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: Retrotransposons were found to be transcriptionally active in all the four tissues, namely leaf, root, spica and stem (Fig. 2; Supplementary Tables S11–S15). A maximum of Copia-type TEs (∼80%) matched with RNA-HiSeq reads which revealed that Copia-type TEs were prevalently expressed in tissues of foxtail millet. Approximately 49% of Gypsy-type retrotransposons matched with RNA-HiSeq reads. Similarly, ∼10% LINEs, ∼15% SINEs and ∼16% DNA transposons matched with the expressed reads (Fig. 2; Supplementary Tables S11–S15).Figure 2.
Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.