Cytoplasm Types Affect DNA Methylation among Different Cytoplasmic Male Sterility Lines and Their Maintainer Line in Soybean (<i>Glycine max</i> L.)
Chunjing Lin,
Bao Peng,
Yongkuan Li,
Pengnian Wang,
Guolong Zhao,
Xiaoyang Ding,
Rong Li,
Limei Zhao,
Chunbao Zhang
Affiliations
Chunjing Lin
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
Bao Peng
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
Yongkuan Li
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
Pengnian Wang
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
Guolong Zhao
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
Xiaoyang Ding
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
Rong Li
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
Limei Zhao
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
Chunbao Zhang
Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China
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.
