The MITE family<i>Heartbreaker</i>(<i>Hbr</i>): Molecular markers in maize

Casa, Alexandra M.; Brouwer, Cory; Nagel, Alexander; Wang, Lianjiang; Zhang, Qiang; Kresovich, Stephen; Wessler, Susan R.

doi:10.1073/pnas.97.18.10083

Cited by 211 publications

(183 citation statements)

References 51 publications

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“…Instead, transposon display (TD) was used to provide a better estimate of copy number. TD is a modification of the amplified fragment-length polymorphism technique (17), where genomic DNA is digested, ligated to an adapter, and used as template for PCR with a labeled primer that anneals, in this case, near one end of mPing elements (11,18,19). All DNA fragments that are visualized on TD gels should have an adapter primer at one end and an mPing element at the other end.…”

Section: Resultsmentioning

confidence: 99%

“…mPing copy number was determined by TD and performed as described (18,19). Final annealing temperature for selective amplification was 58°C with the 33 Plabeled primer.…”

Section: Methodsmentioning

confidence: 99%

“…DNA fragments from TD gels were excised, reamplified, and cloned as described (18,19). Sequences of cloned fragments were determined by the Molecular Genetics Instrumentation Facility (University of Georgia).…”

Section: Methodsmentioning

confidence: 99%

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Dramatic amplification of a rice transposable element during recent domestication

Naito

Cho

Yang

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Despite the prevalence of transposable elements in the genomes of higher eukaryotes, what is virtually unknown is how they amplify to very high copy numbers without killing their host. Here, we report the discovery of rice strains where a miniature invertedrepeat transposable element (mPing) has amplified from Ϸ50 to Ϸ1,000 copies in four rice strains. We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented. Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors: (i) the rapid selection against detrimental insertions, (ii) the neutral or minimal effect of the remaining insertions on gene transcription, and (iii) the continued mobility of mPing elements in strains that already have >1,000 copies. The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice. genome evolution ͉ miniature inverted-repeat transposable element ͉ transposon

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Section: Resultsmentioning

confidence: 99%

“…mPing copy number was determined by TD and performed as described (18,19). Final annealing temperature for selective amplification was 58°C with the 33 Plabeled primer.…”

Section: Methodsmentioning

confidence: 99%

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Dramatic amplification of a rice transposable element during recent domestication

Naito

Cho

Yang

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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221

239

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“…Analysis of Stowaway elements present in the extensively sequenced rice genome revealed that they predominantly occur in the vicinity of potential gene sequences (Mao et al 2000). This makes the Stowaway elements attractive for designing molecular markers based on insertional or inter-MITE polymorphisms (Casa et al 2000;Chang et al 2001) that could be targeted into gene-rich euchromatic regions. Our findings suggest that this approach is also feasible in pea, as at least part of the identified elements are located near potential gene sequences.…”

Section: Discussionmentioning

confidence: 99%

Characterization ofStowawayMITEs in pea (Pisum sativumL.) and identification of their potential master elements

Macas¹,

Koblížková²,

Neumann³

2005

Genome

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Abstract:We have investigated miniature inverted-repeat transposable elements (MITEs) of the Stowaway family and corresponding Mariner-like master elements that could potentially facilitate their mobilization in the genome of the garden pea (Pisum sativum L.). The population of pea Stowaway MITEs consists of 10 3 -10 4 copies dispersed in the genome. Judging from a sequence analysis of 17 isolated Stowaway elements and their flanking genomic regions, the elements are relatively uniform in size and sequence and occur in the vicinity of genes as well as within repetitive sequences. Insertional polymorphism of several elements was detected among various Pisum accessions, suggesting they were still transpositionally active during diversification of these taxa. The identification of several Mariner-like elements (MLEs) harboring intact open reading frames, capable of encoding a transposase, further supports a recent mobilization of the Stowaway elements. Using transposase-coding sequences as a hybridization probe, we estimated that there are about 50 MLE sequences in the pea genome. Among the 5 elements sequenced, 3 distinct subfamilies showing mutual similarities within their transposase-coding regions, but otherwise diverged in sequence, were distinguished and designated as Psmar-1 to Psmar-3. The terminal inverted repeats (TIRs) of these MLE subfamilies differed in their homology to the TIRs of Stowaway MITEs. The homlogy ranged from 9 bp in Psmar-3 to 30 bp in Psmar-1, which corresponds to the complete Stowaway TIR sequence. Based on this feature, the Psmar-1 elements are believed to be the most likely candidates for the master elements of the Stowaway MITEs in pea.Key words: Mariner-like transposons, master elements, Stowaway MITEs, insertional polymorphism, Pisum sativum. Résumé :Les auteurs ont étudié les transposons MITE (« miniature inverted-repeat transposable elements ») de la famille Stowaway et les éléments autonomes correspondants de type Mariner, lesquels pourraient potentiellement causer la mobilité de ces éléments chez le petit pois (Pisum sativum L.). Le génome du pois compte 10 3 -10 4 copies dispersées de MITE Stowaway. L'analyse de la séquence de 17 éléments Stowaway et de l'ADN génomique qui les borde a révélé que ceux-ci sont relativement uniformes tant en matière de taille que de séquence et qu'ils sont situés à la fois à proximité de gènes et au sein de séquences répétées. Du polymorphisme insertionnel pour plusieurs éléments a été dé-tecté parmi diverses accessions de Pisum, ce qui suggère qu'ils étaient encore mobiles lors de la différenciation de ces taxons. L'identification de plusieurs éléments de type Mariner (MLE, « Mariner-like elements ») ayant des cadres de lecture ouverts intacts, capables de coder pour une transposase, vient appuyer davantage l'hypothèse d'une récente mobilité de ces éléments Stowaway. En employant la séquence codant pour la transposase comme sonde, les auteurs estiment qu'il y aurait environ 50 séquences MLE au sein du génome du pois. Parmi les 5 éléments séquenc...

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“…TD 기술을 활용하여 MITE(Miniature Inverted-repeat Transposable Elements)라고 불리는 특이한 특성을 갖는 TE가 개발되었다 (Casa et al, 2000).…”

Section: Sscp(single Strand Conformation Polymorphism)unclassified

Genetic Improvement of Maize by Marker-Assisted Breeding

Kim¹,

Moon²,

Baek³

et al. 2014

Korean Journal of Crop Science

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Maize is one of the most important food and feed crops in the world including Southeast Asia. In spite of numberous efforts with conventional breeding, the maize productions remain low and the loss of yields by drought and downy mildew are still severe in Asia. Genetic improvement of maize has been performed with molecular marker and genetic engineering. Because maize is one of the most widely studied crop for its own genome and has tremendous diversity and variant, maize is considered as a forefront crop in development and estimation of molecular markers for agricultural useful trait in genetics and breeding. Using QTL (Quantitative Trait Loci) and MAS (Marker Assisted Breeding), molecular breeders are able to accelerate the development of drought tolerance or downy mildew resistance maize genotype. The present paper overviews QTL/MAS approaches towards improvement of maize production against drought and downy mildew. We also discuss here the trends and importance of molecular marker and mapping population in maize breeding.

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The MITE familyHeartbreaker(Hbr): Molecular markers in maize

Cited by 211 publications

References 51 publications

Dramatic amplification of a rice transposable element during recent domestication

Dramatic amplification of a rice transposable element during recent domestication

Characterization ofStowawayMITEs in pea (Pisum sativumL.) and identification of their potential master elements

Genetic Improvement of Maize by Marker-Assisted Breeding

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