Abstract
Main conclusion
In 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.
Abstract
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.
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Data availability
The DNA methylation data that support the findings of this study are available in NCBI Gene Expression Omnibus (GEO) www.ncbi.nlm.nih.gov/geo (accession no. GSE72993). Genomic sequencing data in NCBI under accession no. GSE74551 and GSE72993.
Abbreviations
- CAPS:
-
Cleaved amplified polymorphic sequences
- CO:
-
Crossing over
- DMR:
-
Differentially methylated region
- SNP:
-
Single-nucleotide polymorphism
- SD:
-
Segregation distortion
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Acknowledgements
We thank all the members of Qingzhu Zhang lab Northeast Forestry University Harbin, China, especially Jie Zou, Dr. Bowei Chen, Dr. Min Wang, Wei Zhou, Dr. Lishan Wang, and Dr. Wang Yu for useful discussion.
Funding
This work was supported by the National Natural Science Foundation of China (31871220); the National Nonprofit Institute Research Grant of the Chinese Academy of Forestry (CAFYBB2019ZY003); the Fundamental Research Funds for the Central Universities (2572017DA06 and 2572020DP01). CL receives BBSRC grant-aided support as part of the Institute Strategic Program Designing Future Wheat Grant (BB/P016855/1).
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Ali, S., Zhang, T., Lambing, C. et al. Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana. Planta 254, 107 (2021). https://doi.org/10.1007/s00425-021-03763-5
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DOI: https://doi.org/10.1007/s00425-021-03763-5