Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

Abstract

Transposable elements (TEs) are common mobile genetic elements comprising several classes and making up the majority of eukaryotic genomes. The movement and accumulation of TEs has been a major force shaping the genes and genomes of most organisms. Most eukaryotic genomes are dominated by retrotransposons and minimal DNA transposon accumulation. The ‘copy and paste’ lifecycle of replicative transposition produces new genome insertions without excising the original element. Horizontal TE transfer among lineages is rare. TEs represent a reservoir of potential genomic instability and RNA-level toxicity. Many TEs appear static and nonfunctional, but some are capable of replicating and mobilising to new positions, and somatic transposition events have been observed. The overall structure of retrotransposons and the domains responsible for the phases of their replication are highly conserved in all eukaryotes. TEs are important drivers of species diversity and exhibit great variety in their structure, size and transposition mechanisms, making them important putative actors in evolution. Because TEs are abundant in plant genomes, various applications have been developed to exploit polymorphisms in TE insertion patterns, including conventional or anchored PCR, and quantitative or digital PCR with primers for the 5ʹ or 3ʹ junction. Alternatively, the retrotransposon junction can be mapped using high-throughput next-generation sequencing and bioinformatics. With these applications, TE insertions can be rapidly, easily and accurately identified, or new TE insertions can be found. This review provides an overview of the TE-based applications developed for plant species and assesses the contributions of TEs to the analysis of plants’ genetic diversity.

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

“…It has been reported that LTR-retroelements get activated by environmental stress [48][49][50]. Therefore, in the course of genome evolution, LTR-retrotransposon activity could accumulate several variations, making them an ideal source for genome-wide molecular markers [51][52][53][54].…”

Genetic analysis of the grapevine genotypes of the Russian Vitis ampelographic collection using iPBS markers

“…The advent of molecular markers has offered a powerful tool to address these issues; these markers have frequently been used by ampelographers and grapevine geneticists (Cipriani et al 2010;Drabek et al 2016;De Lorenzis et al 2015). Among the many classes of molecular markers proposed in the last 20 years, a relatively new universal retrotransposon-based marker system for DNA fingerprinting, inter-primer binding sites (iPBS), was used by Kalendar et al (Kalendar and Schulman 2014;Kalendar et al 2010Kalendar et al , 2019.…”

“…Retrotransposons are ubiquitous throughout the plant kingdom and exist in vast numbers of copies in any plant genome (Kalendar et al 2019). Thus, they are a well-suited source of genetic markers (Vuorinen et al 2018;Mandoulakani et al 2015;Smykal et al 2011).…”

Copy Number Variation of Transposable Elements in Thinopyrum intermedium and Its Diploid Relative Species

“…The comparison of the TE's abundance between the genomes of diploids and subgenomes in polyploids is of great interest as it may help to understand the speciation after the divergence from the common ancestor and the contribution of a particular genome in polyploid formation. Different molecular techniques ranging from conventional PCR to digital PCR as well as bioinformatic approaches have been applied to study TE's polymorphisms that enable rapid and accurate identification of different TE's insertions in the genome that helps to estimate genome modifications during evolution [72]. Recently, we demonstrated different abundance of Ty3/Gypsy centromeric retrotransposon on the individual chromosomes of particular subgenomes of Th.…”

“…The abundance of transposable elements (TEs) can be assessed using different approaches [72]. The computational analysis using NGS sequencing data have been successfully applied in Triticum, Hordeum and Secale studies [27,31,56,76].…”