AUTHOR=Agius Dolores Rita , Kapazoglou Aliki , Avramidou Evangelia , Baranek Miroslav , Carneros Elena , Caro Elena , Castiglione Stefano , Cicatelli Angela , Radanovic Aleksandra , Ebejer Jean-Paul , Gackowski Daniel , Guarino Francesco , Gulyás Andrea , Hidvégi Norbert , Hoenicka Hans , Inácio Vera , Johannes Frank , Karalija Erna , Lieberman-Lazarovich Michal , Martinelli Federico , Maury Stéphane , Mladenov Velimir , Morais-Cecílio Leonor , Pecinka Ales , Tani Eleni , Testillano Pilar S. , Todorov Dimitar , Valledor Luis , Vassileva Valya TITLE=Exploring the crop epigenome: a comparison of DNA methylation profiling techniques JOURNAL=Frontiers in Plant Science VOLUME=14 YEAR=2023 URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1181039 DOI=10.3389/fpls.2023.1181039 ISSN=1664-462X ABSTRACT=

Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.