title: Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database.
abstract: 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.
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.
authors.forename: Chandra Bhan
authors.initials: CB
authors.lastname: Yadav
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.
authors.forename: Venkata Suresh
authors.initials: VS
authors.lastname: Bonthala
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.
authors.forename: Mehanathan
authors.initials: M
authors.lastname: Muthamilarasan
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.
authors.forename: Garima
authors.initials: G
authors.lastname: Pandey
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India.
authors.forename: Yusuf
authors.initials: Y
authors.lastname: Khan
authors.affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110 067, India manoj_prasad@nipgr.ac.in.
authors.forename: Manoj
authors.initials: M
authors.lastname: Prasad
mesh_terms: D004251:DNA Transposable Elements; D030561:Databases, Nucleic Acid; D005819:Genetic Markers; D055106:Genome-Wide Association Study; D011110:Polymorphism, Genetic; D018626:Retroelements; D032983:Setaria Plant / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D005819:Genetic Markers; D018626:Retroelements
keywords: DNA transposons; database; foxtail millet (Setaria italica L.); retrotransposons; transposable element-based markers