Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution

Yaakov, Beery; Ceylan, Elif; Domb, Katherine; Kashkush, Khalil

doi:10.1007/s00122-012-1793-y

Cited by 35 publications

(29 citation statements)

References 59 publications

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“…Moreover, makers developed from IP approach have been used for various molecular breeding studies such as genetic diversity analysis, trait identification, and candidate gene analysis (Monden et al 2009;Yaakov et al 2012;. Our analysis based on the genome-specific MITE insertion showed high genetic diversity among various B. rapa accessions suggesting the importance of the MIP markers for the diversity analysis (Fig.…”

Section: Application Of Ip-bs2 Makers For Various Molecular Breeding mentioning

confidence: 79%

“…DNA markers are used in a wide range of genomic and breeding applications such as construction of genetic linkage maps, genomics assisted breeding, genome-wide association studies and evolutionary studies (Purugganan and Wessler 1995;Casa et al 2000;Kwon et al 2007;Yaakov et al 2012;Varshney et al 2013). DNA markers have been developed using various methods like random amplified polymorphic DNA, restriction fragment length polymorphism, simple sequence repeats, amplified fragment length polymorphism (AFLP), sequence characterized amplified region, and single nucleotide polymorphism (Agarwal et al 2008;Kalendar et al 2011;Varshney et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

Perumal¹,

Waminal²,

Lee³

et al. 2016

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea ABSTRACT Miniature transposable elements (mTEs) such as miniature inverted-repeat transposable element (MITE), terminal repeat retrotransposon in miniature, and short interspersed element are exquisite sources for marker development. mTEs are short, non-autonomous and stably inherited. The high-copy members are widely distributed into the gene rich euchromatic regions. Here, we conducted a modified transposon display (TD) for a high-copy MITE family, BraSto-2 (Bs2). The Bs2-specific primers derived from conserved sequences of Bs2 members as well as MseI adapter primers were used for polymerase chain reaction (PCR) in two Brassica rapa accessions, 'Chiifu' and 'Kenshin'. The pooled PCR products were sequenced by Illumina sequencing platform instead of high-resolution gel electrophoresis. Subsequent in silico-based insertion polymorphism (IP) analysis (next-generation sequencing [NGS]-based Bs2 transposon display) was conducted, which generated more than 99 putative polymorphic insertion sites between 'Chiifu' and 'Kenshin'. Among 90 successful PCR amplification, 34 showed Bs2 IP (IP-Bs2) between 'Chiifu' and 'Kenshin' accessions, 27 and seven 'Chiifu'-and 'Kenshin'-unique insertions, respectively. When the 90 IP-Bs2 primer sets were applied to 10 Brassica accessions, including four additional B. rapa and B. oleracea accessions, 69 (76%) showed insertion olymorphism among accessions. The IP-Bs2 were evenly distributed through all the chromosomes and provide rich polymorphism among various B. rapa and B. oleracea accessions demonstrating the usefulness of these markers for various genetic diversity and molecular breeding studies in Brassica. In addition, NGS-based TD will be applicable to various high copy transposable elements family for high throughput and rapid polymorphic marker development which will be helpful for efficient plant genomics and breeding purposes.

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Section: Application Of Ip-bs2 Makers For Various Molecular Breeding mentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

Perumal¹,

Waminal²,

Lee³

et al. 2016

Plant Breed. Biotech.

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“…Insertion polymorphism inter- and intra- Brassica species due to insertion or absence of a mTE in specific accessions was surveyed by PCR using flanking primers [48]. For MITE insertion polymorphism (MIP) analysis, 187 and 145 MITE targets were surveyed from B. rapa and B. oleracea members, respectively [30,45].…”

Section: Resultsmentioning

confidence: 99%

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

et al. 2014

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BackgroundMITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops.FindingsWe have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences.ConclusionsBrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species. BrassicaTED can be accessed at http://im-crop.snu.ac.kr/BrassicaTED/index.php.

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“…The specific distribution of these families could be considered an important evolutionary feature in the wheat genome. Furthermore, the specific distributed MITEs may be useful to develop chromosome-specific molecular markers for biodiversity and evolutionary studies (Yaakov et al, 2012;Ben-David et al, 2013). In total, 16, 17, and 17 MITE families were identified on 7A, 7B, and 7D, respectively, while the copy number of MITEs on these chromosomes was 587, 714, and 725, respectively.…”

Section: Comparative Analysis Of Mites In Wheat Group 7 Chromosomesmentioning

confidence: 99%

“…Several studies have been carried out to investigate MITEs in wheat. Yaakov et al (2012) identified some MITEs from wheat and assessed the utility of MITEs for marker development. They further systematically identified the Stowaway-like MITEs in the wheat genome using 454 survey sequences (Yaakov et al, 2013a), which provided comprehensive information about the abundance, composition, and diversity of MITEs.…”

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confidence: 99%

Comparative analysis of Stowaway‐like miniature inverted repeat transposable elements in wheat group 7 chromosomes: Abundance, composition, and evolution

Wang

Yue

et al. 2014

J of Sytematics Evolution

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Miniature inverted repeat transposable elements (MITEs) are the most ubiquitous transposable elements in eukaryotic genomes; they play a prominent role in sequence divergence and genome evolution. There are many wellcharacterized Stowaway-like MITE families in wheat, but their distribution, abundance, and composition at the chromosome level are still not well understood. In this study, we systematically investigated the Stowaway-like MITEs in wheat group 7 chromosomes based on the survey sequences of isolated wheat chromosomes, to compare them at the chromosome level and to reveal their evolutionary role on wheat polyploidization. In summary, 2026 MITEs were identified, of which 587, 714, and 725 were distributed on 7A, 7B, and 7D chromosomes, respectively. There are more MITEs present on 7D, compared to 7A and 7B, suggesting A and B subgenomes eliminated some repetitive elements during two hybridization processes. Furthermore, some chromosome/arm-specific MITEs were also identified, providing information on the function and evolution of MITEs in wheat genomes. The sequence diversity of the MITE insertions was also investigated. This study for the first time investigated the abundance and composition of MITEs at the chromosome level, which will be beneficial to improve our understanding of the distribution of wheat MITEs and their evolutionary role in polyploidization.

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Marker utility of miniature inverted-repeat transposable elements for wheat biodiversity and evolution

Cited by 35 publications

References 59 publications

Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

Next-Generation Sequencing Based Transposon Display to Detect High-Throughput Insertion Polymorphism Markers in Brassica

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

Comparative analysis of Stowaway‐like miniature inverted repeat transposable elements in wheat group 7 chromosomes: Abundance, composition, and evolution

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