Rim 2/Hipa CACTA transposon display ; A new genetic marker technique in Oryza species

Abstract

Background: Transposons constitute the major fractions of repetitive sequences in eukaryotes, and have been crucial in the shaping of current genomes. Transposons are generally divided into two classes according to the mechanism underlying their transposition: RNA intermediate class 1 and DNA intermediate class 2. CACTA is a class 2 transposon superfamily, which is found exclusively in plants. As some transposons, including the CACTA superfamily, are highly abundant in plant species, and their nucleotide sequences are highly conserved within a family, they can be utilized as genetic markers, using a slightly modified version of the conventional AFLP protocol. Rim2 /Hipa is a CACTA transposon family having 16 bp consensus TIR sequences to be present in high copy numbers in rice genome. This research was carried out in order to develop a Rim2/Hipa CACTA-AFLP or Rim2/ Hipa CACTA-TD (transposon display, hereafter Rim2/Hipa-TD) protocol for the study of genetic markers in map construction and the study of genetic diversity in rice.

Construction of genetic linkage map and identification of QTLs related to agronomic traits in maize using DNA transposon-based markers

“…Several characteristics of TEs make them especially useful for generating molecular markers, including their ability to create unique insertion polymorphisms and their wide distribution throughout the genome. With a variety of molecular techniques, both RNA and DNA transposon superfamilies have been utilized to develop new genetic markers for agriculturally important crops ( Kalendar and Schulman 2006 , Kwon et al 2005 , Lee et al 2005 , Queen et al 2004 , Yaakov et al 2012 ).…”

The DcMaster Transposon Display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome

“…Rice Rim2/Hipa elements produced 60 to 80 bands per primer combination, when the adaptor-specific primer carried two selective nucleotides (Kwon et al, 2005). On average 52 Hbr markers per primer combination were obtained using Transposon Display for the MITE family Heartbreaker in maize, using only one selective nucleotide (Casa et al, 2000).…”

“…Some transposon families are present in numerous copies in the host genome, thus potentially hundreds of markers can be generated. Several systems for identifying transposon insertion sites have been developed over the last ten years, including those based on a simple PCR: IRAP (Inter Retrotransposon Polymorphism) and REMAP (Retrotransposon Microsatellite Polymorphism, Kalendar et al, 1999); IMP (Inter MITE Polymorphism, Chang et al, 2001); those using an AFLP-like approach: S-SAP (Site-Specific Amplified Polymorphism, Waugh et al, 1997) and Transposon Display (Casa et al, 2000;Biedler et al, 2003;Park et al, 2003;Kwon et al, 2005); and those identifying polymorphisms in the specific sequence-characterized regions: RBIP (Retrotransposon-Based Insertion Polymorphism, Flavell et al, 1998).…”

DcMaster transposon display markers as a tool for diversity evaluation of carrot breeding materials and for hybrid seed purity testing

“…Successful examples of the use of TD systems tailored towards various groups of transposable elements include reports on Petunia hybrida (Van den Broeck et al 1998), Zea mays, and Arabidopsis thaliana (Yephremov and Saedler 2000). TD markers were also used to infer genetic relationships among maize inbreds, by using the MITE family Heartbreaker (Casa et al 2002) and to study rice diversity by using Rim2/Hipa CACTA TD (Kwon et al 2005).…”