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; ). Taken together, this study would serve as a valuable resource for large-scale genotyping applications in foxtail millet and related grass species.

Foxtail millet: nutritional and eating quality, and prospects for genetic improvement

“…Both SNPs [66] and microsatellites [67][68][69] have been developed and utilized as molecular markers. In addition, some novel marker types such as miRNA-based [70] and transposable elements-based markers [71] were developed along with construction of web-based databases [70][71][72] for the access of the foxtail millet research community. A haplotype map of genomic variations has been proposed [66] .…”

Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects

“…Therefore, the Beijing Genomics Institute, China and the US Department of Energy–Joint Genome Institute have sequenced the foxtail millet genome (Bennetzen et al, 2012 ; Zhang et al, 2012 ). As foxtail millet serves as a rich source of genes, alleles, or QTL for genetic improvement of major cereals and bioenergy grasses, large-scale genomic resources were developed including simple sequence repeats (SSRs) (Pandey et al, 2013 ; Zhang et al, 2014b ), intron length polymorphisms (Muthamilarasan et al, 2014 ), eSSRs (Kumari et al, 2013 ), miRNA-based markers (Yadav et al, 2014 ), and transposable-elements based markers (Yadav et al, 2015 ). Moreover, open access online databases such as foxtail millet marker database (FmMDb) (Suresh et al, 2013 ), foxtail millet miRNA database (FmMiRNADb) (Khan et al, 2014 ) and foxtail millet transposable elements-based marker database (FmTEMDb) (Yadav et al, 2015 ) have been constructed.…”

Advances in Omics for Enhancing Abiotic Stress Tolerance in Millets

“…Since then several groups reported on development of various genomic or EST based simple sequence repeat (SSR) markers to be used in diverse genotyping applications, phylogenetic and transferability studies in foxtail millet and other grass species (Jia et al, 2007;Jia et al, 2009;Heng et al, 2011;Gupta et al, 2012;Gupta et al, 2013). Considering the importance of intron length polymorphic (ILP) markers as genomic resources, Gupta et al (2011) andMuthamilarasan et al (2014a) developed 98 and 5123 ILP markers respectively in foxtail millet. The ILP markers from both studies showed to be useful in cross-species transferability, germplasm characterization, comparative mapping and genomic relationships studies between millets and non-millets.…”

“…Xu et al (2013) developed a total of 9,576 and 7,056 SSR markers from 42,754 transcripts generated from referenced based assembly using foxtail millet genome and 60,751 transcripts from de novo assembly, respectively. Several other researchers also reported on identification of several microsatellite repeat motifs (Pandey et al, 2013;Zhang et al, 2014), eSSRs , and transposable elements (TE)-based markers (Yadav et al, 2014a) using Setaria genome sequence data. In another interesting study, 176 microRNA (miRNA)-based molecular markers have been developed (Yadav et al, 2014b) from a set of 335 mature miRNAs (Khan et al, 2014).…”