Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns
Summary Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth perfor...
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Online Access: | http://dx.doi.org/10.1111/pbi.14229 https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14229 |
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crwiley:10.1111/pbi.14229 2024-04-21T08:01:00+00:00 Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns Vu, Giang Thi Ha Cao, Hieu Xuan Hofmann, Martin Steiner, Wilfried Gailing, Oliver Fachagentur Nachwachsende Rohstoffe 2023 http://dx.doi.org/10.1111/pbi.14229 https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14229 en eng Wiley http://creativecommons.org/licenses/by-nc/4.0/ Plant Biotechnology Journal volume 22, issue 4, page 863-875 ISSN 1467-7644 1467-7652 Plant Science Agronomy and Crop Science Biotechnology journal-article 2023 crwiley https://doi.org/10.1111/pbi.14229 2024-03-26T09:14:44Z Summary Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth performance of long‐lived trees remains unclear. In this study, a comparative analysis of targeted DNA genotyping, DNA methylation and mRNAseq profiling for needles of 44‐year‐old Douglas‐fir trees ( Pseudotsuga menziesii (Mirb.) Franco) having contrasting growth characteristics was performed. In total, we identified 195 differentially expressed genes (DEGs) and 115 differentially methylated loci (DML) that are associated with genes involved in fitness‐related processes such as growth, stress management, plant development and energy resources. Interestingly, all four intronic DML were identified in mega‐sized (between 100 and 180 kbp in length) and highly expressed genes, suggesting specialized regulation mechanisms of these long intron genes in gymnosperms. DNA repetitive sequences mainly comprising long‐terminal repeats of retroelements are involved in growth‐associated DNA methylation regulation (both hyper‐ and hypomethylation) of 99 DML (86.1% of total DML). Furthermore, nearly 14% of the DML was not tagged by single nucleotide polymorphisms, suggesting a unique contribution of the epigenetic variation in tree growth. Article in Journal/Newspaper DML Wiley Online Library Plant Biotechnology Journal 22 4 863 875 |
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Plant Science Agronomy and Crop Science Biotechnology |
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Plant Science Agronomy and Crop Science Biotechnology Vu, Giang Thi Ha Cao, Hieu Xuan Hofmann, Martin Steiner, Wilfried Gailing, Oliver Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns |
topic_facet |
Plant Science Agronomy and Crop Science Biotechnology |
description |
Summary Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth performance of long‐lived trees remains unclear. In this study, a comparative analysis of targeted DNA genotyping, DNA methylation and mRNAseq profiling for needles of 44‐year‐old Douglas‐fir trees ( Pseudotsuga menziesii (Mirb.) Franco) having contrasting growth characteristics was performed. In total, we identified 195 differentially expressed genes (DEGs) and 115 differentially methylated loci (DML) that are associated with genes involved in fitness‐related processes such as growth, stress management, plant development and energy resources. Interestingly, all four intronic DML were identified in mega‐sized (between 100 and 180 kbp in length) and highly expressed genes, suggesting specialized regulation mechanisms of these long intron genes in gymnosperms. DNA repetitive sequences mainly comprising long‐terminal repeats of retroelements are involved in growth‐associated DNA methylation regulation (both hyper‐ and hypomethylation) of 99 DML (86.1% of total DML). Furthermore, nearly 14% of the DML was not tagged by single nucleotide polymorphisms, suggesting a unique contribution of the epigenetic variation in tree growth. |
author2 |
Fachagentur Nachwachsende Rohstoffe |
format |
Article in Journal/Newspaper |
author |
Vu, Giang Thi Ha Cao, Hieu Xuan Hofmann, Martin Steiner, Wilfried Gailing, Oliver |
author_facet |
Vu, Giang Thi Ha Cao, Hieu Xuan Hofmann, Martin Steiner, Wilfried Gailing, Oliver |
author_sort |
Vu, Giang Thi Ha |
title |
Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns |
title_short |
Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns |
title_full |
Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns |
title_fullStr |
Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns |
title_full_unstemmed |
Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns |
title_sort |
uncovering epigenetic and transcriptional regulation of growth in douglas‐fir: identification of differential methylation regions in mega‐sized introns |
publisher |
Wiley |
publishDate |
2023 |
url |
http://dx.doi.org/10.1111/pbi.14229 https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14229 |
genre |
DML |
genre_facet |
DML |
op_source |
Plant Biotechnology Journal volume 22, issue 4, page 863-875 ISSN 1467-7644 1467-7652 |
op_rights |
http://creativecommons.org/licenses/by-nc/4.0/ |
op_doi |
https://doi.org/10.1111/pbi.14229 |
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Plant Biotechnology Journal |
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22 |
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4 |
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863 |
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875 |
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1796941376962691072 |