| Literature DB >> 28621722 |
Fengqing Han1,2, Xiaoli Zhang3, Xing Liu4,5, Henan Su6, Congcong Kong7, Zhiyuan Fang8, Limei Yang9, Mu Zhuang10, Yangyong Zhang11, Yumei Liu12, Zhansheng Li13, Honghao Lv14.
Abstract
Methylation modifications play an important role in multiple biological processes. Several studies have reported altered methylation patterns in male sterile plants such as rice and wheat, but little is known about the global methylation profiles and their possible roles in the cabbage (Brassicaoleracea) male sterile line. In this study, single-base-resolution bisulfite sequencing (BS-Seq) was adopted to identify the pattern and degree of cytosine methylation in the male sterile line 01-20S and its near-isogenic fertile line 01-20F. Similar methylation patterns were profiled, with some changes observed in local positions. In total, 505 differentially methylated genomic regions (DMRs) and 106 DMR-associated genes were detected. Nine genes related to pollen development were discovered and further validated by a quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Among these, four were downregulated in 01-20S. In particular, Bol039180 (an invertase/pectin methylesterase inhibitor family protein) is likely involved in pectin degradation, and might play an important role in the pollen separation defects of 01-20S. This study facilitates a better understanding of DNA methylation alterations and their possible roles in genic male sterility in cabbages.Entities:
Keywords: Brassica oleracea; DNA methylation; genic male sterility
Year: 2017 PMID: 28621722 PMCID: PMC5485523 DOI: 10.3390/genes8060159
Source DB: PubMed Journal: Genes (Basel) ISSN: 2073-4425 Impact factor: 4.096
Figure 1DNA methylation patterns of 01-20F (F) and 01-20S (S). (a) The cytosine methylation level (mC) percentage for each sequence context; (b) Levels of CG, CHG and CHH methylation in the whole cabbage genome.
Figure 2Genomic methylation levels of 01-20F and 01-20S. (a) Global DNA methylation patterns of 01-20F and 01-20S; (b) DNA methylation levels in nine chromosomes; (c) Methylcytosines density in chromosome 8 and 9. The blue dots represent methylcytosine density. The smoothed lines represent the methylcytosine density of the three contexts.
Information on nine differentially methylated genomic region (DMR)-associated genes involved in pollen development.
| ID | Different Methylation Region | Hyper or Hypo in S | Homologous Gene in | Predicted Functional Description | ||
|---|---|---|---|---|---|---|
| Intron | hyper | 1.74 × 10−3 | 1.00 × 10−16 | Endoglucanase 21 | ||
| Upstream | hyper | 5.09 × 10−12 | 1.00 × 10−117 | ADP-ribosylation factor GTPase-activating protein AGD10 | ||
| Upstream | hyper | 1.84 × 10−7 | 1.00 × 10−55 | Unknown protein; expressed in sperm cell, male gametophyte, pollen tube | ||
| Intron | hyper | 2.76 × 10−8 | 0.00 | ABC transporter; multidrug and toxin efflux family transporter DTX35 | ||
| Intron | hyper | 1.98 × 10−7 | 0.00 | Endo-1,4-beta-xylanase A | ||
| Upstream | hyper | 6.36 × 10−5 | 0.00 | Homeobox-leucine zipper protein HDG10 | ||
| downstream | hypo | 2.62 × 10−5 | 0.00 | Pectinesterase, active site | ||
| downstream | hyper | 1.16 × 10−5 | 0.00 | Transcription factor jumonji | ||
| downstream | hyper | 1.93 × 10−11 | 0.38 | invertase/pectin methylesterase inhibitor family protein |
Hyper: Hypermethylated; Hypo: Hypomethylated; S: sterile line 01-20S.
Figure 3Gene expression and DNA methylation patterns of differentially methylated genomic regions (DMR)-associated genes involved in pollen development. (a) Expression analysis of nine genes related to pollen development; (b) DNA methylation at specific sites of four genes by bisulfite sequencing (BS-seq). The asterisk indicates a significant difference between F and S (* p-value < 0.05; ** p-value < 0.01).