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Arora I, Li S, Crowley MR, Li Y, Tollefsbol TO. Genome-Wide Analysis on Transcriptome and Methylome in Prevention of Mammary Tumor Induced by Early Life Combined Botanicals. Cells 2022; 12:cells12010014. [PMID: 36611809 PMCID: PMC9818885 DOI: 10.3390/cells12010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the most common malignancy and the second leading cause of cancer death among women in the United States. The consumption of natural dietary components such as broccoli sprouts (BSp) and green tea polyphenols (GTPs) has demonstrated exciting potential in reducing the risk of BC through the regulation of epigenetic mechanisms. However, little is known about their impacts on reversing epigenomic aberrations that are centrally involved in the initiation and progression of BC. Previously, we have determined the efficacy of combined BSp and GTPs treatment on the inhibition of the growth of a mammary tumor in a transgenic Her2/neu mouse model. We sought to extend our previous study to identify universal biomarkers that represent common mechanistic changes among different mouse models in response to this dietary regime by including a new transgenic mouse model, C3(1)-SV40 TAg (SV40). As a result, we identified novel target genes that were differentially expressed and methylated in response to dietary botanicals when administered singly (BSp and GTPs) and in combination (BSp + GTPs) in both mouse models. We discovered more differentially expressed and methylated genes in the combination treatment group compared to the singly administered groups. Subsequently, several biological pathways related to epigenetic regulations were identified in response to the combination treatment. Furthermore, when compared to the BSp and GTPs treatment alone, the combinatorial treatment showed a more significant impact on the regulation of the epigenetic modifier activities involved in DNA methylation and histone modifications. Our study provides key insights about the impact of the combined administration of BSp and GTPs on BC using a multi-omics analysis, suggesting a combinatorial approach is more efficacious in preventing and inhibiting BC by impacting key tumor-related genes at transcriptomic and methylomic levels. Our findings could be further extrapolated as a comprehensive source for understanding the epigenetic modifications that are associated with the effects of these dietary botanicals on BC prevention.
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Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael R. Crowley
- Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yuanyuan Li
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
- Correspondence: (Y.L.); (T.O.T.)
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Integrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence: (Y.L.); (T.O.T.)
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Global DNA Methylation and mRNA-miRNA Variations Activated by Heat Shock Boost Early Microspore Embryogenesis in Cabbage ( Brassica oleracea). Int J Mol Sci 2022; 23:ijms23095147. [PMID: 35563550 PMCID: PMC9103256 DOI: 10.3390/ijms23095147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 12/05/2022] Open
Abstract
Microspore culture, a type of haploid breeding, is extensively used in the cultivation of cruciferous crops such as cabbage. Heat shock (HS) treatment is essential to improve the embryo rate during the culture process; however, its molecular role in boosting early microspore embryogenesis (ME) remains unknown. Here we combined DNA methylation levels, miRNAs, and transcriptome profiles in isolated microspores of cabbage ‘01-88’ under HS (32 °C for 24 h) and normal temperature (25 °C for 24 h) to investigate the regulatory roles of DNA methylation and miRNA in early ME. Global methylation levels were significantly different in the two pre-treatments, and 508 differentially methylated regions (DMRs) were identified; 59.92% of DMRs were correlated with transcripts, and 39.43% of miRNA locus were associated with methylation levels. Significantly, the association analysis revealed that 31 differentially expressed genes (DEGs) were targeted by methylation and miRNA and were mainly involved in the reactive oxygen species (ROS) response and abscisic acid (ABA) signaling, indicating that HS induced DNA methylation, and miRNA might affect ME by influencing ROS and ABA. This study revealed that DNA methylation and miRNA interfered with ME by modulating key genes and pathways, which could broaden our understanding of the molecular regulation of ME induced by HS pre-treatment.
