TY  - JOUR
AU  - Agius, Dolores Rita
AU  - Kapazoglou, Aliki
AU  - Avramidou, Evangelia
AU  - Baranek, Miroslav
AU  - Carneros, Elena
AU  - Caro, Elena
AU  - Castiglione, Stefano
AU  - Cicatelli, Angela
AU  - Radanović, Aleksandra
AU  - Ebejer, Jean-Paul
AU  - Gackowski, Daniel
AU  - Guarino, Francesco
AU  - Gulya, Andrea
AU  - Hidvegi, Norbert
AU  - Hoenicka, Hans
AU  - Inacio, Vera
AU  - Johannes, Frank
AU  - Karalija, Erna
AU  - Lieberman-Lazarovich, Michal
AU  - Martinelli, Federico
AU  - Maury, Stephane
AU  - Mladenov, Velimir
AU  - Morais-Cecılio, Leonor
AU  - Pecinka, Ales
AU  - Tani, Eleni
AU  - Testillano, Pilar S.
AU  - Todorov, Dimitar
AU  - Valledor, Luis
AU  - Vassileva, Valya
PY  - 2023
UR  - http://fiver.ifvcns.rs/handle/123456789/3777
AB  - 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.
PB  - Frontiers Media S.A.
T2  - Frontiers in Plant Science
T1  - Exploring the crop epigenome: a comparison of DNA methylation profiling techniques
SP  - 1181039
VL  - 14
DO  - 10.3389/fpls.2023.1181039
ER  - 

@article{
author = "Agius, Dolores Rita and Kapazoglou, Aliki and Avramidou, Evangelia and Baranek, Miroslav and Carneros, Elena and Caro, Elena and Castiglione, Stefano and Cicatelli, Angela and Radanović, Aleksandra and Ebejer, Jean-Paul and Gackowski, Daniel and Guarino, Francesco and Gulya, Andrea and Hidvegi, Norbert and Hoenicka, Hans and Inacio, Vera and Johannes, Frank and Karalija, Erna and Lieberman-Lazarovich, Michal and Martinelli, Federico and Maury, Stephane and Mladenov, Velimir and Morais-Cecılio, Leonor and Pecinka, Ales and Tani, Eleni and Testillano, Pilar S. and Todorov, Dimitar and Valledor, Luis and Vassileva, Valya",
year = "2023",
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.",
publisher = "Frontiers Media S.A.",
journal = "Frontiers in Plant Science",
title = "Exploring the crop epigenome: a comparison of DNA methylation profiling techniques",
pages = "1181039",
volume = "14",
doi = "10.3389/fpls.2023.1181039"
}

Agius, D. R., Kapazoglou, A., Avramidou, E., Baranek, M., Carneros, E., Caro, E., Castiglione, S., Cicatelli, A., Radanović, A., Ebejer, J., Gackowski, D., Guarino, F., Gulya, A., Hidvegi, N., Hoenicka, H., Inacio, V., Johannes, F., Karalija, E., Lieberman-Lazarovich, M., Martinelli, F., Maury, S., Mladenov, V., Morais-Cecılio, L., Pecinka, A., Tani, E., Testillano, P. S., Todorov, D., Valledor, L.,& Vassileva, V.. (2023). Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. in Frontiers in Plant Science
Frontiers Media S.A.., 14, 1181039.
https://doi.org/10.3389/fpls.2023.1181039

Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanović A, Ebejer J, Gackowski D, Guarino F, Gulya A, Hidvegi N, Hoenicka H, Inacio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecılio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. in Frontiers in Plant Science. 2023;14:1181039.
doi:10.3389/fpls.2023.1181039 .

Agius, Dolores Rita, Kapazoglou, Aliki, Avramidou, Evangelia, Baranek, Miroslav, Carneros, Elena, Caro, Elena, Castiglione, Stefano, Cicatelli, Angela, Radanović, Aleksandra, Ebejer, Jean-Paul, Gackowski, Daniel, Guarino, Francesco, Gulya, Andrea, Hidvegi, Norbert, Hoenicka, Hans, Inacio, Vera, Johannes, Frank, Karalija, Erna, Lieberman-Lazarovich, Michal, Martinelli, Federico, Maury, Stephane, Mladenov, Velimir, Morais-Cecılio, Leonor, Pecinka, Ales, Tani, Eleni, Testillano, Pilar S., Todorov, Dimitar, Valledor, Luis, Vassileva, Valya, "Exploring the crop epigenome: a comparison of DNA methylation profiling techniques" in Frontiers in Plant Science, 14 (2023):1181039,
https://doi.org/10.3389/fpls.2023.1181039 . .

TY  - JOUR
AU  - Varotto, Serena
AU  - Krugman, Tamar
AU  - Cigliano, Riccardo Aiese
AU  - Kashkush, Khalil
AU  - Kondić-Špika, Ankica
AU  - Aravanopoulos, Fillipos A.
AU  - Pradillo, Monica
AU  - Consiglio, Federica
AU  - Aversano, Riccardo
AU  - Pecinka, Ales
AU  - Miladinović, Dragana
PY  - 2022
UR  - http://fiver.ifvcns.rs/handle/123456789/4050
AB  - Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.
PB  - Springer
T2  - Theoretical and Applied Genetics
T1  - Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation
EP  - 4003
SP  - 3987
VL  - 135
DO  - 10.1007/s00122-022-04122-y
ER  - 

@article{
author = "Varotto, Serena and Krugman, Tamar and Cigliano, Riccardo Aiese and Kashkush, Khalil and Kondić-Špika, Ankica and Aravanopoulos, Fillipos A. and Pradillo, Monica and Consiglio, Federica and Aversano, Riccardo and Pecinka, Ales and Miladinović, Dragana",
year = "2022",
abstract = "Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.",
publisher = "Springer",
journal = "Theoretical and Applied Genetics",
title = "Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation",
pages = "4003-3987",
volume = "135",
doi = "10.1007/s00122-022-04122-y"
}

Varotto, S., Krugman, T., Cigliano, R. A., Kashkush, K., Kondić-Špika, A., Aravanopoulos, F. A., Pradillo, M., Consiglio, F., Aversano, R., Pecinka, A.,& Miladinović, D.. (2022). Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation. in Theoretical and Applied Genetics
Springer., 135, 3987-4003.
https://doi.org/10.1007/s00122-022-04122-y

Varotto S, Krugman T, Cigliano RA, Kashkush K, Kondić-Špika A, Aravanopoulos FA, Pradillo M, Consiglio F, Aversano R, Pecinka A, Miladinović D. Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation. in Theoretical and Applied Genetics. 2022;135:3987-4003.
doi:10.1007/s00122-022-04122-y .

Varotto, Serena, Krugman, Tamar, Cigliano, Riccardo Aiese, Kashkush, Khalil, Kondić-Špika, Ankica, Aravanopoulos, Fillipos A., Pradillo, Monica, Consiglio, Federica, Aversano, Riccardo, Pecinka, Ales, Miladinović, Dragana, "Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation" in Theoretical and Applied Genetics, 135 (2022):3987-4003,
https://doi.org/10.1007/s00122-022-04122-y . .