Genome-wide high-resolution mapping of DNA methylation reveals epigenetic variation in the offspring of sexual and asexual propagation in Robinia pseudoacacia.

Zijie Zhang, Jie Liu, Yuhan Sun, Shaoming Wang, Xiuxia Xing, Xiaojing Feng, José Manuel Pérez-Pérez, Yun Li

Abstract read

In one paragraph

Article in Plant cell reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

0.9field-weighted citation impact, top 20% of its field

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 4 citations in OpenAlex.

The RpTOE1-International journal of molecular sciences · 2022
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 4 institutions in 2 countries.

Zijie ZhangNational Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China.

Jie LiuNational Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China.

Yuhan SunNational Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China.

Shaoming WangState-Owned Quanbaoshan Forestry Station in Luoning County of He'nan Province, Luoyang, 471717, People's Republic of China.

Xiuxia XingAgricultural Service Center of Wangfan Hui Town in Luoning County of He'nan Province, Luoyang, 471700, People's Republic of China.

Xiaojing FengState-Owned Lvcun Forestry Station in Luoning County of He'nan Province, Luoyang, 471700, People's Republic of China.

José Manuel Pérez-PérezInstituto de Bioingeniería, Universidad Miguel Hernández de Elche, Alicante, Spain.

Yun LiNational Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China. yunli@bjfu.edu.cn.ORCID http://orcid.org/0000-0002-8426-565X

Beijing Forestry University · CNExperimental Center of Forestry in North China · CNLuye Pharma (China) · CNUniversitat de Miguel Hernández d'Elx · ES

Funding

national key R&D program of china 2017YFD0600503the long-term research program for young teachers of beijing forestry university 2015ZCQ-SW-03the national nature science foundation of china 31971675

6 · The paper itself

Abstract

key messageWe detected the genome-wide pattern of DNA methylation and its association with gene expression in sexual and asexual progenies of mature Robinia pseudoacacia trees. DNA methylation plays an important role in plant reproduction and development. Although some studies on sexual reproduction have been carried out in model plants, little is known about the dynamic changes in DNA methylation and their effect on gene expression in sexual and asexual progeny of woody plants. Here, through whole-genome bisulfite sequencing, we revealed DNA methylation patterns in the sexual and asexual progenies of mature Robinia pseudoacacia to understand the regulation of gene expression by DNA methylation in juvenile seedlings. An average of 53% CG, 34% CHG and 5% CHH contexts was methylated in the leaves of mature and juvenile individuals. The CHH methylation level of asexually propagated seedlings was significantly lower than that of seed-derived seedlings and mature trees. The intergenic regions had the highest methylation level. Analysis of differentially methylated regions (DMRs) showed that most of them were hypermethylated and located in the gene upstream and introns. A total of 24, 108 and 162 differentially expressed genes containing DMRs were identified in root sprouts (RSs), root cuttings (RCs) and seed-derived seedlings (SSs), respectively, and a large proportion of them showed hypermethylation. In addition, DMRs were enriched within GO subcategories including catalytic activity, metabolic process and cellular process. The results reveal widespread DNA methylation changes between mature plants and their progenies through sexual/asexual reproduction, which provides novel insights into DNA methylation reprogramming and the regulation of gene expression in woody plants.

Indexed as

DNA MethylationEpigenesis, GeneticGene Expression Regulation, PlantGenome, PlantGenome-Wide Association StudyGerminationPlant ProteinsReproduction, AsexualRobiniaSeedlingsPlant ProteinsBlack locust (Robinia pseudoacacia L.)DNA methylationGene expressionSexual and asexual propagation

Identifiers

PMID34524479

DOI10.1007/s00299-021-02787-1

OpenAlexW3201009127

What OpenQuestion holds

Textmetadata

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.