ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
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- Genome-wide identification and expression profiling of the MADS-box gene family in Lavandula angustifolia.BMC genomics · 2025Article
- Genome-wide identification and comparative evolution of 14-3-3 gene family members in five Brassicaceae species.BMC genomics · 2025Article
- Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.The plant genome · 2025Article
- Foxtail millet research in supporting climate change resilience efforts: Bibliometric analysis and focused literature review.Heliyon · 2025Review
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- Genome-Wide Identification and Analysis of Family Members with Juvenile Hormone Binding Protein Domains inInsects · 2024Article
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- Genome-wide identification of AAAP gene family and expression analysis in response to saline-alkali stress in foxtail millet (Setaria italica L.).Scientific reports · 2024Article
- Diversification of plant SUPPRESSOR OF MAX2 1 (SMAX1)-like genes and genome-wide identification and characterization of cotton SMXL gene family.BMC plant biology · 2023Article
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- Genome-Wide Identification and Abiotic Stress Response Analysis of PP2C Gene Family in Woodland and Pineapple Strawberries.International journal of molecular sciences · 2023Article
- Molecular characterization and expression analysis of theFrontiers in plant science · 2023Article
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- Genome-Wide Identification and Expression Analysis of Wall-Associated Kinase (WAK) Gene Family inPlants (Basel, Switzerland) · 2022Article
- Genome-wide identification and expression analysis of the cucumber PP2C gene family.BMC genomics · 2022Article
- Development of molecular markers based on LTR retrotransposon in the Cleistogenes songorica genome.Journal of applied genetics · 2022Article
- Multi-omics intervention inFrontiers in plant science · 2022Review
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Authors and funding
6 authors.
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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.
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