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.

• Klíčová slova
• DNA methylation modulation, DNA methylation profiling, bisulfite sequencing, crop epigenome, immunological techniques, mass spectrometry, next-generation sequencing,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Herbicide resistance is broadly recognized as the adaptive evolution of weed populations to the intense selection pressure imposed by the herbicide applications. Here, we tested whether transcriptional gene silencing (TGS) and RNA-directed DNA Methylation (RdDM) pathways modulate resistance to commonly applied herbicides. Using Arabidopsis thaliana wild-type plants exposed to sublethal doses of glyphosate, imazethapyr, and 2,4-D, we found a partial loss of TGS and increased susceptibility to herbicides in six out of 11 tested TGS/RdDM mutants. Mutation in REPRESSOR OF SILENCING 1 (ROS1), that plays an important role in DNA demethylation, leading to strongly increased susceptibility to all applied herbicides, and imazethapyr in particular. Transcriptomic analysis of the imazethapyr-treated wild type and ros1 plants revealed a relation of the herbicide upregulated genes to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis, and epigenetic processes. Hypersensitivity to imazethapyr of the flavonoid biosynthesis component TRANSPARENT TESTA 4 (TT4) mutant plants strongly suggests that ROS1-dependent accumulation of flavonoids is an important mechanism for herbicide stress response in A. thaliana. In summary, our study shows that herbicide treatment affects transcriptional gene silencing pathways and that misregulation of these pathways makes Arabidopsis plants more sensitive to herbicide treatment.

• Klíčová slova
• 2,4-D, ROS1, chromatin mutants, epigenetics, glyphosate, herbicide resistance, imazethapyr,
• MeSH
• acyltransferasy genetika   MeSH
• Arabidopsis účinky léků   genetika   MeSH
• chromatin chemie   MeSH
• demetylace DNA MeSH
• genetická transkripce MeSH
• herbicidy farmakologie   MeSH
• jaderné proteiny genetika   MeSH
• kyselina 2,4-dichlorfenoxyoctová farmakologie   MeSH
• kyseliny nikotinové farmakologie   MeSH
• metylace DNA MeSH
• mutace MeSH
• proteiny huseníčku genetika   MeSH
• regulace genové exprese u rostlin * MeSH
• RNA rostlin genetika   MeSH
• sekvenování transkriptomu MeSH
• umlčování genů * MeSH
• vysokoúčinná kapalinová chromatografie MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• acyltransferasy MeSH
• AT5G13930 protein, Arabidopsis MeSH Prohlížeč
• chromatin MeSH
• herbicidy MeSH
• imazethapyr MeSH Prohlížeč
• jaderné proteiny MeSH
• kyselina 2,4-dichlorfenoxyoctová MeSH
• kyseliny nikotinové MeSH
• proteiny huseníčku MeSH
• RNA rostlin MeSH
• ROS1 protein, Arabidopsis MeSH Prohlížeč