Cytoplasm Types Affect DNA Methylation among Different Cytoplasmic Male Sterility Lines and Their Maintainer Line in Soybean (Glycine max L.).

Chunjing Lin,Limei Zhao,Yongkuan Li,Pengnian Wang,Guolong Zhao,Xiaoyang Ding,Bao Peng,Rong Li,Chunbao Zhang

doi:10.3390/plants9030385

Chunjing Lin, Limei Zhao + Show 7 more

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https://doi.org/10.3390/plants9030385

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Abstract

Cytoplasmic male sterility (CMS) lines and their maintainer line have the same nucleus but different cytoplasm types. We used three soybean (Glycine max L.) CMS lines, JLCMS9A, JLCMSZ9A, and JLCMSPI9A, and their maintainer line, JLCMS9B, to explore whether methylation levels differed in their nuclei. Whole-genome bisulfite sequencing of these four lines was performed. The results show that the cytosine methylation level in the maintainer line was lower than in the CMS lines. Compared with JLCMS9B, the Gene Ontology (GO) enrichment analysis of DMR (differentially methylated region, DMR)-related genes of JLCMS9A revealed that their different 5-methylcytosine backgrounds were enriched in molecular function, whereas JLCMSZ9A and JLCMSPI9A were enriched in biological process and cellular component. The Kyoto Encyclopedia of Genes and Genome (KEGG) analysis of DMR-related genes and different methylated promoter regions in different cytosine contexts, hypomethylation or hypermethylation, showed that the numbers of DMR-related genes and promoter regions were clearly different. According to the DNA methylation and genetic distances separately, JLCMS9A clustered with JLCMS9B, and JLCMSPI9A with JLCMSZ9A. Thus, the effects of different cytoplasm types on DNA methylation were significantly different. This may be related to their genetic distances revealed by re-sequencing these lines. The detected DMR-related genes and pathways that are probably associated with CMS are also discussed.

Highlights

Instead of traditional sexual cross-breeding, the seed industry primarily uses cytoplasmic male sterility (CMS) for hybrid seed production [1]
The results show that JLCMSZ9A and JLCMSPI9A, as well as JLCMS9A and JLCMS9B were closest, with correlation coefficients of >0.88 in the three methylated cytosine (mC) contexts (Figure S1)
These results indicate that different cytoplasm types can affect nuclear DNA methylation levels and that differentially methylated region (DMR) may lead to sterility–fertility transitions

Summary

Introduction

Instead of traditional sexual cross-breeding, the seed industry primarily uses cytoplasmic male sterility (CMS) for hybrid seed production [1]. Because CMS lines generate pollen abortion, using a CMS system avoids the need to artificially remove the maternal line pollen in cross-breeding programs. CMS systems improve the genetic purity of hybrid seeds and increase seed yield. The A line is controlled by both nuclear and cytoplasmic genes and is the donor of the sterile genes in the cytoplasm. The B line is the donor of the fertility genes in the cytoplasm and nucleus. To reproduce an A line, the A line (maternal line) is crossed to obtain fertile pollen from the B line (paternal line). The first CMS systems were reported by Davis [3], but no further reported

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