Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database.
Bottom Line: Transposable elements (TEs) are major components of plant genome and are reported to play significant roles in functional genome diversity and phenotypic variations.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.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.Show MeSH
Mentions: Using the three-level schema of Apache, PHP and MySQL, open access Foxtail millet Transposable Element-based Marker Database (FmTEMDb; http://126.96.36.199/ltrdb/index.html) was constructed (Fig. 8). The database is a repository of complete TE data along with respective marker information. The details of TEs can be searched using six different search criteria such as TE IDs, type of TE, chromosome, etc. For each TE, the database will provide preliminary information of TE ID, chromosomal location, orientation of the coding strand, subclass (if any) and hyperlinks to retrieve the primers and view the physical map. Under primer details, the database will display the primer type, junction, TE type, TE source, strand orientation, start and end position of primers, melting temperature and GC percentage. The CMap feature of FmTEMDb allows the interactive visualization of physical and comparative map of TEs (Fig. 9). The map could be browsed either by type of TE or chromosome-wise. Further, all the data stored in the database are available for download. Although the database is user friendly, a tutorial is also provided (Supplementary Fig. S12).Figure 8.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.