Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana

A - Papers appearing in refereed journals

Ali, S., Zhang, T., Lambing, C., Wang, W., Zhang, P., Xie, L., Wang, J., Khan, N. and Zhang, Q. 2021. Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana. Planta. 254 (5), p. 107. https://doi.org/10.1007/s00425-021-03763-5

AuthorsAli, S., Zhang, T., Lambing, C., Wang, W., Zhang, P., Xie, L., Wang, J., Khan, N. and Zhang, Q.
Abstract

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. 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.

KeywordsCAPS marker ; DNA methylation; DDM1; Mendelian law; Segregation distortion; SNPs
Year of Publication2021
JournalPlanta
Journal citation254 (5), p. 107
Digital Object Identifier (DOI)https://doi.org/10.1007/s00425-021-03763-5
PubMed ID34694462
Web address (URL)https://link.springer.com/content/pdf/10.1007/s00425-021-03763-5.pdf
Open accessPublished as non-open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or codeDesigning Future Wheat (DFW) [ISPG]
Output statusPublished
Publication dates
Online25 Oct 2021
Publication process dates
Accepted18 Oct 2021
PublisherSpringer
ISSN0032-0935

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