Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.
Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.
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DOI：
10.1093/jxb/erv283
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发表时间：
2015-07
影响因子：
6.9
通讯作者：
Van Sluys MA
中科院分区：
文献类型：
--
作者：
Metcalfe CJ;Oliveira SG;Gaiarsa JW;Aitken KS;Carneiro MS;Zatti F;Van Sluys MA
qPCR-RBIP 用于检查甘蔗属和相关属、花茅属和芒属中特定标记的剂量和进化历史。它还区分了 S. spontaneum 和 S. officinarum。甘蔗是世界糖的主要来源，作为生物燃料的来源变得越来越重要。甘蔗基因组的高度多倍体和杂合性意味着该基因组的表征落后于其他重要作物。在这里，我们开发了一种方法，结合使用定量 PCR 和转座标记系统，对特定基因座上存在转座元件 (TE) 的等位基因的相对数量进行评分。我们筛选了与甘蔗密切相关的两个属（芒草属和毛茅属）、野生甘蔗属、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。我们展示了如何以多种方式使用此方法。首先，我们证明该方法可以扩展为基因分型系统的一部分。其次，所检查的三个 TE 的插入历史和时间支持了我们目前对糖复合体进化的理解。第三，所有三个 TE 仅在导致现代甘蔗品种的两个主要谱系之一中发现，因此是第一个确定的可用作自发糖标记的 TE。
qPCR-RBIP was used to examine the dosage of particular markers and evolutionary history in Saccharum and the related genera, Erianthus and Miscanthus. It also differentiated between S. spontaneum and S. officinarum. 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.
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影响因子：
3.7
作者：
Cardoso-Silva CB;Costa EA;Mancini MC;Balsalobre TW;Canesin LE;Pinto LR;Carneiro MS;Garcia AA;de Souza AP;Vicentini R
通讯作者：
Vicentini R
影响因子：
1.9
作者：
BREMER, G
通讯作者：
BREMER, G
影响因子：
2
作者：
Berkman, Paul J.;Bundock, Peter C.;Aitken, Karen S.
通讯作者：
Aitken, Karen S.
影响因子：
2
作者：
Devarumath, Rachayya M.;Kalwade, Sachin B.;Henry, Robert
通讯作者：
Henry, Robert
影响因子：
3.1
作者：
D'Hont, A;Ison, D;Glaszmann, JC
通讯作者：
Glaszmann, JC