Changes in DNA methylation pattern of apple long-term in vitro shoot culture and acclimatized plants

Andrea Gulyás; Judit Dobránszki; Erzsébet Kiss; Jaime A Teixeira da Silva; Katalin Posta; Norbert Hidvégi

doi:10.1016/j.jplph.2019.05.007

Changes in DNA methylation pattern of apple long-term in vitro shoot culture and acclimatized plants

J Plant Physiol. 2019 Aug:239:18-27. doi: 10.1016/j.jplph.2019.05.007. Epub 2019 May 23.

Authors

Andrea Gulyás¹, Judit Dobránszki², Erzsébet Kiss³, Jaime A Teixeira da Silva⁴, Katalin Posta⁵, Norbert Hidvégi⁶

Affiliations

¹ Research Institute of Nyíregyháza, IAREF, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary. Electronic address: gulyas.andrea@agr.unideb.hu.
² Research Institute of Nyíregyháza, IAREF, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary. Electronic address: dobranszki@freemail.hu.
³ Institute of Genetics, Microbiology and Biotechnology, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Páter Károly u.1., H-2100, Hungary. Electronic address: kiss.erzsebet@mkk.szie.hu.
⁴ Research Institute of Nyíregyháza, IAREF, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary. Electronic address: jaimetex@yahoo.com.
⁵ Institute of Genetics, Microbiology and Biotechnology, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Páter Károly u.1., H-2100, Hungary. Electronic address: posta.katalin@mkk.szie.hu.
⁶ Research Institute of Nyíregyháza, IAREF, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary. Electronic address: hidvegi.norbert@agr.unideb.hu.

PMID: 31177027
DOI: 10.1016/j.jplph.2019.05.007

Abstract

DNA methylation is a process of epigenetic modification that can alter the functionality of a genome. Using whole-genome bisulfite sequencing, this study quantify the level of DNA methylation in the epigenomes of two diploid apple (Malus x domestica) scion cultivars ('McIntosh' and 'Húsvéti rozmaring') derived from three environmental conditions: in vivo mother plants in an orchard, in vitro culture, and acclimatized in vitro plants. The global DNA methylation levels were not dependent on the source of plant material, and the average level of DNA methylation was 49.77%, 34.65% and 8.77% in CpG, CHG and CHH contexts, respectively. Significant differences in DNA methylation were identified in 586 (specifically 334, 201 and 131 in CpG, CHG and CHH contexts, respectively) out of 45,116 genes, including promoter and coding sequences. These were classified as differentially methylated genes (DMGs). This is a 1.3% difference in the level of DNA methylation of genes in response to a change in the environment. Differential methylation was visualised by MA plots and functional genomic maps were established for biological processes, molecular functions and cellular components. When the DMGs were considered, in vitro tissue culture resulted in the highest level of methylation, but it was lower in acclimatized in vitro plants which was similar to that in the mother tree. Methylation patterns of the two scions differed, indicating cultivar-specific epigenetic regulation of gene expression during adaptation to various environments. After selecting genes that displayed differences larger than ±10% in CpG and CHG contexts, or larger than ±1.35% in the CHH context from among the DMGs, they were annotated in Blast2 GO v5.1.12 for Gene Ontology. DMGs identified as MD07G1113000 (protein transport), MD08G1041600 (extracellular space), MD09G1054800 (phosphatidic acid binding), and MD10G1265800 (not annotated) were methylated in all three contexts in in vitro shoots. These DNA methylation results suggest that epigenetic changes may contribute to the adaptation of apple to environmental changes by modifying the epigenome and thereby gene expression.

Keywords: Epigenetic; Malus sp.; Tissue culture; Whole-genome bisulfite sequencing.

MeSH terms

Acclimatization*
Cell Culture Techniques
DNA Methylation / physiology*
Epigenesis, Genetic
Gene Expression Profiling
Gene Expression Regulation, Plant
Genome, Plant*
Malus / genetics*
Plant Shoots / metabolism