Evidence map›Paper›PMID 34694462›Full record

ArticlePlanta2021

Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana.

Shahid Ali, Tianxu Zhang, Christophe Lambing, Wanpeng Wang, Peng Zhang, Linan Xie, Jiang Wang, Naeem Khan, Qingzhu Zhang

Abstract read
PubMed Publisher
In one paragraph

Article in Planta, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Epigenetic regulation during meiosis and crossover.Physiology and molecular biology of plants : an international journal of functional plant biology · 2023
    Review
  2. Article
  3. Epidemiology of Δ8THC-Related Carcinogenesis in USA: A Panel Regression and Causal Inferential Study.International journal of environmental research and public health · 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

9 authors.

Shahid Ali *Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
Tianxu Zhang *State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
Christophe LambingPlant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK.
Wanpeng WangKey Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
Peng ZhangKey Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
Linan XieKey Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
Jiang WangKey Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
Naeem KhanDepartment of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, 32611, USA.
Qingzhu ZhangState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China. qingzhu.zhang@nefu.edu.cn.ORCID http://orcid.org/0000-0001-8246-6688

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

MAIN

conclusionIn ddm1 mutants, the DNA methylation is primarily affected in the heterochromatic region of the chromosomes, which is associated with the segregation distortion of SNPs in the F2 progenies. Segregation distortion (SD) is common in most genetic mapping experiments and a valuable resource to determine how gene loci induce deviation. Meiotic DNA crossing over and SD are under the control of several types of epigenetic modifications. DNA methylation is an important regulatory epigenetic modification that is inherited across generations. In the present study, we investigated the relationship between SD and DNA methylation. The ecotypes Col-0/C24 and chromatin remodeler mutants ddm1-10/Col and ddm1-15/C24 were reciprocally crossed to obtain F2 generations. A total of 300 plants for each reciprocally crossed plant in the F2 generations were subjected to next-generation sequencing to detect the single-nucleotide polymorphisms (SNPs) as DNA markers. All SNPs were analyzed using the Chi-square test method to determine their segregation ratio in F2 generations. Through the segregation ratio, whole-genome SNPs were classified into 16 classes. In class 10, the SNPs in the reciprocal crosses of wild type showed the expected Mendelian ratio of 1:2:1, while those in the reciprocal crosses of ddm1 mutants showed distortion. In contrast, all SNPs in class 16 displayed a normal 1:2:1 ratio, and class 1 showed SD, regardless of wild type or mutants, as assessed using CAPS (cleaved amplified polymorphic sequences) marker analysis to confirm the next-generation sequencing. In ddm1 mutants, the DNA methylation is highly reduced throughout the whole genome and more significantly in the heterochromatic regions of chromosomes. Our results showed that the ddm1 mutants exhibit low levels of DNA methylation, which facilitates the SD of SNPs primarily located in the heterochromatic region of chromosomes by reducing the heterozygous ratio. The present study will provide a strong base for future research focusing on the impact of DNA methylation on trait segregation and plant evolution.

Indexed as

ArabidopsisArabidopsis ProteinsChromatinDNA-Binding ProteinsDNA MethylationMutationTranscription FactorsArabidopsis ProteinsChromatinDDM1 protein, ArabidopsisDNA-Binding ProteinsTranscription FactorsCAPS markerDDM1DNA methylationMendelian lawSegregation distortionSNPs

Identifiers

PMID34694462

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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.