Metcalfe Cushla J, Oliveira Sarah G, Gaiarsa Jonas W, Aitken Karen S, Carneiro Monalisa S, Zatti Fernanda, Van Sluys Marie-Anne
GaTE-Lab, Departamento de Botânica, IBUSP, Universidade de São Paulo, rua do Matao 277, 05508-090, SP, Brazil.
CSIRO Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4072, Australia.
J Exp Bot. 2015 Jul;66(14):4239-50. doi: 10.1093/jxb/erv283. Epub 2015 Jun 19.
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.
甘蔗是全球食糖的主要来源，并且作为生物燃料来源正变得愈发重要。甘蔗基因组高度多倍体且杂合的特性意味着其基因组特征的研究落后于其他重要作物。在此，我们开发了一种方法，该方法结合了定量PCR与转座标记系统，以确定特定位点上存在的带有转座元件（TE）的等位基因的相对数量。我们筛选了与甘蔗属密切相关的两个属（芒属和蔗茅属）、野生甘蔗、传统品种，以及来自巴西和澳大利亚育种计划的127个现代品种。我们展示了该方法可以有多种用途。首先，我们表明该方法可扩展用作基因分型系统的一部分。其次，所检测的三种TE的插入历史和时间支持了我们目前对甘蔗复合体进化的理解。第三，在导致现代甘蔗品种的两个主要谱系中，仅在其中一个谱系中发现了所有三种TE，因此它们是首批被鉴定出的有可能用作野生甘蔗标记的TE。
