Yadav Chandra Bhan, Bonthala Venkata Suresh, Muthamilarasan Mehanathan, Pandey Garima, Khan Yusuf, Prasad Manoj
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India
DNA Res. 2015 Feb;22(1):79-90. doi: 10.1093/dnares/dsu039. Epub 2014 Nov 26.
Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations. Several TEs are highly polymorphic for insert location in the genome and this facilitates development of TE-based markers for various genotyping purposes. Considering this, a genome-wide analysis was performed in the model plant foxtail millet. A total of 30,706 TEs were identified and classified as DNA transposons (24,386), full-length Copia type (1,038), partial or solo Copia type (10,118), full-length Gypsy type (1,570), partial or solo Gypsy type (23,293) and Long- and Short-Interspersed Nuclear Elements (3,659 and 53, respectively). Further, 20,278 TE-based markers were developed, namely Retrotransposon-Based Insertion Polymorphisms (4,801, ∼24%), Inter-Retrotransposon Amplified Polymorphisms (3,239, ∼16%), Repeat Junction Markers (4,451, ∼22%), Repeat Junction-Junction Markers (329, ∼2%), Insertion-Site-Based Polymorphisms (7,401, ∼36%) and Retrotransposon-Microsatellite Amplified Polymorphisms (57, 0.2%). A total of 134 Repeat Junction Markers were screened in 96 accessions of Setaria italica and 3 wild Setaria accessions of which 30 showed polymorphism. Moreover, an open access database for these developed resources was constructed (Foxtail millet Transposable Elements-based Marker Database; http://59.163.192.83/ltrdb/index.html). Taken together, this study would serve as a valuable resource for large-scale genotyping applications in foxtail millet and related grass species.
转座元件（TEs）是植物基因组的主要组成部分，据报道在功能基因组多样性和表型变异中发挥着重要作用。一些转座元件在基因组中的插入位置具有高度多态性，这有利于开发用于各种基因分型目的的基于转座元件的标记。考虑到这一点，在模式植物谷子中进行了全基因组分析。共鉴定出30706个转座元件，并将其分类为DNA转座子（24386个）、全长Copia型（1038个）、部分或单独的Copia型（10118个）、全长Gypsy型（1570个）、部分或单独的Gypsy型（23293个）以及长散在核元件和短散在核元件（分别为3659个和53个）。此外，开发了20278个基于转座元件的标记，即基于反转录转座子的插入多态性（4801个，约24%）、反转录转座子间扩增多态性（3239个，约16%）、重复连接标记（4451个，约22%）、重复连接-连接标记（329个，约2%）、基于插入位点的多态性（7401个，约36%）和反转录转座子-微卫星扩增多态性（57个，0.2%）。在96份谷子种质和3份野生狗尾草种质中筛选了总共134个重复连接标记，其中30个表现出多态性。此外，还构建了一个用于这些开发资源的开放获取数据库（谷子转座元件标记数据库；http://59.163.192.83/ltrdb/index.html）。综上所述，本研究将为谷子及相关禾本科物种的大规模基因分型应用提供有价值的资源。
