Marker utility of transposable elements for plant genetics, breeding, and ecology: a review

Abstract

Variation is the primary source for plant and animal breeding and evolution, and hence, the detection of variation is an integral part of genetics, breeding, and ecology. Various molecular marker systems have been developed to detect genetic variation. They detect sequence variations (e.g., restriction fragment length polymorphism, randomly amplified polymorphic DNA, amplified fragment length polymorphism) or simple sequence motif variations. However, a large portion of genomic variation is derived from the transposition of transposable elements (TEs), which are major denizens of most eukaryote genomes. Therefore, molecular markers derived from TEs are valuable resources for dissecting genomes in plants and animals. Because class I retrotransposons transpose by a ''copy-and-paste'' semi-conservative manner, retrotransposon-based markers (e.g., Inter-retrotransposon amplified polymorphism, retrotransposon-microsatellite amplified polymorphism, sequence-specific amplified polymorphism) can reveal highly accurate phylogenetic relationships among related taxa as well as among accessions within a species. Transposon display based on class II DNA transposons has also been used in various genetics fields. A large amount of fairly accurate genome sequences are now being generated, and computational biology allows us to mine the TEs on a genome-wide scale. Thus, TE-based molecular markers are adding another venue to the other marker systems used for the molecular dissection of genomes.

LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species

“…Retrotransposon-based markers have been proved as excellent tools for analyzing plant diversity and marker-assisted breeding (Syed and Flavell 2006;Paux et al 2010;Roy et al 2015). Unlike the sequence variation based on markers (e.g., RFLP, AFLP, SNPs), transposon-based markers detect the variations derived from transpositions.…”

DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing

“…LTR retrotransposons contain ORFs, POL and GAG, as they are widely distributed within plant genomes [58]. LTR retrotransposons are further divided into Ty1/copia and Ty3/gypsy retrotransposons on the basis of encoded gene order [59]. Class II of transposable elements is further divided into terminal inverted repeat (TIR) and non-TIR subclasses [60].…”

“…The REMAP protocol is similar to IRAP; however, in REMAP, SSRs (microsatellites) are used in conjunction with specific primers of LTR during PCR [62,64]. During REMAP PCR, those primers are selected for microsatellite loci which contain a repeat motif anchored nucleotide at the 3' end aiming to avoid the primer slippage between individual SSR motifs [59].…”

Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers

“…They have the advantage of having a high level of allelic variation, reliability, reproducibility, and discrimination (Enoki et al, 2002). In addition, transposable element-based molecular markers have been recently successfully applied for accessing the genetic diversity of many plants (Roy et al, 2015). Several types of transposable element-based molecular markers have been developed from retrotransposons, including retrotransposon-based insertion polymorphisms (RBIP) (Paux et al, 2010), inter-retrotransposon amplified polymorphism (IRAP) (Kalendar et al, 1999), retrotransposonmicrosatellite amplified polymorphism (REMAP) (Kalendar and Schulman, 2006), and sequence specific amplified polymorphism (SSAP) (Waugh et al, 1997).…”