined. (This figure is available in colour at JXB online.)
Mentions: Modern sugarcane cultivars are highly polyploid or aneuploid hybrids derived from interspecific hybridization between Saccharum officinarum and Saccharum spontaneum, a wild sugarcane (Moore et al., 2014) (Fig. 1). S. officinarium and S. spontaneum have contrasting attributes in terms of sucrose and fibre content: S. officinarium has high sucrose and low fibre content, while S. spontaneum has low sucrose and high fibre content (Moore et al., 2014). Hybrids between S. officinarum and S. spontaneum show 2n+n transmission, where 2n is the entire genome of S. officinarum. This phenomena remains true in the first backcross between the 2n+n F1 and the female S. officinarum, but generally breaks down in subsequent backcrosses (Bremer, 1961; Piperidis et al., 2010). Early breeders used this phenomenon to introduce vigour and resistance genes from S. spontaneum, while quickly recovering the high sugar content of S. officinarum (Roach, 1972). The modern sugarcane cultivar has chromosome numbers ranging from 100 to 120, 70–80% of which are from S. officinarum, 10–23% from S. spontaneum, and a small portion being recombinants (D’Hont, 2005; Piperidis et al., 2010). The number of alleles most likely varies from 8 to 14 (Aitken et al., 2014b). For almost all cultivars the genome size is unknown; the modern R570 cultivar has a genome size of ~10 Gb (D’Hont and Glaszmann, 2001). Current molecular evidence suggests that S. officinarum itself is derived from the wild sugarcane, Saccharum robustum (Lu et al., 1994; D’Hont et al., 1998). The older traditional cultivars Saccharum barberi (North India) and Saccharum sinense (China) are thought to be natural hybrids (D’Hont et al., 2002).

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