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DNA-only Transposons02:57

DNA-only Transposons

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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
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Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane.

Cushla J Metcalfe1, Sarah G Oliveira1, Jonas W Gaiarsa1

  • 1GaTE-Lab, Departamento de Botânica, IBUSP, Universidade de São Paulo, rua do Matao 277, 05508-090, SP, Brazil.

Journal of Experimental Botany
|June 21, 2015
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Summary

Researchers developed a new method using quantitative PCR and transposable markers to analyze the sugarcane genome. This technique aids in sugarcane genotyping and understanding its evolution, identifying potential markers for Saccharum spontaneum.

Keywords:
Markerpolyploidreal-time PCRretrotransposon-based insertion polymorphismsugarcanetransposable element.

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Area of Science:

  • Genetics
  • Plant Science
  • Genomics

Background:

  • Sugarcane is a vital crop for sugar and biofuel production.
  • Its complex polyploid and heterozygous genome hinders comprehensive characterization.
  • Previous genomic studies have been limited by these complexities.

Purpose of the Study:

  • To develop a novel method for analyzing the sugarcane genome.
  • To utilize transposable elements (TEs) for genotyping and evolutionary studies.
  • To identify potential molecular markers for sugarcane breeding.

Main Methods:

  • Developed a quantitative PCR-based method combined with a transposable marker system.
  • Scored the relative number of alleles with specific transposable elements (TEs) at loci.
  • Screened diverse sugarcane relatives, wild types, and modern cultivars.

Main Results:

  • The method was successfully applied for sugarcane genotyping.
  • Analysis of TE insertion history provided insights into the evolution of the Saccharum complex.
  • Identified three TEs present in only one major lineage, potentially serving as markers for Saccharum spontaneum.

Conclusions:

  • The developed method offers a valuable tool for sugarcane genomic analysis.
  • TEs can be effectively used for genotyping and understanding sugarcane evolutionary history.
  • Specific TEs show promise as molecular markers for Saccharum spontaneum, aiding breeding programs.