Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley.

Renata Orłowska,Wioletta M Dynkowska,Katarzyna A Pachota,Piotr T Bednarek,Agnieszka Niedziela

doi:10.3390/ijms22136783

Abstract

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.

Highlights

Plant tissue cultures are a well-established model to study distinct genetic [1,2] and epigenetic [3] changes related to abiotic factors that may be exhibited at the morphological level [4]
Plant regeneration via anther cultures is subjected to somaclonal variation [75], or tissue culture-induced variation [76], manifested at the level of plant morphology, genotype, or both simultaneously
The plants derived via anther culture were identical in shape to donor plants

Summary

Introduction

Plant tissue cultures are a well-established model to study distinct genetic [1,2] and epigenetic [3] changes related to abiotic factors that may be exhibited at the morphological level [4]. DNA sequence changes may originate from the activation of retrotransposons [11]. Transposable elements (TEs) are the most common repeat sequences in the plant genome. Systematics of TEs distinguish classes, subclasses, orders, superfamilies, families, and subfamilies [17]. Transposable elements are divided into Class I, which includes retroelements (retroviruses and retrotransposons) and class II, encompassing DNA transposons. Phylogenetic analyses based on reverse transcriptase amino acid sequences resolve the Long Terminal Repat (LTR) retrotransposons into families: the Ty3-gypsy retrotransposons (Metaviridae) and the Ty1-copia elements (Pseudoviridae) [18,19,20].

Methods

Results

Conclusion