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细胞质类型对大豆（L.）不同细胞质雄性不育系及其保持系DNA甲基化的影响

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

作者信息

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

机构信息

Soybean Research Institute, The National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, No. 1363, Shengtai St., Changchun 130000, China.

出版信息

Plants (Basel). 2020 Mar 20;9(3):385. doi: 10.3390/plants9030385.

DOI:10.3390/plants9030385
PMID:32245080
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7155767/
Abstract

Cytoplasmic male sterility (CMS) lines and their maintainer line have the same nucleus but different cytoplasm types. We used three soybean ( 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.

摘要

细胞质雄性不育（CMS）系与其保持系具有相同的细胞核，但细胞质类型不同。我们使用了三个大豆（L.）CMS系JLCMS9A、JLCMSZ9A和JLCMSPI9A及其保持系JLCMS9B，来探究它们细胞核中的甲基化水平是否存在差异。对这四个品系进行了全基因组亚硫酸氢盐测序。结果表明，保持系中的胞嘧啶甲基化水平低于CMS系。与JLCMS9B相比，对JLCMS9A的差异甲基化区域（DMR）相关基因进行基因本体（GO）富集分析发现，它们不同的5-甲基胞嘧啶背景在分子功能方面富集，而JLCMSZ9A和JLCMSPI9A在生物学过程和细胞组分方面富集。对不同胞嘧啶背景（低甲基化或高甲基化）下的DMR相关基因和不同甲基化启动子区域进行京都基因与基因组百科全书（KEGG）分析表明，DMR相关基因和启动子区域的数量明显不同。根据DNA甲基化和遗传距离分别来看，JLCMS9A与JLCMS9B聚类，JLCMSPI9A与JLCMSZ9A聚类。因此，不同细胞质类型对DNA甲基化的影响显著不同。这可能与通过对这些品系重新测序所揭示的它们的遗传距离有关。还讨论了检测到的可能与CMS相关的DMR相关基因和途径。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/caba/7155767/80a1fcb78376/plants-09-00385-g003a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/caba/7155767/acbd08c07220/plants-09-00385-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/caba/7155767/530fee5164fb/plants-09-00385-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/caba/7155767/80a1fcb78376/plants-09-00385-g003a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/caba/7155767/acbd08c07220/plants-09-00385-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/caba/7155767/530fee5164fb/plants-09-00385-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/caba/7155767/80a1fcb78376/plants-09-00385-g003a.jpg

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