Genomic and Epigenomic Changes in the Progeny of Cold-Stressed <i>Arabidopsis thaliana</i> Plants
Plants are continuously exposed to various environmental stresses. Because they can not escape stress, they have to develop mechanisms of remembering stress exposures somatically and passing it to the progeny. We studied the <i>Arabidopsis thaliana</i> ecotype Columbia plants exposed to...
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MDPI AG
2024-02-01
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| Series: | International Journal of Molecular Sciences |
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| author | Ashif Rahman Narendra Singh Yadav Boseon Byeon Yaroslav Ilnytskyy Igor Kovalchuk |
| author_facet | Ashif Rahman Narendra Singh Yadav Boseon Byeon Yaroslav Ilnytskyy Igor Kovalchuk |
| author_sort | Ashif Rahman |
| collection | DOAJ |
| description | Plants are continuously exposed to various environmental stresses. Because they can not escape stress, they have to develop mechanisms of remembering stress exposures somatically and passing it to the progeny. We studied the <i>Arabidopsis thaliana</i> ecotype Columbia plants exposed to cold stress for 25 continuous generations. Our study revealed that multigenerational exposure to cold stress resulted in the changes in the genome and epigenome (DNA methylation) across generations. Main changes in the progeny were due to the high frequency of genetic mutations rather than epigenetic changes; the difference was primarily in single nucleotide substitutions and deletions. The progeny of cold-stressed plants exhibited the higher rate of missense non-synonymous mutations as compared to the progeny of control plants. At the same time, epigenetic changes were more common in the CHG (C = cytosine, H = cytosine, adenine or thymine, G = guanine) and CHH contexts and favored hypomethylation. There was an increase in the frequency of C to T (thymine) transitions at the CHH positions in the progeny of cold stressed plants; because this type of mutations is often due to the deamination of the methylated cytosines, it can be hypothesized that environment-induced changes in methylation contribute to mutagenesis and may be to microevolution processes and that RNA-dependent DNA methylation plays a crucial role. Our work supports the existence of heritable stress response in plants and demonstrates that genetic changes prevail. |
| first_indexed | 2024-04-25T00:28:50Z |
| format | Article |
| id | doaj.art-5cbea36a4fa8499b9772ebe42b3a8822 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-04-25T00:28:50Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-5cbea36a4fa8499b9772ebe42b3a88222024-03-12T16:46:21ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-02-01255279510.3390/ijms25052795Genomic and Epigenomic Changes in the Progeny of Cold-Stressed <i>Arabidopsis thaliana</i> PlantsAshif Rahman0Narendra Singh Yadav1Boseon Byeon2Yaroslav Ilnytskyy3Igor Kovalchuk4Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, CanadaDepartment of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, CanadaBiomedical and Health Informatics, Computer Science Department, State University of New York, 2 S Clinton St, Syracuse, NY 13202, USADepartment of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, CanadaDepartment of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, CanadaPlants are continuously exposed to various environmental stresses. Because they can not escape stress, they have to develop mechanisms of remembering stress exposures somatically and passing it to the progeny. We studied the <i>Arabidopsis thaliana</i> ecotype Columbia plants exposed to cold stress for 25 continuous generations. Our study revealed that multigenerational exposure to cold stress resulted in the changes in the genome and epigenome (DNA methylation) across generations. Main changes in the progeny were due to the high frequency of genetic mutations rather than epigenetic changes; the difference was primarily in single nucleotide substitutions and deletions. The progeny of cold-stressed plants exhibited the higher rate of missense non-synonymous mutations as compared to the progeny of control plants. At the same time, epigenetic changes were more common in the CHG (C = cytosine, H = cytosine, adenine or thymine, G = guanine) and CHH contexts and favored hypomethylation. There was an increase in the frequency of C to T (thymine) transitions at the CHH positions in the progeny of cold stressed plants; because this type of mutations is often due to the deamination of the methylated cytosines, it can be hypothesized that environment-induced changes in methylation contribute to mutagenesis and may be to microevolution processes and that RNA-dependent DNA methylation plays a crucial role. Our work supports the existence of heritable stress response in plants and demonstrates that genetic changes prevail.https://www.mdpi.com/1422-0067/25/5/2795multigenerational cold stressstress memory<i>Arabidopsis thaliana</i>intergenerational inheritanceepigenetic variationsgenetic variations |
| spellingShingle | Ashif Rahman Narendra Singh Yadav Boseon Byeon Yaroslav Ilnytskyy Igor Kovalchuk Genomic and Epigenomic Changes in the Progeny of Cold-Stressed <i>Arabidopsis thaliana</i> Plants International Journal of Molecular Sciences multigenerational cold stress stress memory <i>Arabidopsis thaliana</i> intergenerational inheritance epigenetic variations genetic variations |
| title | Genomic and Epigenomic Changes in the Progeny of Cold-Stressed <i>Arabidopsis thaliana</i> Plants |
| title_full | Genomic and Epigenomic Changes in the Progeny of Cold-Stressed <i>Arabidopsis thaliana</i> Plants |
| title_fullStr | Genomic and Epigenomic Changes in the Progeny of Cold-Stressed <i>Arabidopsis thaliana</i> Plants |
| title_full_unstemmed | Genomic and Epigenomic Changes in the Progeny of Cold-Stressed <i>Arabidopsis thaliana</i> Plants |
| title_short | Genomic and Epigenomic Changes in the Progeny of Cold-Stressed <i>Arabidopsis thaliana</i> Plants |
| title_sort | genomic and epigenomic changes in the progeny of cold stressed i arabidopsis thaliana i plants |
| topic | multigenerational cold stress stress memory <i>Arabidopsis thaliana</i> intergenerational inheritance epigenetic variations genetic variations |
| url | https://www.mdpi.com/1422-0067/25/5/2795 |
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