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You J, Li M, Li H, Bai Y, Zhu X, Kong X, Chen X, Zhou R. Integrated Methylome and Transcriptome Analysis Widen the Knowledge of Cytoplasmic Male Sterility in Cotton ( Gossypium barbadense L.). FRONTIERS IN PLANT SCIENCE 2022; 13:770098. [PMID: 35574131 PMCID: PMC9093596 DOI: 10.3389/fpls.2022.770098] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
DNA methylation is defined as a conserved epigenetic modification mechanism that plays a key role in maintaining normal gene expression without altering the DNA sequence. Several studies have reported that altered methylation patterns were associated with male sterility in some plants such as rice and wheat, but global methylation profiles and their possible roles in cytoplasmic male sterility (CMS), especially in cotton near-isogenic lines, remain unclear. In this study, bisulfite sequencing technology and RNA-Seq were used to investigate CMS line 07-113A and its near-isogenic line 07-113B. Using integrated methylome and transcriptome analyses, we found that the number of hypermethylated genes in the differentially methylated regions, whether in the promoter region or in the gene region, was more in 07-113A than the number in 07-113B. The data indicated that 07-113A was more susceptible to methylation. In order to further analyze the regulatory network of male sterility, transcriptome sequencing and DNA methylation group data were used to compare the characteristics of near-isogenic lines 07-113A and 07-113B in cotton during the abortion stage. Combined methylation and transcriptome analysis showed that differentially expressed methylated genes were mainly concentrated in vital metabolic pathways including the starch and sucrose metabolism pathways and galactose metabolism. And there was a negative correlation between gene methylation and gene expression. In addition, five key genes that may be associated with CMS in cotton were identified. These data will support further understanding of the effect of DNA methylation on gene expression and their potential roles in cotton CMS.
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Affiliation(s)
- Jingyi You
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Min Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hongwei Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Yulin Bai
- Xinjiang Yida Textile Co., Ltd, Urumqi, China
| | - Xuan Zhu
- Dali Bai Autonomous Prefecture Agricultural Science Extension Institute, Dali, China
| | - Xiangjun Kong
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaoyan Chen
- Dali Bai Autonomous Prefecture Agricultural Science Extension Institute, Dali, China
| | - Ruiyang Zhou
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
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Ren C, Tang X, Lan H. Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer. PeerJ 2021; 9:e11377. [PMID: 33987034 PMCID: PMC8103922 DOI: 10.7717/peerj.11377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 11/20/2022] Open
Abstract
Background Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq. Methods We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset. Results We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using STITCH. Higher infiltration rates of CD8 T cells, plasma cells, and monocytes were found in the lower quartile WT1 group and the favorable 6-gene signature group. In conclusion, we demonstrated that WT1 is hypermethylated and up-regulated in the four BC molecular subtypes and a 6-gene signature may predict BC prognosis.
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Affiliation(s)
- Chongyang Ren
- Department of Breast Cancer, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaojiang Tang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Haitao Lan
- Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
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Mohd Saad NS, Severn-Ellis AA, Pradhan A, Edwards D, Batley J. Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment. Front Genet 2021; 12:600789. [PMID: 33679880 PMCID: PMC7930750 DOI: 10.3389/fgene.2021.600789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences Western Australia and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton. Int J Mol Sci 2019; 20:ijms20236070. [PMID: 31810186 PMCID: PMC6928835 DOI: 10.3390/ijms20236070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
DNA methylation is an important epigenetic modification involved in multiple biological processes. Altered methylation patterns have been reported to be associated with male sterility in some plants, but their role in cotton cytoplasmic male sterility (CMS) remains unclear. Here, integrated methylome and transcriptome analyses were conducted between the CMS-D2 line ZBA and its near-isogenic maintainer line ZB in upland cotton. More methylated cytosine sites (mCs) and higher methylation levels (MLs) were found among the three sequence contexts in ZB compared to ZBA. A total of 4568 differentially methylated regions (DMRs) and 2096 differentially methylated genes (DMGs) were identified. Among the differentially expressed genes (DEGs) associated with DMRs (DMEGs), 396 genes were upregulated and 281 genes were downregulated. A bioinformatics analysis of these DMEGs showed that hyper-DEGs were significantly enriched in the “oxidative phosphorylation” pathway. Further qRT-PCR validation indicated that these hypermethylated genes (encoding the subunits of mitochondrial electron transport chain (ETC) complexes I and V) were all significantly upregulated in ZB. Our biochemical data revealed a higher extent of H2O2 production but a lower level of adenosine triphosphate (ATP) synthesis in CMS-D2 line ZBA. On the basis of the above results, we propose that disrupted DNA methylation in ZBA may disrupt the homeostasis of reactive oxygen species (ROS) production and ATP synthesis in mitochondria, triggering a burst of ROS that is transferred to the nucleus to initiate programmed cell death (PCD) prematurely, ultimately leading to microspore abortion. This study illustrates the important role of DNA methylation in cotton CMS.
