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.

BioISI BioSystems and Integrative Sciences Institute Faculdade de Ciências Universidade de Lisboa Lisbon Portugal

Biology Department Ġ F Abela Junior College Msida Malta

Center for Biological Research Madrid Spain

Centre for Agricultural Genomics and Biotechnology Faculty of Agricultural and Food Sciences and Environmental Management University of Debrecen Nyíregyháza Hungary

Centre of Molecular Medicine and Biobanking University of Malta Msida Malta

Centre of Plant Structural and Functional Genomics Institute of Experimental Botany of the Czech Academy of Sciences Olomouc Czechia

Centro de Biotecnología y Genómica de Plantas Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria Madrid Spain

Department of Biology University of Florence Sesto Fiorentino Italy

Department of Chemistry and Biology 'A Zambelli' University of Salerno Fisciano Italy

Department of Clinical Biochemistry Faculty of Pharmacy Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Toruń Bydgoszcz Poland

Department of Molecular Biology and Genetics Institute of Plant Physiology and Genetics Bulgarian Academy of Sciences Sofia Bulgaria

Department of Vegetables and Field Crops Agricultural Research Organization Volcani Center Institute of Plant Sciences Rishon LeZion Israel

Department of Vitis Institute of Olive Tree Subtropical Crops and Viticulture Athens Greece

Faculty of Agriculture University of Novi Sad Novi Sad Serbia

Faculty of Science University of Sarajevo Sarajevo Bosnia and Herzegovina

Genomic Research Department Thünen Institute of Forest Genetics Grosshansdorf Germany

Institute of Field and Vegetable Crops National Institute of Republic of Serbia Novi Sad Serbia

Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328 INRAE Université d'Orléans Orléans France

Laboratory of Forest Genetics and Biotechnology Institute of Mediterranean Forest Ecosystems Hellenic Agricultural Organization DIMITRA Athens Greece

Laboratory of Plant Breeding and Biometry Department of Crop Science Agricultural University of Athens Athens Greece

Linking Landscape Environment Agriculture and Food Institute of Agronomy University of Lisbon Lisbon Portugal

Mendeleum Insitute of Genetics Faculty of Horticulture Mendel University in Brno Lednice Czechia

Plant Epigenomics Technical University of Munich Freising Germany

Plant Physiology Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias University of Oviedo Oviedo Spain

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