Limits...
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

Mauve visualization of the region around the scIvana elements in sugarcane BACS and other grass genomes (S. bicolor, Z. mays, and O. sativa). The BAC sequence and each genome are laid out in a horizontal track. Annotated coding regions are shown as white boxes and TEs as pink boxes. A coloured similarity plot (locally collinear blocks) is shown for each genome, the height of which is proportional to the level of sequence identity in that region. The same colour represents regions of highest similarity. (A) BAC SCHRBa_011_K15 (scIvana1.1); (B) SCHRBa_044_D02 (scIvana1.2). Orange boxes, SHCRBa_011_K15.13, Sobic.008G106700, and GRMZM2G326116, translation initiation factors; green boxes, SHCRBa_044_D02.1, Sobic.007G192200, LOC_Os08g42040, and GRMZM2G083725, similar to lipid transfer protein-like; purple boxes, SHCRBa_044_D02.4, Sobic.007G192100, LOC_Os08g42050, and GRMZM2G083551), similar to coated vesicle membrane protein-like; bright pink boxes, SHCRBa_044_D02.7, Sobic.007G192000, LOC_Os08g42080, and GRMZM2G083538, ACT domain repeats.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: Mauve visualization of the region around the scIvana elements in sugarcane BACS and other grass genomes (S. bicolor, Z. mays, and O. sativa). The BAC sequence and each genome are laid out in a horizontal track. Annotated coding regions are shown as white boxes and TEs as pink boxes. A coloured similarity plot (locally collinear blocks) is shown for each genome, the height of which is proportional to the level of sequence identity in that region. The same colour represents regions of highest similarity. (A) BAC SCHRBa_011_K15 (scIvana1.1); (B) SCHRBa_044_D02 (scIvana1.2). Orange boxes, SHCRBa_011_K15.13, Sobic.008G106700, and GRMZM2G326116, translation initiation factors; green boxes, SHCRBa_044_D02.1, Sobic.007G192200, LOC_Os08g42040, and GRMZM2G083725, similar to lipid transfer protein-like; purple boxes, SHCRBa_044_D02.4, Sobic.007G192100, LOC_Os08g42050, and GRMZM2G083551), similar to coated vesicle membrane protein-like; bright pink boxes, SHCRBa_044_D02.7, Sobic.007G192000, LOC_Os08g42080, and GRMZM2G083538, ACT domain repeats.

Mentions: Based on published reports of cultivar traits, we were unable to find a particular trait or groups of traits associated with the scIvana elements examined. We therefore extended our search for traits by identifying regions syntenic to and 100kb 5′ and 3′ to the BACs in three other grass genomes. Sorghum bicolor (v.2.1) and Z. mays (v.6a) are the closest fully sequenced genomes to Saccharum. Oryza sativa (v.7.0) was also chosen because it is the best annotated of the grass genomes and has been used previously in synteny analyses with sugarcane (D’Hont et al., 2010; Aitken et al., 2014a). Coding regions were then queried against the Phytozome v.10 database for functional annotation (Supplementary Table S3, available at JXB online). Syntenic regions to the BAC SCHRBa_015_O15 in the three grass genomes could not be identified with any confidence. The regions identified by the Mauve program (Darling et al., 2010) contained coding regions in putatively syntenic regions to other genomes that were not listed as protein homologues in the Phytozome database. For BACs SCHRBa_011_K15 (scIvana1.1) and SCHRBa_044_D02 (scIvana1.2), a 3–4kb region around the element is illustrated in Fig. 5. Supplementary Table S3 lists in more detail the locus, location, and functional annotation from the Panther, PFAM, and KEGG databases (Kanehisa and Goto, 2000; Punta et al., 2012; Mi et al., 2013) for each coding region identified in the BACs and 100kb 5′ and 3′ to the BACs in the three grass genomes.


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)

Mauve visualization of the region around the scIvana elements in sugarcane BACS and other grass genomes (S. bicolor, Z. mays, and O. sativa). The BAC sequence and each genome are laid out in a horizontal track. Annotated coding regions are shown as white boxes and TEs as pink boxes. A coloured similarity plot (locally collinear blocks) is shown for each genome, the height of which is proportional to the level of sequence identity in that region. The same colour represents regions of highest similarity. (A) BAC SCHRBa_011_K15 (scIvana1.1); (B) SCHRBa_044_D02 (scIvana1.2). Orange boxes, SHCRBa_011_K15.13, Sobic.008G106700, and GRMZM2G326116, translation initiation factors; green boxes, SHCRBa_044_D02.1, Sobic.007G192200, LOC_Os08g42040, and GRMZM2G083725, similar to lipid transfer protein-like; purple boxes, SHCRBa_044_D02.4, Sobic.007G192100, LOC_Os08g42050, and GRMZM2G083551), similar to coated vesicle membrane protein-like; bright pink boxes, SHCRBa_044_D02.7, Sobic.007G192000, LOC_Os08g42080, and GRMZM2G083538, ACT domain repeats.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: Mauve visualization of the region around the scIvana elements in sugarcane BACS and other grass genomes (S. bicolor, Z. mays, and O. sativa). The BAC sequence and each genome are laid out in a horizontal track. Annotated coding regions are shown as white boxes and TEs as pink boxes. A coloured similarity plot (locally collinear blocks) is shown for each genome, the height of which is proportional to the level of sequence identity in that region. The same colour represents regions of highest similarity. (A) BAC SCHRBa_011_K15 (scIvana1.1); (B) SCHRBa_044_D02 (scIvana1.2). Orange boxes, SHCRBa_011_K15.13, Sobic.008G106700, and GRMZM2G326116, translation initiation factors; green boxes, SHCRBa_044_D02.1, Sobic.007G192200, LOC_Os08g42040, and GRMZM2G083725, similar to lipid transfer protein-like; purple boxes, SHCRBa_044_D02.4, Sobic.007G192100, LOC_Os08g42050, and GRMZM2G083551), similar to coated vesicle membrane protein-like; bright pink boxes, SHCRBa_044_D02.7, Sobic.007G192000, LOC_Os08g42080, and GRMZM2G083538, ACT domain repeats.
Mentions: Based on published reports of cultivar traits, we were unable to find a particular trait or groups of traits associated with the scIvana elements examined. We therefore extended our search for traits by identifying regions syntenic to and 100kb 5′ and 3′ to the BACs in three other grass genomes. Sorghum bicolor (v.2.1) and Z. mays (v.6a) are the closest fully sequenced genomes to Saccharum. Oryza sativa (v.7.0) was also chosen because it is the best annotated of the grass genomes and has been used previously in synteny analyses with sugarcane (D’Hont et al., 2010; Aitken et al., 2014a). Coding regions were then queried against the Phytozome v.10 database for functional annotation (Supplementary Table S3, available at JXB online). Syntenic regions to the BAC SCHRBa_015_O15 in the three grass genomes could not be identified with any confidence. The regions identified by the Mauve program (Darling et al., 2010) contained coding regions in putatively syntenic regions to other genomes that were not listed as protein homologues in the Phytozome database. For BACs SCHRBa_011_K15 (scIvana1.1) and SCHRBa_044_D02 (scIvana1.2), a 3–4kb region around the element is illustrated in Fig. 5. Supplementary Table S3 lists in more detail the locus, location, and functional annotation from the Panther, PFAM, and KEGG databases (Kanehisa and Goto, 2000; Punta et al., 2012; Mi et al., 2013) for each coding region identified in the BACs and 100kb 5′ and 3′ to the BACs in the three grass genomes.

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