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Singh S, Dey SS, Bhatia R, Kumar R, Behera TK. Current understanding of male sterility systems in vegetable Brassicas and their exploitation in hybrid breeding. PLANT REPRODUCTION 2019; 32:231-256. [PMID: 31053901 DOI: 10.1007/s00497-019-00371-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Overview of the current status of GMS and CMS systems available in Brassica vegetables, their molecular mechanism, wild sources of sterile cytoplasm and exploitation of male sterility in hybrid breeding. The predominantly herbaceous family Brassicaceae (crucifers or mustard family) encompasses over 3700 species, and many of them are scientifically and economically important. The genus Brassica is an economically important genus within the tribe Brassicaceae that comprises important vegetable, oilseed and fodder crops. Brassica vegetables display strong hybrid vigor, and heterosis breeding is the integral part in their improvement. Commercial production of F1 hybrid seeds in Brassica vegetables requires an effective male sterility system. Among the available male sterility systems, cytoplasmic male sterility (CMS) is the most widely exploited in Brassica vegetables. This system is maternally inherited and studied intensively. A limited number of reports about the genic male sterility (GMS) are available in Brassica vegetables. The GMS system is reported to be dominant, recessive and trirecessive in nature in different species. In this review, we discuss the available male sterility systems in Brassica vegetables and their potential use in hybrid breeding. The molecular mechanism of mt-CMS and causal mitochondrial genes of CMS has been discussed in detail. Finally, the exploitation of male sterility system in heterosis breeding of Brassica vegetables, future prospects and need for further understanding of these systems are highlighted.
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Affiliation(s)
- Saurabh Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India.
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Raj Kumar
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
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Han F, Yuan K, Kong C, Zhang X, Yang L, Zhuang M, Zhang Y, Li Z, Wang Y, Fang Z, Lv H. Fine mapping and candidate gene identification of the genic male-sterile gene ms3 in cabbage 51S. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2651-2661. [PMID: 30238254 DOI: 10.1007/s00122-018-3180-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 09/03/2018] [Indexed: 05/27/2023]
Abstract
The ms3 gene responsible for a male-sterile phenotype in cabbage was mapped to a 187.4-kb genomic fragment. The gene BoTPD1, a homolog of Arabidopsis TPD1, was identified as a strong candidate gene. Cabbage 51S is a spontaneous male-sterile mutant. Phenotypic investigation revealed defects in anther cell differentiation, with failure to form the tapetum layer and complete abortion of microsporocytes before the tetrad stage. Genetic analysis indicated that this male sterility was controlled by a single recessive gene, ms3. Using an F2 population, we mapped ms3 to a 187.4-kb interval. BoTPD1 was identified as a candidate from this interval. Sequence analysis revealed an intronic 182-bp insertion in 51S that interrupted the conserved motif at the 5' splicing site of the third intron, possibly resulting in a truncated transcript. Analyses of BoTPD1 homologous proteins revealed evolutionarily conserved roles in anther cell fate determination during reproductive development. RT-PCR showed that BoTPD1 was expressed in various tissues, excluding the root, and high expression levels were detected in anthers and buds. A BoTPD1-specific marker based on the 182-bp insertion cosegregated with male sterility and can be used for marker-assisted selection.
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Affiliation(s)
- Fengqing Han
- Germplasm Innovation in Northwest China, Ministry of Agriculture; College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Kaiwen Yuan
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Congcong Kong
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Xiaoli Zhang
- Tianjin Kernel Vegetable Research Institute, Jinjing Road, Xiqing District, Tianjin, 300384, China
| | - Limei Yang
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Zhansheng Li
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Yong Wang
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China
| | - Zhiyuan Fang
- Germplasm Innovation in Northwest China, Ministry of Agriculture; College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China.
| | - Honghao Lv
- Institute of Vegetables and Flowers, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081, China.
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Genome-Wide DNA Methylation Comparison between Brassica napus Genic Male Sterile Line and Restorer Line. Int J Mol Sci 2018; 19:ijms19092689. [PMID: 30201884 PMCID: PMC6165103 DOI: 10.3390/ijms19092689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/30/2018] [Accepted: 09/04/2018] [Indexed: 12/29/2022] Open
Abstract
DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during plant development. However, few studies have determined the DNA methylation profiles of male-sterile rapeseed. Here, we conducted a global comparison of DNA methylation patterns between the rapeseed genic male sterile line 7365A and its near-isogenic fertile line 7365B by whole-genome bisulfite sequencing (WGBS). Profiling of the genome-wide DNA methylation showed that the methylation level in floral buds was lower than that in leaves and roots. Besides, a total of 410 differentially methylated region-associated genes (DMGs) were identified in 7365A relative to 7365B. Traditional bisulfite sequencing polymerase chain reaction (PCR) was performed to validate the WGBS data. Eleven DMGs were found to be involved in anther and pollen development, which were analyzed by quantitative PCR. In particular, Bnams4 was hypo-methylated in 7365A, and its expression was up-regulated, which might affect other DMGs and thus control the male sterility. This study provided genome-wide DNA methylation profiles of floral buds and important clues for revealing the molecular mechanism of genic male sterility in rapeseed.
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