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Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database

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Title Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database
 
Creator Yadav, Chandra Bhan
Bonthala, Venkata Suresh
Muthamilarasan, Mehanathan
Pandey, Garima
Khan, Yusuf
Prasad, Manoj
 
Subject foxtail millet (Setaria italica L.)
transposable element-based markers
retrotransposons
DNA transposons
database
 
Description Accepted date: October 27, 2014
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.
The authors’ work in this area was supported by the core grant of National
Institute of Plant Genome Research (NIPGR), New Delhi, India. Funding to
pay the Open Access publication charges for this article was provided by the National Institute of Plant Genome Research, New Delhi, India.
 
Date 2016-01-27T05:53:13Z
2016-01-27T05:53:13Z
2015
 
Type Article
 
Identifier DNA Res., 22(1): 79-90
1340-2838
http://172.16.0.77:8080/jspui/handle/123456789/594
http://dnaresearch.oxfordjournals.org/content/22/1/79.long
10.1093/dnares/dsu039
 
Language en_US
 
Publisher Oxford University Press