title: Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.
abstract: Sugarcane is the main source of the world's sugar and is becoming increasingly important as a source of biofuel. The highly polyploid and heterozygous nature of the sugarcane genome has meant that characterization of the genome has lagged behind that of other important crops. Here we developed a method using a combination of quantitative PCR with a transposable marker system to score the relative number of alleles with a transposable element (TE) present at a particular locus. 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. We showed how this method could be used in various ways. First, we showed that the method could be extended to be used as part of a genotyping system. 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.
authors.affiliation: GaTE-Lab, Departamento de Botânica, IBUSP, Universidade de São Paulo, rua do Matao 277, 05508-090, SP, Brazil.
authors.forename: Cushla J
authors.identifier: http://orcid.org/0000-0001-9375-3332
authors.initials: CJ
authors.lastname: Metcalfe
authors.affiliation: GaTE-Lab, Departamento de Botânica, IBUSP, Universidade de São Paulo, rua do Matao 277, 05508-090, SP, Brazil.
authors.forename: Sarah G
authors.initials: SG
authors.lastname: Oliveira
authors.affiliation: GaTE-Lab, Departamento de Botânica, IBUSP, Universidade de São Paulo, rua do Matao 277, 05508-090, SP, Brazil.
authors.forename: Jonas W
authors.initials: JW
authors.lastname: Gaiarsa
authors.affiliation: CSIRO Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4072, Australia.
authors.forename: Karen S
authors.initials: KS
authors.lastname: Aitken
authors.affiliation: Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, 13600-970, SP, Brazil.
authors.forename: Monalisa S
authors.initials: MS
authors.lastname: Carneiro
authors.affiliation: Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, 13600-970, SP, Brazil.
authors.forename: Fernanda
authors.initials: F
authors.lastname: Zatti
authors.affiliation: GaTE-Lab, Departamento de Botânica, IBUSP, Universidade de São Paulo, rua do Matao 277, 05508-090, SP, Brazil mavsluys@usp.br.
authors.forename: Marie-Anne
authors.identifier: http://orcid.org/0000-0002-6506-2734
authors.initials: MA
authors.lastname: Van Sluys
mesh_terms: D005819:Genetic Markers; D016254:Mutagenesis, Insertional; D016133:Polymerase Chain Reaction / Q000379:methods*; D011110:Polymorphism, Genetic; D031786:Saccharum / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: Marker; polyploid; real-time PCR; retrotransposon-based insertion polymorphism; sugarcane; transposable element.