Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane

Autor(es)

Metcalfe, Cushla J. ; Oliveira, Sarah G. ; Gaiarsa, Jonas W. ; Aitken, Karen S. ; Carneiro, Monalisa S. ; Zatti, Fernanda ; Van Sluys, Marie-Anne

• Tipo de documento: Artigo Científico
• Fonte: Journal of Experimental Botany; v. 66, n. 14, p. 12-pg., 2015-07-01.

Resumo

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. (AU)

• Processo FAPESP: 08/52074-0 - Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function
• Beneficiário: Marie-Anne Van Sluys
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOEN - Temático
• Processo FAPESP: 13/09391-2 - Uso de Real Time PCR para quantificação polimorfismo derivados da inserção de retrotransposons em cultivares poliplóides modernas de cana de açúcar
• Beneficiário: Cushla J Metcalfe
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 09/09217-7 - Estudos sobre a organização do genoma de cana de açúcar e expressão gênica associada a presença de elementos de transposição
• Beneficiário: Cushla J Metcalfe
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 13/18322-4 - Anotação de 1000 clones BAC do genoma da cana de açúcar: banco de dados, integração e interface web.
• Beneficiário: Jonas Weissmann Gaiarsa
• Modalidade de apoio: Bolsas no Brasil - Programa Capacitação - Treinamento Técnico