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Open AccessArticle

Exploring the Biochemical Origin of DNA Sequence Variation in Barley Plants Regenerated via in Vitro Anther Culture

1
Department of Plant Physiology and Biochemistry, Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland
2
Institute of Biology and Biotechnology, University of Rzeszow, Al. Rejtana 16c A, 35-959 Rzeszow, Poland
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(16), 5770; https://doi.org/10.3390/ijms21165770
Received: 22 June 2020 / Revised: 6 August 2020 / Accepted: 10 August 2020 / Published: 11 August 2020
(This article belongs to the Section Molecular Plant Sciences)
Tissue culture is an essential tool for the regeneration of uniform plant material. However, tissue culture conditions can be a source of abiotic stress for plants, leading to changes in the DNA sequence and methylation patterns. Despite the growing evidence on biochemical processes affected by abiotic stresses, how these altered biochemical processes affect DNA sequence and methylation patterns remains largely unknown. In this study, the methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach was used to investigate de novo methylation, demethylation, and sequence variation in barley regenerants derived by anther culture. Additionally, we used Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy to identify the spectral features of regenerants, which were then analyzed by mediation analysis. The infrared spectrum ranges (710–690 and 1010–940 cm−1) identified as significant in the mediation analysis were most likely related to β-glucans, cellulose, and S-adenosyl-L-methionine (SAM). Additionally, the identified compounds participated as predictors in moderated mediation analysis, explaining the role of demethylation of CHG sites (CHG_DMV) in in vitro tissue culture-induced sequence variation, depending on the duration of tissue culture. The data demonstrate that ATR-FTIR spectroscopy is a useful tool for studying the biochemical compounds that may affect DNA methylation patterns and sequence variation, if combined with quantitative characteristics determined using metAFLP molecular markers and mediation analysis. The role of β-glucans, cellulose, and SAM in DNA methylation, and in cell wall, mitochondria, and signaling, are discussed to highlight the putative cellular mechanisms involved in sequence variation. View Full-Text
Keywords: ATR-FTIR spectroscopy; β-glucans; cellulose; DNA demethylation; S-adenosyl L-methionine; sequence variation; time of in vitro culture ATR-FTIR spectroscopy; β-glucans; cellulose; DNA demethylation; S-adenosyl L-methionine; sequence variation; time of in vitro culture
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Bednarek, P.T.; Zebrowski, J.; Orłowska, R. Exploring the Biochemical Origin of DNA Sequence Variation in Barley Plants Regenerated via in Vitro Anther Culture. Int. J. Mol. Sci. 2020, 21, 5770.

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